Starting phenix.real_space_refine on Tue Mar 12 13:12:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g05_3388/03_2024/5g05_3388.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g05_3388/03_2024/5g05_3388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g05_3388/03_2024/5g05_3388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g05_3388/03_2024/5g05_3388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g05_3388/03_2024/5g05_3388.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g05_3388/03_2024/5g05_3388.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 389 5.16 5 C 40476 2.51 5 N 10792 2.21 5 O 11521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 63181 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1569, 11890 Classifications: {'peptide': 1569} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'CIS': 7, 'PCIS': 3, 'PTRANS': 86, 'TRANS': 1472} Chain breaks: 14 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 470 Unresolved non-hydrogen angles: 588 Unresolved non-hydrogen dihedrals: 364 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 13, 'ASP:plan': 18, 'GLU:plan': 30, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 313 Chain: "B" Number of atoms: 649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 84, 644 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 84, 644 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 660 Chain: "C" Number of atoms: 4306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4306 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 508} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 450 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3618 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 444} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 220 Classifications: {'peptide': 25} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 21} Chain: "H" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3879 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 473} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "I" Number of atoms: 5634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5634 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 696} Chain breaks: 2 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 12, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 124 Chain: "J" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4053 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 489} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "K" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3988 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1435 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 168} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 481 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 4767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4767 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 566} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 15, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 138 Chain: "O" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5400 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 668} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'HIS:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "P" Number of atoms: 4046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 4046 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 478} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 79 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'TRANS': 12} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 218 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3767 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "Y" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3862 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 480} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12065 SG CYS B 23 142.039 55.029 108.895 1.00500.00 S ATOM 12083 SG CYS B 26 142.837 58.030 111.559 1.00452.68 S ATOM 12328 SG CYS B 59 139.667 56.297 113.069 1.00500.00 S ATOM 12437 SG CYS B 73 137.510 51.383 101.314 1.00500.00 S ATOM 12458 SG CYS B 76 137.312 50.240 97.263 1.00465.43 S Time building chain proxies: 24.59, per 1000 atoms: 0.39 Number of scatterers: 63181 At special positions: 0 Unit cell: (236.64, 186.32, 217.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 389 16.00 O 11521 8.00 N 10792 7.00 C 40476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.12 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.28 Conformation dependent library (CDL) restraints added in 8.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1085 " pdb="ZN ZN B1085 " - pdb=" SG CYS B 23 " pdb="ZN ZN B1085 " - pdb=" SG CYS B 26 " pdb="ZN ZN B1085 " - pdb=" SG CYS B 59 " pdb="ZN ZN B1085 " - pdb=" ND1 HIS B 56 " pdb=" ZN B1086 " pdb="ZN ZN B1086 " - pdb=" SG CYS B 73 " pdb="ZN ZN B1086 " - pdb=" ND1 HIS B 53 " pdb="ZN ZN B1086 " - pdb=" SG CYS B 76 " Number of angles added : 3 15828 Ramachandran restraints generated. 7914 Oldfield, 0 Emsley, 7914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15370 Finding SS restraints... Secondary structure from input PDB file: 389 helices and 26 sheets defined 71.7% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 removed outlier: 4.132A pdb=" N ASP A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 630 through 647 Processing helix chain 'A' and resid 655 through 668 Processing helix chain 'A' and resid 673 through 677 Processing helix chain 'A' and resid 704 through 713 removed outlier: 3.637A pdb=" N LEU A 711 " --> pdb=" O TRP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 758 through 777 removed outlier: 3.844A pdb=" N ILE A 762 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 764 " --> pdb=" O PRO A 760 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 795 Processing helix chain 'A' and resid 800 through 810 removed outlier: 3.759A pdb=" N HIS A 805 " --> pdb=" O PRO A 801 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 806 " --> pdb=" O TYR A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 815 removed outlier: 4.238A pdb=" N VAL A 814 " --> pdb=" O TYR A 810 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG A 815 " --> pdb=" O PRO A 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 810 through 815' Processing helix chain 'A' and resid 843 through 854 Processing helix chain 'A' and resid 867 through 881 removed outlier: 3.525A pdb=" N LEU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 937 removed outlier: 3.740A pdb=" N VAL A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 945 removed outlier: 3.564A pdb=" N GLU A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 965 Proline residue: A 954 - end of helix removed outlier: 3.501A pdb=" N ALA A 958 " --> pdb=" O PRO A 954 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 965 " --> pdb=" O HIS A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 978 removed outlier: 3.566A pdb=" N CYS A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 992 removed outlier: 3.971A pdb=" N GLN A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 992 " --> pdb=" O CYS A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1032 through 1042 removed outlier: 3.769A pdb=" N ASP A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1088 removed outlier: 3.783A pdb=" N GLU A1064 " --> pdb=" O HIS A1060 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A1065 " --> pdb=" O GLU A1061 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A1076 " --> pdb=" O GLN A1072 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A1079 " --> pdb=" O GLN A1075 " (cutoff:3.500A) Proline residue: A1081 - end of helix removed outlier: 3.735A pdb=" N MET A1086 " --> pdb=" O VAL A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1146 Processing helix chain 'A' and resid 1149 through 1154 removed outlier: 3.697A pdb=" N ASP A1154 " --> pdb=" O ALA A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1183 Processing helix chain 'A' and resid 1183 through 1188 removed outlier: 3.912A pdb=" N LYS A1187 " --> pdb=" O GLY A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1200 Processing helix chain 'A' and resid 1201 through 1217 removed outlier: 3.550A pdb=" N LYS A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1232 removed outlier: 3.536A pdb=" N LEU A1227 " --> pdb=" O SER A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1261 removed outlier: 3.604A pdb=" N ALA A1252 " --> pdb=" O ASN A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1278 removed outlier: 3.751A pdb=" N GLY A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1307 removed outlier: 3.788A pdb=" N TYR A1294 " --> pdb=" O ASP A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1331 Processing helix chain 'A' and resid 1359 through 1375 removed outlier: 3.890A pdb=" N THR A1363 " --> pdb=" O ASN A1359 " (cutoff:3.500A) Proline residue: A1365 - end of helix Processing helix chain 'A' and resid 1380 through 1387 Processing helix chain 'A' and resid 1392 through 1399 removed outlier: 3.794A pdb=" N ASP A1397 " --> pdb=" O MET A1393 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A1398 " --> pdb=" O TYR A1394 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1415 removed outlier: 3.752A pdb=" N LEU A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 3.968A pdb=" N VAL A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A1427 " --> pdb=" O SER A1423 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A1429 " --> pdb=" O TRP A1425 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL A1430 " --> pdb=" O VAL A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1437 Processing helix chain 'A' and resid 1456 through 1476 removed outlier: 3.533A pdb=" N HIS A1461 " --> pdb=" O LEU A1457 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A1462 " --> pdb=" O SER A1458 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A1463 " --> pdb=" O GLN A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1501 Processing helix chain 'A' and resid 1503 through 1508 removed outlier: 4.392A pdb=" N THR A1507 " --> pdb=" O ASN A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1527 Processing helix chain 'A' and resid 1532 through 1546 removed outlier: 4.231A pdb=" N THR A1546 " --> pdb=" O LEU A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1566 Processing helix chain 'A' and resid 1567 through 1570 Processing helix chain 'A' and resid 1578 through 1588 removed outlier: 3.525A pdb=" N CYS A1586 " --> pdb=" O ALA A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1608 removed outlier: 3.600A pdb=" N LEU A1606 " --> pdb=" O LEU A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1613 removed outlier: 3.883A pdb=" N ALA A1613 " --> pdb=" O LEU A1609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1609 through 1613' Processing helix chain 'A' and resid 1684 through 1693 removed outlier: 3.636A pdb=" N ILE A1690 " --> pdb=" O HIS A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1742 removed outlier: 3.549A pdb=" N PHE A1741 " --> pdb=" O THR A1737 " (cutoff:3.500A) Processing helix chain 'A' and resid 1744 through 1754 removed outlier: 3.504A pdb=" N PHE A1750 " --> pdb=" O ALA A1746 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A1751 " --> pdb=" O LEU A1747 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A1752 " --> pdb=" O LEU A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1781 Processing helix chain 'A' and resid 1785 through 1803 removed outlier: 4.182A pdb=" N ALA A1789 " --> pdb=" O GLU A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1808 through 1821 removed outlier: 3.528A pdb=" N TRP A1812 " --> pdb=" O THR A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1828 Processing helix chain 'A' and resid 1844 through 1863 Processing helix chain 'A' and resid 1864 through 1873 Processing helix chain 'A' and resid 1880 through 1893 removed outlier: 3.915A pdb=" N MET A1884 " --> pdb=" O SER A1880 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS A1887 " --> pdb=" O SER A1883 " (cutoff:3.500A) Processing helix chain 'A' and resid 1911 through 1921 removed outlier: 3.566A pdb=" N LYS A1919 " --> pdb=" O LEU A1915 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A1920 " --> pdb=" O PHE A1916 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1935 removed outlier: 3.555A pdb=" N LEU A1928 " --> pdb=" O PRO A1924 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A1929 " --> pdb=" O VAL A1925 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A1930 " --> pdb=" O ARG A1926 " (cutoff:3.500A) Proline residue: A1933 - end of helix Processing helix chain 'B' and resid 57 through 68 Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.573A pdb=" N ILE C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 62 removed outlier: 3.501A pdb=" N LEU C 58 " --> pdb=" O TRP C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 96 removed outlier: 4.877A pdb=" N ASP C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ALA C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 111 through 137 removed outlier: 3.539A pdb=" N VAL C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 removed outlier: 4.153A pdb=" N VAL C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 182 Processing helix chain 'C' and resid 184 through 199 removed outlier: 3.542A pdb=" N ASP C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.649A pdb=" N TRP C 206 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 222 Processing helix chain 'C' and resid 228 through 242 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 258 through 261 removed outlier: 4.310A pdb=" N LYS C 261 " --> pdb=" O GLY C 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 258 through 261' Processing helix chain 'C' and resid 262 through 276 Processing helix chain 'C' and resid 278 through 293 removed outlier: 3.610A pdb=" N ILE C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 310 Processing helix chain 'C' and resid 312 through 327 Processing helix chain 'C' and resid 330 through 344 Processing helix chain 'C' and resid 346 through 361 Processing helix chain 'C' and resid 364 through 379 removed outlier: 4.419A pdb=" N TRP C 368 " --> pdb=" O TYR C 364 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS C 373 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 398 through 413 Processing helix chain 'C' and resid 414 through 429 removed outlier: 4.193A pdb=" N TYR C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR C 421 " --> pdb=" O TYR C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 447 removed outlier: 4.072A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 463 Processing helix chain 'C' and resid 467 through 480 removed outlier: 4.001A pdb=" N VAL C 471 " --> pdb=" O LYS C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 500 Processing helix chain 'C' and resid 509 through 524 Processing helix chain 'C' and resid 525 through 539 Processing helix chain 'C' and resid 541 through 557 removed outlier: 4.104A pdb=" N GLU C 545 " --> pdb=" O ASP C 541 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LYS C 547 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 549 " --> pdb=" O GLU C 545 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C 555 " --> pdb=" O ARG C 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 46 Processing helix chain 'E' and resid 52 through 92 removed outlier: 3.796A pdb=" N GLU E 90 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 98 through 103 Processing helix chain 'F' and resid 5 through 18 Processing helix chain 'F' and resid 20 through 35 Processing helix chain 'F' and resid 37 through 51 Processing helix chain 'F' and resid 53 through 63 Processing helix chain 'F' and resid 68 through 82 Processing helix chain 'F' and resid 84 through 93 removed outlier: 3.626A pdb=" N LEU F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 111 removed outlier: 3.740A pdb=" N VAL F 107 " --> pdb=" O HIS F 103 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 128 Processing helix chain 'F' and resid 130 through 145 Processing helix chain 'F' and resid 149 through 159 Processing helix chain 'F' and resid 163 through 168 Processing helix chain 'F' and resid 455 through 478 Processing helix chain 'F' and resid 480 through 491 Processing helix chain 'F' and resid 492 through 497 Processing helix chain 'F' and resid 498 through 512 Processing helix chain 'F' and resid 514 through 529 Processing helix chain 'F' and resid 535 through 546 Processing helix chain 'F' and resid 548 through 561 removed outlier: 3.509A pdb=" N ASP F 561 " --> pdb=" O LYS F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 580 removed outlier: 3.595A pdb=" N TRP F 570 " --> pdb=" O SER F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 597 Processing helix chain 'F' and resid 600 through 614 removed outlier: 4.359A pdb=" N TYR F 604 " --> pdb=" O TYR F 600 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR F 605 " --> pdb=" O ALA F 601 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR F 614 " --> pdb=" O GLU F 610 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 631 Processing helix chain 'F' and resid 634 through 649 removed outlier: 4.170A pdb=" N TRP F 638 " --> pdb=" O HIS F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 665 removed outlier: 3.655A pdb=" N MET F 656 " --> pdb=" O SER F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 667 through 682 removed outlier: 4.493A pdb=" N LEU F 671 " --> pdb=" O GLN F 667 " (cutoff:3.500A) Processing helix chain 'F' and resid 691 through 699 removed outlier: 3.962A pdb=" N ILE F 696 " --> pdb=" O LEU F 692 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 716 removed outlier: 3.654A pdb=" N LYS F 706 " --> pdb=" O ASN F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 733 removed outlier: 3.541A pdb=" N ILE F 732 " --> pdb=" O GLU F 728 " (cutoff:3.500A) Processing helix chain 'F' and resid 736 through 751 removed outlier: 3.728A pdb=" N TYR F 740 " --> pdb=" O GLU F 736 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 743 " --> pdb=" O VAL F 739 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS F 749 " --> pdb=" O LYS F 745 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 23 removed outlier: 3.763A pdb=" N GLU G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE G 19 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU G 20 " --> pdb=" O ILE G 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 18 Processing helix chain 'H' and resid 20 through 36 Processing helix chain 'H' and resid 37 through 51 Processing helix chain 'H' and resid 53 through 64 Processing helix chain 'H' and resid 68 through 82 Processing helix chain 'H' and resid 84 through 94 removed outlier: 3.679A pdb=" N ILE H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 111 Processing helix chain 'H' and resid 113 through 129 Processing helix chain 'H' and resid 130 through 145 removed outlier: 3.739A pdb=" N GLU H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER H 141 " --> pdb=" O CYS H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 158 removed outlier: 4.098A pdb=" N PHE H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 174 removed outlier: 3.892A pdb=" N PHE H 168 " --> pdb=" O PRO H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 479 removed outlier: 3.516A pdb=" N GLY H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU H 462 " --> pdb=" O ALA H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 490 removed outlier: 3.517A pdb=" N ILE H 485 " --> pdb=" O CYS H 481 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 493 through 498 Processing helix chain 'H' and resid 498 through 513 Processing helix chain 'H' and resid 514 through 529 Processing helix chain 'H' and resid 535 through 547 Processing helix chain 'H' and resid 548 through 563 Processing helix chain 'H' and resid 566 through 580 removed outlier: 3.652A pdb=" N TRP H 570 " --> pdb=" O SER H 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 597 removed outlier: 3.538A pdb=" N PHE H 589 " --> pdb=" O ILE H 585 " (cutoff:3.500A) Processing helix chain 'H' and resid 600 through 615 removed outlier: 4.420A pdb=" N TYR H 604 " --> pdb=" O TYR H 600 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR H 605 " --> pdb=" O ALA H 601 " (cutoff:3.500A) Processing helix chain 'H' and resid 616 through 631 removed outlier: 3.554A pdb=" N ALA H 622 " --> pdb=" O ASP H 618 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS H 623 " --> pdb=" O LYS H 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 634 through 649 removed outlier: 3.764A pdb=" N TRP H 638 " --> pdb=" O HIS H 634 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 665 removed outlier: 3.575A pdb=" N MET H 656 " --> pdb=" O SER H 652 " (cutoff:3.500A) Processing helix chain 'H' and resid 668 through 682 Processing helix chain 'H' and resid 684 through 699 Processing helix chain 'H' and resid 702 through 717 removed outlier: 3.672A pdb=" N LYS H 706 " --> pdb=" O ASN H 702 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG H 709 " --> pdb=" O CYS H 705 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA H 710 " --> pdb=" O LYS H 706 " (cutoff:3.500A) Processing helix chain 'H' and resid 718 through 733 removed outlier: 3.629A pdb=" N GLU H 728 " --> pdb=" O GLN H 724 " (cutoff:3.500A) Processing helix chain 'H' and resid 736 through 751 removed outlier: 3.798A pdb=" N TYR H 740 " --> pdb=" O GLU H 736 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS H 749 " --> pdb=" O LYS H 745 " (cutoff:3.500A) Processing helix chain 'H' and resid 752 through 767 removed outlier: 3.715A pdb=" N ALA H 763 " --> pdb=" O ASN H 759 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 52 Processing helix chain 'I' and resid 122 through 139 removed outlier: 3.590A pdb=" N LEU I 138 " --> pdb=" O GLU I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 169 removed outlier: 3.508A pdb=" N LEU I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU I 168 " --> pdb=" O ILE I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 244 Processing helix chain 'I' and resid 244 through 295 removed outlier: 4.434A pdb=" N PHE I 290 " --> pdb=" O ARG I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 310 Processing helix chain 'I' and resid 315 through 325 removed outlier: 3.535A pdb=" N THR I 319 " --> pdb=" O ALA I 315 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 350 Processing helix chain 'I' and resid 350 through 372 Processing helix chain 'I' and resid 372 through 377 Processing helix chain 'I' and resid 382 through 429 Processing helix chain 'I' and resid 441 through 457 removed outlier: 3.948A pdb=" N PHE I 447 " --> pdb=" O LYS I 443 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL I 448 " --> pdb=" O ASP I 444 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU I 452 " --> pdb=" O VAL I 448 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR I 453 " --> pdb=" O ALA I 449 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU I 454 " --> pdb=" O GLU I 450 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N HIS I 455 " --> pdb=" O PHE I 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 473 through 480 removed outlier: 3.814A pdb=" N TYR I 478 " --> pdb=" O ARG I 474 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU I 479 " --> pdb=" O VAL I 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 503 Processing helix chain 'I' and resid 521 through 548 removed outlier: 3.814A pdb=" N CYS I 536 " --> pdb=" O ILE I 532 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU I 537 " --> pdb=" O ILE I 533 " (cutoff:3.500A) Proline residue: I 540 - end of helix removed outlier: 4.126A pdb=" N MET I 548 " --> pdb=" O ILE I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 672 through 674 No H-bonds generated for 'chain 'I' and resid 672 through 674' Processing helix chain 'I' and resid 679 through 683 Processing helix chain 'J' and resid 2 through 17 Processing helix chain 'J' and resid 18 through 34 Processing helix chain 'J' and resid 36 through 50 Processing helix chain 'J' and resid 52 through 64 removed outlier: 3.591A pdb=" N ARG J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 70 removed outlier: 3.522A pdb=" N LEU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 84 removed outlier: 3.621A pdb=" N LEU J 75 " --> pdb=" O ALA J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 94 Processing helix chain 'J' and resid 124 through 144 Processing helix chain 'J' and resid 145 through 161 Processing helix chain 'J' and resid 163 through 173 removed outlier: 4.221A pdb=" N PHE J 167 " --> pdb=" O CYS J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 188 removed outlier: 3.566A pdb=" N GLU J 186 " --> pdb=" O LYS J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 224 through 230 removed outlier: 3.766A pdb=" N GLN J 228 " --> pdb=" O VAL J 224 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU J 229 " --> pdb=" O ASP J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 245 Processing helix chain 'J' and resid 246 through 261 removed outlier: 3.567A pdb=" N VAL J 256 " --> pdb=" O LYS J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 279 removed outlier: 4.479A pdb=" N VAL J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 295 Processing helix chain 'J' and resid 298 through 313 removed outlier: 3.936A pdb=" N TRP J 302 " --> pdb=" O ASN J 298 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL J 312 " --> pdb=" O TYR J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 330 Processing helix chain 'J' and resid 333 through 348 removed outlier: 3.666A pdb=" N TRP J 337 " --> pdb=" O TYR J 333 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE J 344 " --> pdb=" O TYR J 340 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 364 Processing helix chain 'J' and resid 368 through 382 Processing helix chain 'J' and resid 383 through 397 Processing helix chain 'J' and resid 401 through 416 Processing helix chain 'J' and resid 418 through 434 removed outlier: 3.583A pdb=" N ALA J 434 " --> pdb=" O GLU J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 459 Processing helix chain 'J' and resid 460 through 475 Processing helix chain 'J' and resid 478 through 492 Processing helix chain 'J' and resid 494 through 509 Processing helix chain 'J' and resid 512 through 529 removed outlier: 3.569A pdb=" N VAL J 516 " --> pdb=" O ASP J 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 17 Processing helix chain 'K' and resid 18 through 34 Processing helix chain 'K' and resid 36 through 50 Processing helix chain 'K' and resid 52 through 62 Processing helix chain 'K' and resid 64 through 69 Processing helix chain 'K' and resid 69 through 83 Processing helix chain 'K' and resid 88 through 93 Processing helix chain 'K' and resid 128 through 144 Processing helix chain 'K' and resid 145 through 161 Processing helix chain 'K' and resid 163 through 172 removed outlier: 4.102A pdb=" N PHE K 167 " --> pdb=" O CYS K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 188 Processing helix chain 'K' and resid 193 through 211 removed outlier: 3.966A pdb=" N GLU K 197 " --> pdb=" O LEU K 193 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS K 211 " --> pdb=" O ASN K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 225 removed outlier: 3.542A pdb=" N GLU K 222 " --> pdb=" O THR K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 229 Processing helix chain 'K' and resid 230 through 245 Processing helix chain 'K' and resid 246 through 261 Processing helix chain 'K' and resid 266 through 279 removed outlier: 4.522A pdb=" N VAL K 270 " --> pdb=" O SER K 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 295 Processing helix chain 'K' and resid 298 through 313 removed outlier: 3.991A pdb=" N TRP K 302 " --> pdb=" O ASN K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 330 Processing helix chain 'K' and resid 334 through 348 removed outlier: 3.722A pdb=" N PHE K 344 " --> pdb=" O TYR K 340 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 364 Processing helix chain 'K' and resid 368 through 381 Processing helix chain 'K' and resid 383 through 398 Processing helix chain 'K' and resid 401 through 416 Processing helix chain 'K' and resid 417 through 435 Processing helix chain 'K' and resid 440 through 459 removed outlier: 4.009A pdb=" N TRP K 444 " --> pdb=" O THR K 440 " (cutoff:3.500A) Proline residue: K 446 - end of helix Processing helix chain 'K' and resid 460 through 475 removed outlier: 3.573A pdb=" N LEU K 474 " --> pdb=" O GLN K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 493 Processing helix chain 'K' and resid 494 through 509 Processing helix chain 'K' and resid 512 through 527 Processing helix chain 'L' and resid 12 through 20 removed outlier: 3.851A pdb=" N GLY L 20 " --> pdb=" O LEU L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 Processing helix chain 'L' and resid 145 through 148 removed outlier: 3.768A pdb=" N GLY L 148 " --> pdb=" O HIS L 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 145 through 148' Processing helix chain 'L' and resid 174 through 180 removed outlier: 3.503A pdb=" N MET L 179 " --> pdb=" O ILE L 175 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 16 removed outlier: 4.033A pdb=" N ASP M 16 " --> pdb=" O LEU M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 22 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.739A pdb=" N MET M 55 " --> pdb=" O LYS M 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 29 Processing helix chain 'N' and resid 51 through 66 removed outlier: 3.604A pdb=" N HIS N 65 " --> pdb=" O VAL N 61 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY N 66 " --> pdb=" O LEU N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 86 removed outlier: 4.165A pdb=" N LEU N 71 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU N 72 " --> pdb=" O HIS N 68 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU N 73 " --> pdb=" O SER N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 100 Processing helix chain 'N' and resid 104 through 121 Processing helix chain 'N' and resid 122 through 138 removed outlier: 3.624A pdb=" N GLU N 133 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS N 134 " --> pdb=" O GLU N 130 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU N 138 " --> pdb=" O LYS N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 162 removed outlier: 4.270A pdb=" N VAL N 153 " --> pdb=" O LEU N 149 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N HIS N 154 " --> pdb=" O ARG N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 191 removed outlier: 3.734A pdb=" N GLN N 170 " --> pdb=" O PRO N 166 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU N 171 " --> pdb=" O ARG N 167 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER N 187 " --> pdb=" O VAL N 183 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS N 188 " --> pdb=" O TYR N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 251 Processing helix chain 'N' and resid 253 through 278 removed outlier: 4.000A pdb=" N GLU N 259 " --> pdb=" O ARG N 255 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA N 260 " --> pdb=" O VAL N 256 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR N 263 " --> pdb=" O GLU N 259 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP N 275 " --> pdb=" O GLU N 271 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG N 276 " --> pdb=" O ARG N 272 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 304 removed outlier: 4.237A pdb=" N LYS N 291 " --> pdb=" O ARG N 287 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP N 292 " --> pdb=" O GLU N 288 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE N 293 " --> pdb=" O PHE N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 343 removed outlier: 3.656A pdb=" N ARG N 325 " --> pdb=" O LEU N 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 343 through 350 Processing helix chain 'N' and resid 354 through 368 removed outlier: 3.542A pdb=" N GLU N 366 " --> pdb=" O LYS N 362 " (cutoff:3.500A) Processing helix chain 'N' and resid 371 through 387 Processing helix chain 'N' and resid 392 through 409 removed outlier: 3.585A pdb=" N ARG N 408 " --> pdb=" O ILE N 404 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL N 409 " --> pdb=" O LYS N 405 " (cutoff:3.500A) Processing helix chain 'N' and resid 414 through 431 removed outlier: 4.185A pdb=" N VAL N 419 " --> pdb=" O VAL N 415 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA N 420 " --> pdb=" O ILE N 416 " (cutoff:3.500A) Proline residue: N 423 - end of helix Processing helix chain 'N' and resid 434 through 443 Processing helix chain 'N' and resid 499 through 510 removed outlier: 3.609A pdb=" N SER N 503 " --> pdb=" O SER N 499 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU N 504 " --> pdb=" O ASP N 500 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU N 505 " --> pdb=" O ILE N 501 " (cutoff:3.500A) Processing helix chain 'N' and resid 511 through 530 removed outlier: 3.643A pdb=" N LEU N 528 " --> pdb=" O ALA N 524 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS N 529 " --> pdb=" O ASP N 525 " (cutoff:3.500A) Processing helix chain 'N' and resid 534 through 549 Processing helix chain 'N' and resid 551 through 563 removed outlier: 3.739A pdb=" N PHE N 556 " --> pdb=" O ALA N 552 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL N 559 " --> pdb=" O HIS N 555 " (cutoff:3.500A) Processing helix chain 'N' and resid 564 through 580 Processing helix chain 'N' and resid 581 through 584 Processing helix chain 'N' and resid 612 through 629 removed outlier: 4.141A pdb=" N ALA N 617 " --> pdb=" O GLU N 613 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA N 618 " --> pdb=" O ASP N 614 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 642 removed outlier: 3.550A pdb=" N LEU N 641 " --> pdb=" O LYS N 638 " (cutoff:3.500A) Processing helix chain 'N' and resid 660 through 672 removed outlier: 3.733A pdb=" N ILE N 666 " --> pdb=" O VAL N 662 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU N 667 " --> pdb=" O GLN N 663 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP N 672 " --> pdb=" O LEU N 668 " (cutoff:3.500A) Processing helix chain 'N' and resid 677 through 686 removed outlier: 3.744A pdb=" N VAL N 685 " --> pdb=" O LEU N 681 " (cutoff:3.500A) Processing helix chain 'N' and resid 688 through 703 Processing helix chain 'O' and resid 31 through 45 Processing helix chain 'O' and resid 53 through 70 removed outlier: 3.624A pdb=" N LEU O 63 " --> pdb=" O ARG O 59 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU O 64 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU O 65 " --> pdb=" O ASN O 61 " (cutoff:3.500A) Proline residue: O 66 - end of helix Processing helix chain 'O' and resid 77 through 86 removed outlier: 4.091A pdb=" N SER O 85 " --> pdb=" O LEU O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 103 removed outlier: 3.913A pdb=" N ALA O 90 " --> pdb=" O CYS O 86 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN O 91 " --> pdb=" O PRO O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 122 removed outlier: 3.708A pdb=" N MET O 108 " --> pdb=" O GLU O 104 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER O 118 " --> pdb=" O ASP O 114 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER O 120 " --> pdb=" O SER O 116 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR O 122 " --> pdb=" O SER O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 146 Processing helix chain 'O' and resid 147 through 167 Processing helix chain 'O' and resid 208 through 226 Processing helix chain 'O' and resid 232 through 247 Processing helix chain 'O' and resid 251 through 265 removed outlier: 3.792A pdb=" N TYR O 255 " --> pdb=" O ALA O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 281 removed outlier: 3.689A pdb=" N SER O 270 " --> pdb=" O ASP O 266 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 315 removed outlier: 4.284A pdb=" N ARG O 301 " --> pdb=" O GLY O 297 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR O 302 " --> pdb=" O ARG O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 316 through 335 Processing helix chain 'O' and resid 336 through 351 removed outlier: 3.607A pdb=" N LEU O 340 " --> pdb=" O ASP O 336 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS O 342 " --> pdb=" O VAL O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 360 through 370 removed outlier: 3.983A pdb=" N SER O 364 " --> pdb=" O LEU O 360 " (cutoff:3.500A) Processing helix chain 'O' and resid 373 through 391 Processing helix chain 'O' and resid 402 through 412 removed outlier: 3.982A pdb=" N LEU O 407 " --> pdb=" O LYS O 403 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU O 408 " --> pdb=" O ASP O 404 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS O 412 " --> pdb=" O LEU O 408 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 432 removed outlier: 3.829A pdb=" N ILE O 418 " --> pdb=" O LEU O 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 434 through 448 removed outlier: 3.500A pdb=" N MET O 444 " --> pdb=" O GLN O 440 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU O 445 " --> pdb=" O GLN O 441 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU O 446 " --> pdb=" O ALA O 442 " (cutoff:3.500A) Processing helix chain 'O' and resid 462 through 480 removed outlier: 3.956A pdb=" N PHE O 466 " --> pdb=" O ASN O 462 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA O 467 " --> pdb=" O THR O 463 " (cutoff:3.500A) Processing helix chain 'O' and resid 482 through 497 Processing helix chain 'O' and resid 503 through 523 Processing helix chain 'O' and resid 524 through 540 removed outlier: 3.535A pdb=" N THR O 533 " --> pdb=" O ASP O 529 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY O 534 " --> pdb=" O SER O 530 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU O 538 " --> pdb=" O GLY O 534 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 555 Processing helix chain 'O' and resid 556 through 575 Processing helix chain 'O' and resid 576 through 594 removed outlier: 3.548A pdb=" N VAL O 580 " --> pdb=" O ASN O 576 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG O 593 " --> pdb=" O GLU O 589 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER O 594 " --> pdb=" O LEU O 590 " (cutoff:3.500A) Processing helix chain 'O' and resid 596 through 598 No H-bonds generated for 'chain 'O' and resid 596 through 598' Processing helix chain 'O' and resid 599 through 615 removed outlier: 4.477A pdb=" N MET O 603 " --> pdb=" O ILE O 599 " (cutoff:3.500A) Processing helix chain 'O' and resid 616 through 634 removed outlier: 3.666A pdb=" N ALA O 620 " --> pdb=" O LEU O 616 " (cutoff:3.500A) Processing helix chain 'O' and resid 636 through 654 removed outlier: 4.379A pdb=" N MET O 646 " --> pdb=" O SER O 642 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA O 647 " --> pdb=" O LEU O 643 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU O 649 " --> pdb=" O HIS O 645 " (cutoff:3.500A) Proline residue: O 650 - end of helix removed outlier: 3.570A pdb=" N ASP O 654 " --> pdb=" O PRO O 650 " (cutoff:3.500A) Processing helix chain 'O' and resid 657 through 678 removed outlier: 3.570A pdb=" N SER O 677 " --> pdb=" O ALA O 673 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR O 678 " --> pdb=" O SER O 674 " (cutoff:3.500A) Processing helix chain 'O' and resid 682 through 705 removed outlier: 3.677A pdb=" N ASN O 699 " --> pdb=" O ASN O 695 " (cutoff:3.500A) Processing helix chain 'O' and resid 707 through 725 removed outlier: 3.756A pdb=" N ASP O 712 " --> pdb=" O GLU O 708 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL O 713 " --> pdb=" O ARG O 709 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR O 723 " --> pdb=" O ARG O 719 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU O 724 " --> pdb=" O LEU O 720 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY O 725 " --> pdb=" O TYR O 721 " (cutoff:3.500A) Processing helix chain 'O' and resid 726 through 743 removed outlier: 3.724A pdb=" N ARG O 732 " --> pdb=" O GLN O 728 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU O 736 " --> pdb=" O ARG O 732 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE O 737 " --> pdb=" O CYS O 733 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU O 743 " --> pdb=" O GLN O 739 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 47 Processing helix chain 'P' and resid 48 through 62 Processing helix chain 'P' and resid 77 through 97 removed outlier: 4.016A pdb=" N ASP P 85 " --> pdb=" O ALA P 81 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA P 86 " --> pdb=" O GLN P 82 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU P 89 " --> pdb=" O ASP P 85 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS P 97 " --> pdb=" O TYR P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 107 Processing helix chain 'P' and resid 111 through 134 Processing helix chain 'P' and resid 148 through 165 removed outlier: 3.756A pdb=" N LEU P 154 " --> pdb=" O ALA P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 182 Processing helix chain 'P' and resid 184 through 199 Processing helix chain 'P' and resid 202 through 213 removed outlier: 3.643A pdb=" N TRP P 206 " --> pdb=" O HIS P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 222 Processing helix chain 'P' and resid 228 through 241 Processing helix chain 'P' and resid 243 through 257 Processing helix chain 'P' and resid 262 through 276 removed outlier: 3.807A pdb=" N VAL P 266 " --> pdb=" O SER P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 278 through 293 removed outlier: 3.658A pdb=" N ILE P 285 " --> pdb=" O LYS P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 299 through 310 Processing helix chain 'P' and resid 312 through 327 Processing helix chain 'P' and resid 330 through 344 Processing helix chain 'P' and resid 346 through 361 removed outlier: 3.504A pdb=" N ASN P 361 " --> pdb=" O ALA P 357 " (cutoff:3.500A) Processing helix chain 'P' and resid 364 through 378 removed outlier: 3.837A pdb=" N TRP P 368 " --> pdb=" O TYR P 364 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR P 369 " --> pdb=" O LEU P 365 " (cutoff:3.500A) Processing helix chain 'P' and resid 380 through 395 Processing helix chain 'P' and resid 398 through 412 Processing helix chain 'P' and resid 415 through 429 Processing helix chain 'P' and resid 432 through 447 Processing helix chain 'P' and resid 448 through 463 Processing helix chain 'P' and resid 468 through 480 Processing helix chain 'P' and resid 482 through 500 removed outlier: 3.522A pdb=" N ALA P 486 " --> pdb=" O GLU P 482 " (cutoff:3.500A) Processing helix chain 'P' and resid 511 through 524 Processing helix chain 'P' and resid 525 through 538 Processing helix chain 'W' and resid 12 through 23 removed outlier: 3.679A pdb=" N GLU W 18 " --> pdb=" O ASP W 14 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE W 19 " --> pdb=" O ASP W 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 48 Processing helix chain 'X' and resid 49 through 67 Processing helix chain 'X' and resid 72 through 90 Processing helix chain 'X' and resid 92 through 110 Processing helix chain 'X' and resid 134 through 150 Processing helix chain 'X' and resid 151 through 162 removed outlier: 3.867A pdb=" N ALA X 155 " --> pdb=" O GLN X 151 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE X 162 " --> pdb=" O ILE X 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 168 through 183 Processing helix chain 'X' and resid 184 through 199 Processing helix chain 'X' and resid 202 through 213 Processing helix chain 'X' and resid 214 through 229 removed outlier: 3.571A pdb=" N GLU X 218 " --> pdb=" O VAL X 214 " (cutoff:3.500A) Processing helix chain 'X' and resid 233 through 249 removed outlier: 4.293A pdb=" N SER X 237 " --> pdb=" O LEU X 233 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL X 238 " --> pdb=" O ASP X 234 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS X 241 " --> pdb=" O SER X 237 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY X 249 " --> pdb=" O PHE X 245 " (cutoff:3.500A) Processing helix chain 'X' and resid 250 through 264 removed outlier: 3.650A pdb=" N ALA X 254 " --> pdb=" O ASP X 250 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 285 Processing helix chain 'X' and resid 286 through 301 removed outlier: 3.558A pdb=" N VAL X 291 " --> pdb=" O ASN X 287 " (cutoff:3.500A) Processing helix chain 'X' and resid 304 through 319 removed outlier: 3.875A pdb=" N ASP X 309 " --> pdb=" O ILE X 305 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL X 310 " --> pdb=" O LYS X 306 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR X 313 " --> pdb=" O ASP X 309 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU X 314 " --> pdb=" O VAL X 310 " (cutoff:3.500A) Processing helix chain 'X' and resid 320 through 335 Processing helix chain 'X' and resid 338 through 353 removed outlier: 3.920A pdb=" N TRP X 342 " --> pdb=" O HIS X 338 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE X 350 " --> pdb=" O GLY X 346 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR X 351 " --> pdb=" O CYS X 347 " (cutoff:3.500A) Processing helix chain 'X' and resid 354 through 369 Processing helix chain 'X' and resid 372 through 387 removed outlier: 4.295A pdb=" N LEU X 376 " --> pdb=" O SER X 372 " (cutoff:3.500A) Processing helix chain 'X' and resid 389 through 403 Processing helix chain 'X' and resid 406 through 421 removed outlier: 4.039A pdb=" N TYR X 410 " --> pdb=" O ARG X 406 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU X 413 " --> pdb=" O CYS X 409 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 438 Processing helix chain 'X' and resid 441 through 454 removed outlier: 3.989A pdb=" N THR X 445 " --> pdb=" O ALA X 441 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU X 446 " --> pdb=" O GLN X 442 " (cutoff:3.500A) Processing helix chain 'X' and resid 457 through 472 removed outlier: 4.027A pdb=" N LEU X 464 " --> pdb=" O LYS X 460 " (cutoff:3.500A) Processing helix chain 'X' and resid 475 through 490 removed outlier: 3.566A pdb=" N LEU X 485 " --> pdb=" O LYS X 481 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 506 removed outlier: 3.670A pdb=" N GLY X 495 " --> pdb=" O LYS X 491 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA X 497 " --> pdb=" O GLU X 493 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN X 501 " --> pdb=" O ALA X 497 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN X 505 " --> pdb=" O ASN X 501 " (cutoff:3.500A) Processing helix chain 'X' and resid 509 through 523 removed outlier: 3.915A pdb=" N ARG X 513 " --> pdb=" O CYS X 509 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA X 521 " --> pdb=" O ASP X 517 " (cutoff:3.500A) Processing helix chain 'X' and resid 524 through 539 Processing helix chain 'Y' and resid 36 through 47 Processing helix chain 'Y' and resid 49 through 67 Processing helix chain 'Y' and resid 72 through 91 Processing helix chain 'Y' and resid 92 through 110 Processing helix chain 'Y' and resid 134 through 150 Processing helix chain 'Y' and resid 151 through 162 removed outlier: 4.399A pdb=" N ALA Y 155 " --> pdb=" O GLN Y 151 " (cutoff:3.500A) Processing helix chain 'Y' and resid 168 through 183 Processing helix chain 'Y' and resid 184 through 199 removed outlier: 4.090A pdb=" N CYS Y 199 " --> pdb=" O VAL Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 213 Processing helix chain 'Y' and resid 214 through 229 Processing helix chain 'Y' and resid 235 through 249 removed outlier: 3.750A pdb=" N GLY Y 249 " --> pdb=" O PHE Y 245 " (cutoff:3.500A) Processing helix chain 'Y' and resid 250 through 264 removed outlier: 3.669A pdb=" N ALA Y 254 " --> pdb=" O ASP Y 250 " (cutoff:3.500A) Processing helix chain 'Y' and resid 270 through 285 Processing helix chain 'Y' and resid 286 through 301 Processing helix chain 'Y' and resid 304 through 319 removed outlier: 3.518A pdb=" N MET Y 308 " --> pdb=" O LEU Y 304 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP Y 309 " --> pdb=" O ILE Y 305 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL Y 310 " --> pdb=" O LYS Y 306 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR Y 313 " --> pdb=" O ASP Y 309 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU Y 314 " --> pdb=" O VAL Y 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 320 through 335 Processing helix chain 'Y' and resid 338 through 352 removed outlier: 3.934A pdb=" N TRP Y 342 " --> pdb=" O HIS Y 338 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 369 Processing helix chain 'Y' and resid 372 through 387 Processing helix chain 'Y' and resid 388 through 403 removed outlier: 3.945A pdb=" N HIS Y 395 " --> pdb=" O GLU Y 391 " (cutoff:3.500A) Processing helix chain 'Y' and resid 406 through 421 removed outlier: 3.565A pdb=" N LEU Y 413 " --> pdb=" O CYS Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 422 through 438 Processing helix chain 'Y' and resid 441 through 454 removed outlier: 3.748A pdb=" N THR Y 445 " --> pdb=" O ALA Y 441 " (cutoff:3.500A) Processing helix chain 'Y' and resid 457 through 472 removed outlier: 4.032A pdb=" N LEU Y 464 " --> pdb=" O LYS Y 460 " (cutoff:3.500A) Processing helix chain 'Y' and resid 475 through 490 removed outlier: 3.579A pdb=" N LEU Y 485 " --> pdb=" O LYS Y 481 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 506 removed outlier: 3.642A pdb=" N GLY Y 495 " --> pdb=" O LYS Y 491 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA Y 497 " --> pdb=" O GLU Y 493 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN Y 501 " --> pdb=" O ALA Y 497 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN Y 505 " --> pdb=" O ASN Y 501 " (cutoff:3.500A) Processing helix chain 'Y' and resid 509 through 523 removed outlier: 3.920A pdb=" N ARG Y 513 " --> pdb=" O CYS Y 509 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA Y 521 " --> pdb=" O ASP Y 517 " (cutoff:3.500A) Processing helix chain 'Y' and resid 524 through 539 Processing helix chain 'Y' and resid 542 through 552 removed outlier: 3.906A pdb=" N GLY Y 548 " --> pdb=" O LYS Y 544 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET Y 549 " --> pdb=" O SER Y 545 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET Y 552 " --> pdb=" O GLY Y 548 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 17 through 20 removed outlier: 3.781A pdb=" N MET A 604 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 597 " --> pdb=" O VAL A 605 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG A 594 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASP A 589 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR A 596 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE A 587 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU A 598 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 73 through 78 removed outlier: 3.734A pdb=" N SER A 103 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A 100 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A 116 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP A 102 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 128 through 131 Processing sheet with id= AD, first strand: chain 'A' and resid 180 through 183 Processing sheet with id= AE, first strand: chain 'A' and resid 237 through 238 removed outlier: 6.661A pdb=" N VAL A 268 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 255 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU A 249 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET A 257 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 429 through 434 removed outlier: 3.578A pdb=" N LYS A 429 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS A 440 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 446 " --> pdb=" O GLN A 451 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 451 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU A 452 " --> pdb=" O ASN A 473 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN A 473 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS A 454 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL A 471 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS A 456 " --> pdb=" O GLY A 469 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 478 through 482 removed outlier: 3.793A pdb=" N ASP A 478 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 482 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A 499 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 1047 through 1048 removed outlier: 3.595A pdb=" N THR A1116 " --> pdb=" O ALA A1111 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 1572 through 1574 Processing sheet with id= AJ, first strand: chain 'A' and resid 1620 through 1622 Processing sheet with id= AK, first strand: chain 'A' and resid 1646 through 1652 removed outlier: 3.805A pdb=" N THR A1647 " --> pdb=" O TYR A1638 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU A1633 " --> pdb=" O VAL A1668 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL A1668 " --> pdb=" O LEU A1633 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU A1635 " --> pdb=" O ILE A1666 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE A1666 " --> pdb=" O GLU A1635 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR A1637 " --> pdb=" O LYS A1664 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A1675 " --> pdb=" O VAL A1668 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'B' and resid 3 through 9 removed outlier: 5.051A pdb=" N ILE B 5 " --> pdb=" O ASP N 647 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASP N 647 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS B 7 " --> pdb=" O THR N 645 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU N 655 " --> pdb=" O VAL N 648 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'B' and resid 46 through 48 Processing sheet with id= IA, first strand: chain 'I' and resid 23 through 28 removed outlier: 6.958A pdb=" N VAL I 44 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER I 57 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU I 46 " --> pdb=" O VAL I 55 " (cutoff:3.500A) Processing sheet with id= IB, first strand: chain 'I' and resid 68 through 73 removed outlier: 4.131A pdb=" N CYS I 70 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS I 93 " --> pdb=" O LEU I 80 " (cutoff:3.500A) Processing sheet with id= IC, first strand: chain 'I' and resid 112 through 117 removed outlier: 3.757A pdb=" N GLU I 186 " --> pdb=" O LEU I 178 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE I 185 " --> pdb=" O ARG I 197 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG I 197 " --> pdb=" O ILE I 185 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU I 187 " --> pdb=" O ILE I 195 " (cutoff:3.500A) Processing sheet with id= ID, first strand: chain 'I' and resid 204 through 210 removed outlier: 6.283A pdb=" N CYS I 205 " --> pdb=" O GLU I 222 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLU I 222 " --> pdb=" O CYS I 205 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA I 207 " --> pdb=" O VAL I 220 " (cutoff:3.500A) Processing sheet with id= IE, first strand: chain 'I' and resid 229 through 230 Processing sheet with id= IF, first strand: chain 'I' and resid 574 through 578 removed outlier: 11.927A pdb=" N TYR I 596 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) Processing sheet with id= IG, first strand: chain 'I' and resid 574 through 578 removed outlier: 11.927A pdb=" N TYR I 596 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE I 707 " --> pdb=" O GLY I 621 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE I 623 " --> pdb=" O PHE I 707 " (cutoff:3.500A) Processing sheet with id= IH, first strand: chain 'I' and resid 631 through 632 Processing sheet with id= II, first strand: chain 'I' and resid 636 through 645 removed outlier: 5.621A pdb=" N CYS I 638 " --> pdb=" O LYS I 654 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS I 654 " --> pdb=" O CYS I 638 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR I 648 " --> pdb=" O TYR I 644 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG I 664 " --> pdb=" O LEU I 714 " (cutoff:3.500A) Processing sheet with id= IJ, first strand: chain 'I' and resid 719 through 724 Processing sheet with id= LA, first strand: chain 'L' and resid 22 through 24 removed outlier: 3.833A pdb=" N GLN L 155 " --> pdb=" O TYR L 80 " (cutoff:3.500A) Processing sheet with id= LB, first strand: chain 'L' and resid 30 through 33 removed outlier: 3.636A pdb=" N HIS L 62 " --> pdb=" O VAL L 141 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE L 94 " --> pdb=" O GLN L 110 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLN L 110 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL L 96 " --> pdb=" O ILE L 108 " (cutoff:3.500A) Processing sheet with id= LC, first strand: chain 'L' and resid 73 through 74 removed outlier: 4.149A pdb=" N THR L 132 " --> pdb=" O VAL L 74 " (cutoff:3.500A) 4077 hydrogen bonds defined for protein. 12117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 25.23 Time building geometry restraints manager: 24.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.42: 27239 1.42 - 1.70: 36706 1.70 - 1.97: 593 1.97 - 2.24: 2 2.24 - 2.51: 1 Bond restraints: 64541 Sorted by residual: bond pdb=" C ASP N 563 " pdb=" N MET N 564 " ideal model delta sigma weight residual 1.335 2.508 -1.173 1.31e-02 5.83e+03 8.02e+03 bond pdb=" C VAL K 219 " pdb=" N ILE K 220 " ideal model delta sigma weight residual 1.329 2.003 -0.674 1.13e-02 7.83e+03 3.56e+03 bond pdb=" C ARG C 344 " pdb=" N SER C 345 " ideal model delta sigma weight residual 1.332 2.011 -0.679 1.40e-02 5.10e+03 2.35e+03 bond pdb=" C SER O 116 " pdb=" N ASP O 117 " ideal model delta sigma weight residual 1.335 1.908 -0.573 1.35e-02 5.49e+03 1.80e+03 bond pdb=" C PHE O 135 " pdb=" N LEU O 136 " ideal model delta sigma weight residual 1.335 1.650 -0.315 1.38e-02 5.25e+03 5.20e+02 ... (remaining 64536 not shown) Histogram of bond angle deviations from ideal: 88.49 - 99.06: 67 99.06 - 109.63: 10897 109.63 - 120.21: 49792 120.21 - 130.78: 26306 130.78 - 141.35: 403 Bond angle restraints: 87465 Sorted by residual: angle pdb=" O VAL I 433 " pdb=" C VAL I 433 " pdb=" N PRO I 435 " ideal model delta sigma weight residual 121.10 89.22 31.88 1.14e+00 7.69e-01 7.82e+02 angle pdb=" C VAL I 433 " pdb=" N PRO I 435 " pdb=" CA PRO I 435 " ideal model delta sigma weight residual 119.84 96.63 23.21 1.25e+00 6.40e-01 3.45e+02 angle pdb=" CA GLU N 610 " pdb=" C GLU N 610 " pdb=" N VAL N 611 " ideal model delta sigma weight residual 116.36 136.35 -19.99 1.28e+00 6.10e-01 2.44e+02 angle pdb=" CA VAL I 433 " pdb=" C VAL I 433 " pdb=" N PRO I 435 " ideal model delta sigma weight residual 118.88 98.07 20.81 1.54e+00 4.22e-01 1.83e+02 angle pdb=" C ASP N 563 " pdb=" N MET N 564 " pdb=" CA MET N 564 " ideal model delta sigma weight residual 120.28 103.14 17.14 1.34e+00 5.57e-01 1.64e+02 ... (remaining 87460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 33937 21.24 - 42.49: 3647 42.49 - 63.73: 1138 63.73 - 84.97: 128 84.97 - 106.22: 11 Dihedral angle restraints: 38861 sinusoidal: 15147 harmonic: 23714 Sorted by residual: dihedral pdb=" CA VAL I 433 " pdb=" C VAL I 433 " pdb=" N PRO I 435 " pdb=" CA PRO I 435 " ideal model delta harmonic sigma weight residual 180.00 73.78 106.22 0 5.00e+00 4.00e-02 4.51e+02 dihedral pdb=" CA GLU N 610 " pdb=" C GLU N 610 " pdb=" N VAL N 611 " pdb=" CA VAL N 611 " ideal model delta harmonic sigma weight residual -180.00 -105.33 -74.67 0 5.00e+00 4.00e-02 2.23e+02 dihedral pdb=" C THR L 132 " pdb=" N THR L 132 " pdb=" CA THR L 132 " pdb=" CB THR L 132 " ideal model delta harmonic sigma weight residual -122.00 -103.72 -18.28 0 2.50e+00 1.60e-01 5.35e+01 ... (remaining 38858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 8024 0.126 - 0.252: 1571 0.252 - 0.378: 215 0.378 - 0.504: 36 0.504 - 0.630: 13 Chirality restraints: 9859 Sorted by residual: chirality pdb=" CG LEU I 210 " pdb=" CB LEU I 210 " pdb=" CD1 LEU I 210 " pdb=" CD2 LEU I 210 " both_signs ideal model delta sigma weight residual False -2.59 -3.22 0.63 2.00e-01 2.50e+01 9.92e+00 chirality pdb=" CB VAL I 300 " pdb=" CA VAL I 300 " pdb=" CG1 VAL I 300 " pdb=" CG2 VAL I 300 " both_signs ideal model delta sigma weight residual False -2.63 -2.00 -0.63 2.00e-01 2.50e+01 9.78e+00 chirality pdb=" CA TYR A 860 " pdb=" N TYR A 860 " pdb=" C TYR A 860 " pdb=" CB TYR A 860 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.07e+00 ... (remaining 9856 not shown) Planarity restraints: 11099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL I 433 " 0.142 2.00e-02 2.50e+03 2.40e-01 5.77e+02 pdb=" C VAL I 433 " -0.412 2.00e-02 2.50e+03 pdb=" O VAL I 433 " 0.183 2.00e-02 2.50e+03 pdb=" N PRO I 435 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 433 " 0.153 5.00e-02 4.00e+02 2.61e-01 1.09e+02 pdb=" N PRO I 435 " -0.452 5.00e-02 4.00e+02 pdb=" CA PRO I 435 " 0.141 5.00e-02 4.00e+02 pdb=" CD PRO I 435 " 0.158 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP N 563 " 0.051 2.00e-02 2.50e+03 9.18e-02 8.43e+01 pdb=" C ASP N 563 " -0.157 2.00e-02 2.50e+03 pdb=" O ASP N 563 " 0.075 2.00e-02 2.50e+03 pdb=" N MET N 564 " 0.031 2.00e-02 2.50e+03 ... (remaining 11096 not shown) Histogram of nonbonded interaction distances: 0.61 - 1.47: 36 1.47 - 2.33: 521 2.33 - 3.18: 64051 3.18 - 4.04: 167578 4.04 - 4.90: 302581 Warning: very small nonbonded interaction distances. Nonbonded interactions: 534767 Sorted by model distance: nonbonded pdb=" NZ LYS A 226 " pdb=" C VAL A 236 " model vdw 0.612 3.350 nonbonded pdb=" C HIS I 432 " pdb=" CG PRO I 435 " model vdw 0.737 3.670 nonbonded pdb=" OE1 GLN N 174 " pdb=" OG1 THR N 263 " model vdw 0.869 2.440 nonbonded pdb=" OG1 THR N 677 " pdb=" OE2 GLU N 679 " model vdw 0.925 2.440 nonbonded pdb=" O VAL A 87 " pdb=" OD1 ASP A 88 " model vdw 0.938 3.040 ... (remaining 534762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 26 through 135 or resid 147 through 160 or (resid 161 and \ (name N or name CA or name C or name O or name CB )) or resid 162 through 496 or \ (resid 497 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2)) or resid 498 through 500 or resid 511 through 538)) selection = chain 'P' } ncs_group { reference = (chain 'F' and (resid 5 through 167 or (resid 168 through 459 and (name N or nam \ e CA or name C or name O or name CB )) or resid 460 through 755)) selection = (chain 'H' and (resid 5 through 95 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 through 171 or (resid 455 through 459 and ( \ name N or name CA or name C or name O or name CB )) or resid 460 through 461 or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 463 \ through 470 or (resid 471 and (name N or name CA or name C or name O or name CB \ )) or resid 472 through 477 or (resid 478 and (name N or name CA or name C or n \ ame O or name CB )) or resid 479 through 481 or (resid 482 and (name N or name C \ A or name C or name O or name CB )) or resid 483 through 556 or (resid 557 and ( \ name N or name CA or name C or name O or name CB )) or resid 558 through 587 or \ (resid 588 and (name N or name CA or name C or name O or name CB )) or resid 589 \ through 682 or (resid 691 and (name N or name CA or name C or name O or name CB \ )) or resid 692 or (resid 693 through 701 and (name N or name CA or name C or n \ ame O or name CB )) or resid 702 through 705 or (resid 706 and (name N or name C \ A or name C or name O or name CB )) or resid 707 through 719 or (resid 720 and ( \ name N or name CA or name C or name O or name CB )) or resid 721 through 734 or \ (resid 735 and (name N or name CA or name C or name O or name CB )) or resid 736 \ through 737 or (resid 738 and (name N or name CA or name C or name O or name CB \ )) or resid 739 through 747 or (resid 748 and (name N or name CA or name C or n \ ame O or name CB )) or resid 749 through 753 or (resid 754 and (name N or name C \ A or name C or name O or name CB )) or resid 755)) } ncs_group { reference = (chain 'G' and (resid 1 through 23 or (resid 24 through 25 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'W' and resid 1 through 25) } ncs_group { reference = (chain 'J' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 93 or resid 127 through 227 or (resid 228 and (na \ me N or name CA or name C or name O or name CB )) or resid 229 through 527)) selection = (chain 'K' and (resid 2 through 221 or (resid 222 and (name N or name CA or name \ C or name O or name CB )) or resid 223 through 346 or (resid 347 and (name N or \ name CA or name C or name O or name CB )) or resid 348 through 523 or (resid 52 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 525 through \ 527)) } ncs_group { reference = chain 'X' selection = (chain 'Y' and resid 36 through 540) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.780 Check model and map are aligned: 0.710 Set scattering table: 0.450 Process input model: 146.770 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.173 64541 Z= 1.019 Angle : 1.814 31.876 87465 Z= 1.170 Chirality : 0.104 0.630 9859 Planarity : 0.010 0.261 11099 Dihedral : 18.980 106.217 23488 Min Nonbonded Distance : 0.612 Molprobity Statistics. All-atom Clashscore : 56.69 Ramachandran Plot: Outliers : 1.83 % Allowed : 4.54 % Favored : 93.63 % Rotamer: Outliers : 17.76 % Allowed : 14.85 % Favored : 67.39 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 4.75 % Cis-general : 0.40 % Twisted Proline : 0.34 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.09), residues: 7914 helix: 0.74 (0.06), residues: 5246 sheet: 0.22 (0.26), residues: 404 loop : -2.08 (0.11), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.009 TRP X 239 HIS 0.031 0.005 HIS X 247 PHE 0.055 0.008 PHE I 524 TYR 0.077 0.008 TYR A 500 ARG 0.045 0.003 ARG X 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15828 Ramachandran restraints generated. 7914 Oldfield, 0 Emsley, 7914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15828 Ramachandran restraints generated. 7914 Oldfield, 0 Emsley, 7914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2567 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1181 poor density : 1386 time to evaluate : 5.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 SER cc_start: 0.5870 (m) cc_final: 0.5413 (t) REVERT: A 157 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8474 (p) REVERT: A 213 MET cc_start: 0.9006 (ttt) cc_final: 0.8625 (ttt) REVERT: A 221 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.8986 (t) REVERT: A 254 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7929 (t) REVERT: A 257 MET cc_start: 0.7974 (tpt) cc_final: 0.7614 (mmm) REVERT: A 267 SER cc_start: 0.4995 (OUTLIER) cc_final: 0.4314 (t) REVERT: A 444 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.7311 (p90) REVERT: A 456 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8258 (mtmm) REVERT: A 470 SER cc_start: 0.7517 (OUTLIER) cc_final: 0.6992 (p) REVERT: A 707 TRP cc_start: 0.8306 (OUTLIER) cc_final: 0.6557 (t60) REVERT: A 868 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8178 (tp30) REVERT: A 871 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7295 (ttp80) REVERT: A 945 GLU cc_start: 0.8464 (tp30) cc_final: 0.8261 (mm-30) REVERT: A 957 ASP cc_start: 0.9351 (t0) cc_final: 0.8758 (t0) REVERT: A 989 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8765 (tm-30) REVERT: A 1014 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.5982 (p0) REVERT: A 1017 ASN cc_start: 0.9351 (OUTLIER) cc_final: 0.9149 (m-40) REVERT: A 1033 ARG cc_start: 0.8584 (mtt180) cc_final: 0.8377 (mtm-85) REVERT: A 1049 VAL cc_start: 0.6624 (OUTLIER) cc_final: 0.6249 (p) REVERT: A 1116 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8330 (p) REVERT: A 1165 HIS cc_start: 0.7697 (t-170) cc_final: 0.7487 (t-90) REVERT: A 1203 MET cc_start: 0.5723 (mmp) cc_final: 0.5030 (mmp) REVERT: A 1243 LEU cc_start: 0.5370 (OUTLIER) cc_final: 0.4781 (mm) REVERT: A 1271 GLU cc_start: 0.8698 (tp30) cc_final: 0.8454 (tt0) REVERT: A 1290 ASP cc_start: 0.6755 (m-30) cc_final: 0.6337 (m-30) REVERT: A 1313 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7051 (pt) REVERT: A 1354 GLU cc_start: 0.6706 (tt0) cc_final: 0.6342 (tm-30) REVERT: A 1397 ASP cc_start: 0.9502 (m-30) cc_final: 0.9289 (m-30) REVERT: A 1456 THR cc_start: 0.9615 (m) cc_final: 0.9279 (p) REVERT: A 1479 SER cc_start: 0.9645 (m) cc_final: 0.9427 (p) REVERT: A 1527 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8892 (mmm) REVERT: A 1544 MET cc_start: 0.9142 (mmp) cc_final: 0.8755 (mmp) REVERT: A 1573 SER cc_start: 0.9715 (OUTLIER) cc_final: 0.9424 (p) REVERT: A 1581 ILE cc_start: 0.9605 (mt) cc_final: 0.9338 (mm) REVERT: A 1623 ASP cc_start: 0.9487 (t0) cc_final: 0.9268 (t0) REVERT: A 1645 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8813 (mp0) REVERT: A 1679 ASP cc_start: 0.9078 (OUTLIER) cc_final: 0.8129 (p0) REVERT: A 1754 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.8958 (m-80) REVERT: A 1777 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8440 (tm-30) REVERT: A 1810 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8418 (mt-10) REVERT: A 1813 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.7771 (mm-40) REVERT: A 1926 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8919 (ttp80) REVERT: B 14 TRP cc_start: 0.7090 (OUTLIER) cc_final: 0.5954 (p-90) REVERT: B 16 TRP cc_start: 0.3944 (OUTLIER) cc_final: 0.3675 (m100) REVERT: C 97 LYS cc_start: 0.9090 (pmtt) cc_final: 0.8777 (pttm) REVERT: C 100 ASP cc_start: 0.9742 (m-30) cc_final: 0.9527 (p0) REVERT: C 119 MET cc_start: 0.9628 (tpt) cc_final: 0.9417 (mmm) REVERT: C 129 LYS cc_start: 0.7365 (mttt) cc_final: 0.6765 (mttp) REVERT: C 131 ASP cc_start: 0.8139 (m-30) cc_final: 0.7783 (t0) REVERT: C 213 ILE cc_start: 0.9252 (mm) cc_final: 0.8988 (mm) REVERT: C 217 GLU cc_start: 0.9571 (pt0) cc_final: 0.9320 (pp20) REVERT: C 245 GLU cc_start: 0.9685 (tt0) cc_final: 0.9376 (pm20) REVERT: C 280 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8210 (m-30) REVERT: C 298 GLU cc_start: 0.9315 (tt0) cc_final: 0.9036 (mp0) REVERT: C 300 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8622 (mmp) REVERT: C 358 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9350 (mm) REVERT: C 397 ARG cc_start: 0.9055 (ttt-90) cc_final: 0.8757 (ptt90) REVERT: C 435 MET cc_start: 0.9615 (mpm) cc_final: 0.9409 (mmt) REVERT: C 494 ILE cc_start: 0.7735 (mt) cc_final: 0.7469 (pt) REVERT: C 522 LYS cc_start: 0.9627 (tttt) cc_final: 0.9218 (mmtt) REVERT: C 551 ARG cc_start: 0.8793 (tpt-90) cc_final: 0.8548 (ttp-170) REVERT: C 556 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8249 (mm) REVERT: D 16 LEU cc_start: 0.7648 (pt) cc_final: 0.7281 (pt) REVERT: D 26 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7306 (tp30) REVERT: D 33 GLN cc_start: 0.9146 (mt0) cc_final: 0.8826 (mm-40) REVERT: D 42 GLN cc_start: 0.9502 (mt0) cc_final: 0.9067 (tm-30) REVERT: E 62 GLN cc_start: 0.9379 (mm-40) cc_final: 0.9170 (tp40) REVERT: E 80 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8456 (tp30) REVERT: E 85 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7108 (tp) REVERT: E 86 VAL cc_start: 0.7033 (t) cc_final: 0.6748 (t) REVERT: E 93 GLU cc_start: 0.9492 (tt0) cc_final: 0.9145 (tp30) REVERT: F 30 ARG cc_start: 0.9583 (OUTLIER) cc_final: 0.8939 (mmp80) REVERT: F 34 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8761 (tm-30) REVERT: F 79 CYS cc_start: 0.8810 (m) cc_final: 0.8573 (m) REVERT: F 81 ASP cc_start: 0.8191 (m-30) cc_final: 0.7524 (m-30) REVERT: F 153 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: F 157 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8101 (mm-30) REVERT: F 163 ASP cc_start: 0.9457 (OUTLIER) cc_final: 0.9244 (t0) REVERT: F 476 LEU cc_start: 0.8520 (tp) cc_final: 0.8243 (mt) REVERT: F 481 CYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6276 (p) REVERT: F 516 MET cc_start: 0.8824 (mtt) cc_final: 0.8527 (mmm) REVERT: F 527 ARG cc_start: 0.9454 (ttp80) cc_final: 0.9239 (ttm110) REVERT: F 534 GLU cc_start: 0.9318 (mm-30) cc_final: 0.9047 (mp0) REVERT: F 582 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: F 584 ASP cc_start: 0.9294 (m-30) cc_final: 0.8823 (p0) REVERT: F 602 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.8725 (t80) REVERT: F 616 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8676 (mm-30) REVERT: F 636 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7721 (t0) REVERT: F 649 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8805 (mm-30) REVERT: F 750 LEU cc_start: -0.3616 (OUTLIER) cc_final: -0.3979 (tp) REVERT: H 13 TRP cc_start: 0.9149 (m100) cc_final: 0.8202 (m-10) REVERT: H 61 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9153 (mt) REVERT: H 77 LYS cc_start: 0.8801 (tptt) cc_final: 0.8486 (tppt) REVERT: H 163 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6471 (p0) REVERT: H 469 MET cc_start: 0.8703 (ttm) cc_final: 0.8369 (ttp) REVERT: H 516 MET cc_start: 0.9282 (mmm) cc_final: 0.9010 (ppp) REVERT: H 534 GLU cc_start: 0.9053 (tp30) cc_final: 0.8760 (tp30) REVERT: H 588 LYS cc_start: 0.8129 (mtpp) cc_final: 0.7774 (mttp) REVERT: H 602 TYR cc_start: 0.7710 (t80) cc_final: 0.7436 (t80) REVERT: H 720 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.9023 (tppt) REVERT: H 727 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8945 (tm-30) REVERT: I 80 LEU cc_start: 0.7598 (tp) cc_final: 0.7221 (tp) REVERT: I 97 LYS cc_start: 0.8432 (pttt) cc_final: 0.8181 (pttp) REVERT: I 269 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8977 (mt) REVERT: I 273 CYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8663 (m) REVERT: I 283 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8242 (tmm) REVERT: I 340 SER cc_start: 0.9234 (OUTLIER) cc_final: 0.8776 (t) REVERT: I 429 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7570 (p) REVERT: I 440 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.6438 (ppp) REVERT: I 454 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8349 (tp30) REVERT: I 519 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.6061 (mtp-110) REVERT: I 598 MET cc_start: 0.9327 (ttt) cc_final: 0.9108 (tpp) REVERT: I 736 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7666 (m) REVERT: J 20 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8721 (tm-30) REVERT: J 85 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8247 (mt-10) REVERT: J 91 ASP cc_start: 0.8642 (m-30) cc_final: 0.8296 (m-30) REVERT: J 143 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8998 (mt) REVERT: J 195 ASN cc_start: 0.9397 (m-40) cc_final: 0.9147 (m-40) REVERT: J 199 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9189 (mm-30) REVERT: J 232 ASP cc_start: 0.9038 (m-30) cc_final: 0.8572 (t0) REVERT: J 343 SER cc_start: 0.9495 (OUTLIER) cc_final: 0.9280 (p) REVERT: J 349 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8908 (pm20) REVERT: J 351 ASP cc_start: 0.9349 (OUTLIER) cc_final: 0.9114 (p0) REVERT: J 395 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8609 (mt) REVERT: J 422 GLU cc_start: 0.8916 (tt0) cc_final: 0.8395 (tp30) REVERT: J 477 GLN cc_start: 0.9442 (OUTLIER) cc_final: 0.8990 (mm-40) REVERT: K 87 GLN cc_start: 0.8825 (tt0) cc_final: 0.8474 (tp40) REVERT: K 136 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8775 (ttp-110) REVERT: K 204 LEU cc_start: 0.9464 (mt) cc_final: 0.9186 (mp) REVERT: K 232 ASP cc_start: 0.9514 (m-30) cc_final: 0.9006 (m-30) REVERT: K 263 PHE cc_start: 0.9568 (m-80) cc_final: 0.9288 (m-80) REVERT: K 283 GLU cc_start: 0.9452 (mm-30) cc_final: 0.9153 (mp0) REVERT: K 343 SER cc_start: 0.9137 (OUTLIER) cc_final: 0.8785 (p) REVERT: K 422 GLU cc_start: 0.9622 (tt0) cc_final: 0.9318 (tp30) REVERT: K 458 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8908 (mt) REVERT: K 477 GLN cc_start: 0.9551 (OUTLIER) cc_final: 0.9275 (mm-40) REVERT: K 496 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: L 32 SER cc_start: 0.8355 (m) cc_final: 0.8012 (p) REVERT: L 47 ASP cc_start: 0.8394 (m-30) cc_final: 0.7828 (m-30) REVERT: L 67 GLN cc_start: 0.8989 (mt0) cc_final: 0.8492 (mp10) REVERT: L 78 CYS cc_start: 0.7579 (t) cc_final: 0.7037 (m) REVERT: L 84 LYS cc_start: 0.9469 (OUTLIER) cc_final: 0.9269 (ptpp) REVERT: L 94 ILE cc_start: 0.8460 (mt) cc_final: 0.8047 (mm) REVERT: L 101 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8710 (m-40) REVERT: L 112 GLU cc_start: 0.8168 (tp30) cc_final: 0.7839 (tp30) REVERT: L 159 TYR cc_start: 0.6241 (m-80) cc_final: 0.5916 (m-10) REVERT: M 1 MET cc_start: 0.8093 (tpt) cc_final: 0.7569 (tpp) REVERT: M 7 ARG cc_start: 0.8640 (ptp90) cc_final: 0.8388 (ptp90) REVERT: M 8 ASP cc_start: 0.9324 (t0) cc_final: 0.9040 (t0) REVERT: M 20 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8681 (ptm160) REVERT: M 51 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.9032 (mttp) REVERT: M 53 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8567 (tp40) REVERT: M 63 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8880 (pm20) REVERT: M 64 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.8843 (p90) REVERT: N 65 HIS cc_start: 0.9108 (OUTLIER) cc_final: 0.8372 (m-70) REVERT: N 67 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8167 (pp) REVERT: N 69 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8427 (m) REVERT: N 84 GLN cc_start: 0.9411 (OUTLIER) cc_final: 0.9178 (tm-30) REVERT: N 110 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8306 (tm) REVERT: N 123 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8066 (t0) REVERT: N 126 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8995 (tt) REVERT: N 157 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9334 (pp) REVERT: N 171 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9168 (pt0) REVERT: N 322 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8880 (ttp-110) REVERT: N 415 VAL cc_start: 0.8717 (t) cc_final: 0.8324 (p) REVERT: N 500 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6977 (p0) REVERT: N 523 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9264 (mt) REVERT: N 531 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7188 (t80) REVERT: N 608 LYS cc_start: 0.6222 (mttt) cc_final: 0.5993 (mttm) REVERT: N 640 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8242 (m) REVERT: N 650 LEU cc_start: 0.4079 (OUTLIER) cc_final: 0.1980 (pp) REVERT: N 687 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7239 (ptm) REVERT: O 75 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5672 (tm) REVERT: O 85 SER cc_start: 0.7579 (m) cc_final: 0.7149 (t) REVERT: O 110 GLN cc_start: 0.9200 (tt0) cc_final: 0.8859 (tp40) REVERT: O 126 VAL cc_start: 0.7057 (t) cc_final: 0.6795 (t) REVERT: O 365 VAL cc_start: 0.8742 (m) cc_final: 0.8437 (t) REVERT: O 393 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6845 (tppt) REVERT: O 414 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8186 (pt) REVERT: O 444 MET cc_start: 0.8179 (mtt) cc_final: 0.7601 (mtp) REVERT: O 464 GLU cc_start: 0.9236 (tt0) cc_final: 0.8962 (pm20) REVERT: O 471 CYS cc_start: 0.9724 (m) cc_final: 0.9365 (m) REVERT: O 505 GLN cc_start: 0.9319 (mt0) cc_final: 0.8868 (mp10) REVERT: O 508 MET cc_start: 0.9636 (mtt) cc_final: 0.9312 (mtp) REVERT: O 562 LYS cc_start: 0.9648 (mttt) cc_final: 0.9392 (mptt) REVERT: O 585 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9167 (tp) REVERT: O 586 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8548 (p) REVERT: O 599 ILE cc_start: 0.8976 (mt) cc_final: 0.8736 (tt) REVERT: O 615 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8490 (mtt90) REVERT: O 617 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.9009 (tt0) REVERT: O 621 SER cc_start: 0.9377 (m) cc_final: 0.9136 (p) REVERT: O 732 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7518 (mmm160) REVERT: P 149 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.9041 (mp0) REVERT: P 157 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8515 (mt-10) REVERT: P 203 TRP cc_start: 0.8653 (t-100) cc_final: 0.7970 (t-100) REVERT: P 221 PHE cc_start: 0.9043 (m-80) cc_final: 0.8606 (m-10) REVERT: P 300 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8953 (mmp) REVERT: P 405 LEU cc_start: 0.8845 (mt) cc_final: 0.8589 (tp) REVERT: P 419 LEU cc_start: 0.9470 (tp) cc_final: 0.9145 (mp) REVERT: P 423 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8867 (tpp80) REVERT: P 468 MET cc_start: 0.8068 (tpp) cc_final: 0.7864 (tmm) REVERT: P 524 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8037 (mmtm) REVERT: W 7 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.9110 (p) REVERT: W 10 GLU cc_start: 0.9556 (mm-30) cc_final: 0.9291 (mm-30) REVERT: W 12 LYS cc_start: 0.7557 (mmtm) cc_final: 0.7337 (mmmt) REVERT: W 15 ASP cc_start: 0.9169 (OUTLIER) cc_final: 0.8890 (m-30) REVERT: W 18 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8545 (tm-30) REVERT: W 21 ASN cc_start: 0.8414 (m-40) cc_final: 0.8133 (m110) REVERT: X 76 LYS cc_start: 0.9003 (mttt) cc_final: 0.8212 (ttmm) REVERT: X 88 PHE cc_start: 0.8608 (t80) cc_final: 0.8390 (t80) REVERT: X 91 LYS cc_start: 0.9543 (mttt) cc_final: 0.9051 (tttm) REVERT: X 94 ARG cc_start: 0.8681 (mmt180) cc_final: 0.8474 (tpp80) REVERT: X 185 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8715 (pm20) REVERT: X 233 LEU cc_start: 0.8949 (mt) cc_final: 0.8662 (mt) REVERT: X 259 CYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9050 (m) REVERT: X 281 TYR cc_start: 0.9243 (m-80) cc_final: 0.8982 (m-80) REVERT: X 286 ASP cc_start: 0.9005 (m-30) cc_final: 0.8688 (m-30) REVERT: X 308 MET cc_start: 0.8805 (mmt) cc_final: 0.8405 (mmm) REVERT: X 342 TRP cc_start: 0.8345 (m100) cc_final: 0.7962 (m100) REVERT: X 379 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8430 (mmmm) REVERT: X 386 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8069 (mmt) REVERT: X 398 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7742 (tp30) REVERT: X 401 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6779 (mmt90) REVERT: X 458 GLN cc_start: 0.8905 (mt0) cc_final: 0.8642 (mm-40) REVERT: Y 56 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8472 (tt) REVERT: Y 152 ASP cc_start: 0.9360 (OUTLIER) cc_final: 0.8913 (p0) REVERT: Y 173 MET cc_start: 0.8907 (ttp) cc_final: 0.8671 (tpp) REVERT: Y 243 TYR cc_start: 0.8695 (m-80) cc_final: 0.8201 (m-80) REVERT: Y 259 CYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8748 (m) REVERT: Y 429 MET cc_start: 0.8254 (mtm) cc_final: 0.7917 (ptt) REVERT: Y 451 CYS cc_start: 0.7060 (m) cc_final: 0.6301 (m) REVERT: Y 551 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7563 (tttt) outliers start: 1181 outliers final: 386 residues processed: 2303 average time/residue: 0.7006 time to fit residues: 2674.5100 Evaluate side-chains 1357 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 500 poor density : 857 time to evaluate : 5.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 TRP Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 477 LYS Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 670 TYR Chi-restraints excluded: chain A residue 707 TRP Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 722 HIS Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 827 GLN Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 871 ARG Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 894 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 980 ARG Chi-restraints excluded: chain A residue 988 CYS Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1076 ARG Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1104 LYS Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1110 ARG Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1266 HIS Chi-restraints excluded: chain A residue 1292 GLU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1333 HIS Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1437 ASN Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1527 MET Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1573 SER Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1598 ASP Chi-restraints excluded: chain A residue 1622 VAL Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1645 GLU Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1679 ASP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1705 GLN Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1754 PHE Chi-restraints excluded: chain A residue 1755 CYS Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1778 CYS Chi-restraints excluded: chain A residue 1805 MET Chi-restraints excluded: chain A residue 1813 GLN Chi-restraints excluded: chain A residue 1818 LEU Chi-restraints excluded: chain A residue 1826 HIS Chi-restraints excluded: chain A residue 1827 GLN Chi-restraints excluded: chain A residue 1829 ARG Chi-restraints excluded: chain A residue 1830 LEU Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1840 MET Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1868 VAL Chi-restraints excluded: chain A residue 1899 HIS Chi-restraints excluded: chain A residue 1900 LEU Chi-restraints excluded: chain A residue 1910 SER Chi-restraints excluded: chain A residue 1914 LEU Chi-restraints excluded: chain A residue 1920 GLN Chi-restraints excluded: chain A residue 1923 MET Chi-restraints excluded: chain A residue 1926 ARG Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1934 LEU Chi-restraints excluded: chain A residue 1936 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 PRO Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 479 GLN Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 463 MET Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 481 CYS Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 582 GLU Chi-restraints excluded: chain F residue 602 TYR Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 623 CYS Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 745 LYS Chi-restraints excluded: chain F residue 750 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 163 ASP Chi-restraints excluded: chain H residue 462 LEU Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 481 CYS Chi-restraints excluded: chain H residue 494 HIS Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 536 MET Chi-restraints excluded: chain H residue 686 GLU Chi-restraints excluded: chain H residue 720 LYS Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 LYS Chi-restraints excluded: chain I residue 115 TRP Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 211 SER Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 273 CYS Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 306 HIS Chi-restraints excluded: chain I residue 310 TRP Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 340 SER Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain I residue 435 PRO Chi-restraints excluded: chain I residue 440 MET Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 450 GLU Chi-restraints excluded: chain I residue 454 GLU Chi-restraints excluded: chain I residue 505 SER Chi-restraints excluded: chain I residue 519 ARG Chi-restraints excluded: chain I residue 522 LEU Chi-restraints excluded: chain I residue 526 LYS Chi-restraints excluded: chain I residue 529 MET Chi-restraints excluded: chain I residue 536 CYS Chi-restraints excluded: chain I residue 552 ILE Chi-restraints excluded: chain I residue 736 SER Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 163 CYS Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 318 HIS Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 343 SER Chi-restraints excluded: chain J residue 351 ASP Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain J residue 506 LEU Chi-restraints excluded: chain J residue 515 SER Chi-restraints excluded: chain J residue 518 MET Chi-restraints excluded: chain J residue 521 HIS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 136 ARG Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 164 PHE Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 246 ASP Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 267 CYS Chi-restraints excluded: chain K residue 307 CYS Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 352 GLN Chi-restraints excluded: chain K residue 359 THR Chi-restraints excluded: chain K residue 376 LEU Chi-restraints excluded: chain K residue 388 GLU Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 455 CYS Chi-restraints excluded: chain K residue 458 LEU Chi-restraints excluded: chain K residue 477 GLN Chi-restraints excluded: chain K residue 496 GLU Chi-restraints excluded: chain K residue 510 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 80 TYR Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 20 ARG Chi-restraints excluded: chain M residue 27 GLU Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 63 GLN Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 97 GLN Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 171 GLU Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 185 MET Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 297 VAL Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 322 ARG Chi-restraints excluded: chain N residue 348 VAL Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 367 ARG Chi-restraints excluded: chain N residue 370 GLN Chi-restraints excluded: chain N residue 371 ARG Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 387 LEU Chi-restraints excluded: chain N residue 417 LEU Chi-restraints excluded: chain N residue 500 ASP Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 514 LEU Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 523 LEU Chi-restraints excluded: chain N residue 525 ASP Chi-restraints excluded: chain N residue 531 PHE Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 537 ARG Chi-restraints excluded: chain N residue 544 LEU Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 640 THR Chi-restraints excluded: chain N residue 650 LEU Chi-restraints excluded: chain N residue 662 VAL Chi-restraints excluded: chain N residue 663 GLN Chi-restraints excluded: chain N residue 679 GLU Chi-restraints excluded: chain N residue 680 GLU Chi-restraints excluded: chain N residue 681 LEU Chi-restraints excluded: chain N residue 687 MET Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 214 PHE Chi-restraints excluded: chain O residue 319 GLN Chi-restraints excluded: chain O residue 353 LYS Chi-restraints excluded: chain O residue 354 ARG Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain O residue 393 LYS Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 488 GLU Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 579 MET Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 585 LEU Chi-restraints excluded: chain O residue 586 SER Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 610 LEU Chi-restraints excluded: chain O residue 615 ARG Chi-restraints excluded: chain O residue 616 LEU Chi-restraints excluded: chain O residue 617 GLN Chi-restraints excluded: chain O residue 623 THR Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 632 LEU Chi-restraints excluded: chain O residue 654 ASP Chi-restraints excluded: chain O residue 657 ILE Chi-restraints excluded: chain O residue 658 LEU Chi-restraints excluded: chain O residue 678 TYR Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 732 ARG Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain O residue 752 ILE Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 107 HIS Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 157 GLU Chi-restraints excluded: chain P residue 196 THR Chi-restraints excluded: chain P residue 197 HIS Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 300 MET Chi-restraints excluded: chain P residue 303 PHE Chi-restraints excluded: chain P residue 312 MET Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 362 PRO Chi-restraints excluded: chain P residue 382 SER Chi-restraints excluded: chain P residue 408 THR Chi-restraints excluded: chain P residue 423 ARG Chi-restraints excluded: chain P residue 524 LYS Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 15 ASP Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 158 ILE Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 238 VAL Chi-restraints excluded: chain X residue 245 PHE Chi-restraints excluded: chain X residue 259 CYS Chi-restraints excluded: chain X residue 366 ILE Chi-restraints excluded: chain X residue 379 LYS Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 386 MET Chi-restraints excluded: chain X residue 393 ILE Chi-restraints excluded: chain X residue 398 GLU Chi-restraints excluded: chain X residue 401 ARG Chi-restraints excluded: chain X residue 402 LEU Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 431 ASN Chi-restraints excluded: chain X residue 442 GLN Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 487 SER Chi-restraints excluded: chain Y residue 40 HIS Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 64 SER Chi-restraints excluded: chain Y residue 94 ARG Chi-restraints excluded: chain Y residue 152 ASP Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 259 CYS Chi-restraints excluded: chain Y residue 349 SER Chi-restraints excluded: chain Y residue 383 LEU Chi-restraints excluded: chain Y residue 416 CYS Chi-restraints excluded: chain Y residue 506 GLN Chi-restraints excluded: chain Y residue 551 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 669 optimal weight: 0.9980 chunk 601 optimal weight: 0.7980 chunk 333 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 405 optimal weight: 1.9990 chunk 321 optimal weight: 5.9990 chunk 621 optimal weight: 0.7980 chunk 240 optimal weight: 0.9990 chunk 377 optimal weight: 5.9990 chunk 462 optimal weight: 5.9990 chunk 720 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 HIS ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN A 666 ASN ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 GLN A 846 GLN A 961 HIS ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 HIS A1312 ASN A1333 HIS A1380 ASN A1532 ASN A1558 HIS A1595 HIS A1599 ASN ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1627 ASN A1705 GLN A1727 ASN A1861 GLN A1899 HIS A1920 GLN B 9 ASN C 71 GLN C 202 HIS C 249 GLN C 287 ASN C 299 ASN C 305 ASN C 321 HIS C 361 ASN C 427 GLN C 479 GLN C 488 GLN C 518 GLN C 540 ASN C 552 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN F 64 HIS ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** F 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 ASN F 667 GLN F 702 ASN H 90 GLN ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 HIS H 634 HIS H 648 GLN H 657 HIS H 754 HIS H 759 ASN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 235 GLN I 257 HIS ** I 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 301 GLN I 318 GLN I 323 ASN I 362 HIS ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN J 38 GLN J 54 HIS ** J 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 289 HIS J 316 ASN J 342 HIS J 382 ASN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 HIS J 503 HIS K 45 GLN K 58 HIS K 271 HIS L 28 GLN L 101 ASN L 103 HIS L 146 GLN ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN N 154 HIS N 170 GLN N 541 ASN ** N 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 671 GLN O 69 GLN O 91 ASN O 159 GLN ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 237 GLN O 241 ASN O 242 ASN ** O 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 306 ASN O 325 GLN O 396 ASN O 424 GLN O 449 ASN O 462 ASN O 565 GLN O 617 GLN ** O 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 722 HIS O 753 ASN P 71 GLN P 104 HIS P 148 ASN P 197 HIS P 287 ASN ** P 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 305 ASN P 355 GLN P 361 ASN P 485 GLN P 518 GLN X 50 HIS X 78 GLN X 106 GLN X 151 GLN X 247 HIS X 298 GLN X 337 GLN X 338 HIS X 490 GLN Y 151 GLN Y 198 GLN ** Y 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 296 GLN Y 333 ASN Y 501 ASN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 64541 Z= 0.316 Angle : 0.949 19.662 87465 Z= 0.481 Chirality : 0.049 0.371 9859 Planarity : 0.006 0.155 11099 Dihedral : 12.380 119.969 9789 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.78 % Allowed : 4.05 % Favored : 95.16 % Rotamer: Outliers : 9.88 % Allowed : 19.74 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.75 % Cis-general : 0.40 % Twisted Proline : 0.34 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.09), residues: 7920 helix: 1.18 (0.07), residues: 5416 sheet: 0.24 (0.25), residues: 406 loop : -1.89 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 276 HIS 0.020 0.002 HIS L 152 PHE 0.045 0.003 PHE N 331 TYR 0.036 0.002 TYR A 860 ARG 0.014 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1672 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 657 poor density : 1015 time to evaluate : 6.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7343 (pttm) REVERT: A 92 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6350 (pp20) REVERT: A 125 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: A 157 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.8150 (p) REVERT: A 254 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.7926 (t) REVERT: A 267 SER cc_start: 0.4923 (OUTLIER) cc_final: 0.4632 (p) REVERT: A 273 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7976 (mmm-85) REVERT: A 456 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8646 (mtmm) REVERT: A 459 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8320 (pm20) REVERT: A 470 SER cc_start: 0.7343 (OUTLIER) cc_final: 0.6964 (p) REVERT: A 511 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7673 (pp) REVERT: A 636 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8654 (mp10) REVERT: A 707 TRP cc_start: 0.8252 (OUTLIER) cc_final: 0.7105 (t60) REVERT: A 868 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8001 (tp30) REVERT: A 871 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7340 (ttt-90) REVERT: A 945 GLU cc_start: 0.8597 (tp30) cc_final: 0.8360 (mt-10) REVERT: A 957 ASP cc_start: 0.9183 (t0) cc_final: 0.8805 (t0) REVERT: A 1017 ASN cc_start: 0.9284 (OUTLIER) cc_final: 0.9083 (m-40) REVERT: A 1076 ARG cc_start: 0.6131 (OUTLIER) cc_final: 0.5836 (ttp-110) REVERT: A 1236 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8347 (pt) REVERT: A 1243 LEU cc_start: 0.5751 (OUTLIER) cc_final: 0.5144 (mm) REVERT: A 1279 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7357 (ptm-80) REVERT: A 1290 ASP cc_start: 0.6729 (m-30) cc_final: 0.6035 (m-30) REVERT: A 1292 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6659 (pm20) REVERT: A 1354 GLU cc_start: 0.6767 (tt0) cc_final: 0.6337 (tm-30) REVERT: A 1456 THR cc_start: 0.9527 (m) cc_final: 0.9134 (p) REVERT: A 1532 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8254 (t0) REVERT: A 1601 TYR cc_start: 0.8075 (m-80) cc_final: 0.7625 (m-80) REVERT: A 1623 ASP cc_start: 0.9429 (t0) cc_final: 0.9136 (t0) REVERT: A 1666 ILE cc_start: 0.9228 (tt) cc_final: 0.8980 (mp) REVERT: A 1705 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7565 (mp10) REVERT: A 1777 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8578 (tm-30) REVERT: A 1810 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8396 (mp0) REVERT: A 1827 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8476 (mp10) REVERT: A 1841 ASN cc_start: 0.9539 (t0) cc_final: 0.9135 (p0) REVERT: A 1926 ARG cc_start: 0.9303 (OUTLIER) cc_final: 0.8780 (mtm110) REVERT: B 2 LYS cc_start: 0.8010 (tptt) cc_final: 0.7423 (tptp) REVERT: B 6 LYS cc_start: 0.8102 (ptmm) cc_final: 0.7730 (mtmm) REVERT: B 14 TRP cc_start: 0.7108 (OUTLIER) cc_final: 0.6141 (p-90) REVERT: B 16 TRP cc_start: 0.3433 (OUTLIER) cc_final: 0.2632 (m100) REVERT: B 43 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7946 (p0) REVERT: B 84 GLU cc_start: 0.4243 (OUTLIER) cc_final: 0.3184 (pt0) REVERT: C 100 ASP cc_start: 0.9642 (m-30) cc_final: 0.9432 (p0) REVERT: C 119 MET cc_start: 0.9689 (tpt) cc_final: 0.9370 (mmm) REVERT: C 202 HIS cc_start: 0.8840 (OUTLIER) cc_final: 0.8551 (t70) REVERT: C 213 ILE cc_start: 0.8817 (mm) cc_final: 0.8551 (mm) REVERT: C 218 MET cc_start: 0.9314 (ttp) cc_final: 0.8757 (mtm) REVERT: C 280 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7759 (m-30) REVERT: C 358 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9251 (mt) REVERT: C 397 ARG cc_start: 0.9366 (ttt-90) cc_final: 0.9143 (ptt90) REVERT: C 475 LYS cc_start: 0.7870 (tmtt) cc_final: 0.7603 (mmmm) REVERT: C 522 LYS cc_start: 0.9492 (tttt) cc_final: 0.8980 (mmtm) REVERT: C 536 CYS cc_start: 0.2743 (OUTLIER) cc_final: 0.2312 (t) REVERT: C 542 THR cc_start: 0.5361 (OUTLIER) cc_final: 0.4355 (m) REVERT: D 27 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6553 (tp30) REVERT: D 42 GLN cc_start: 0.9552 (mt0) cc_final: 0.9133 (tm-30) REVERT: D 46 GLU cc_start: 0.9550 (mt-10) cc_final: 0.9331 (pp20) REVERT: E 100 GLU cc_start: 0.9430 (pm20) cc_final: 0.8988 (tm-30) REVERT: F 34 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.9029 (tm-30) REVERT: F 79 CYS cc_start: 0.8871 (m) cc_final: 0.8603 (m) REVERT: F 154 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.7849 (p) REVERT: F 163 ASP cc_start: 0.9598 (OUTLIER) cc_final: 0.9312 (t0) REVERT: F 469 MET cc_start: 0.8400 (mmm) cc_final: 0.8131 (mmp) REVERT: F 481 CYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7369 (t) REVERT: F 494 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.8087 (p90) REVERT: F 527 ARG cc_start: 0.9469 (ttp80) cc_final: 0.9195 (ptp-110) REVERT: F 534 GLU cc_start: 0.9411 (mm-30) cc_final: 0.9045 (mp0) REVERT: F 568 GLU cc_start: 0.9375 (pm20) cc_final: 0.9148 (pm20) REVERT: F 616 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8578 (mm-30) REVERT: F 630 VAL cc_start: 0.7343 (t) cc_final: 0.6711 (t) REVERT: F 633 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7491 (mmm-85) REVERT: F 636 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8126 (t0) REVERT: F 741 PHE cc_start: 0.8471 (m-80) cc_final: 0.8160 (m-10) REVERT: G 20 GLU cc_start: 0.9401 (mt-10) cc_final: 0.9116 (mp0) REVERT: H 87 GLU cc_start: 0.9401 (tt0) cc_final: 0.9102 (tp30) REVERT: H 133 LYS cc_start: 0.9517 (tttt) cc_final: 0.9251 (ttmm) REVERT: H 469 MET cc_start: 0.8578 (ttm) cc_final: 0.8296 (ttp) REVERT: H 524 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8930 (mp0) REVERT: H 527 ARG cc_start: 0.6915 (mtm-85) cc_final: 0.6326 (mtm-85) REVERT: H 581 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7281 (mtm-85) REVERT: H 602 TYR cc_start: 0.7574 (t80) cc_final: 0.6994 (t80) REVERT: H 727 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9054 (tm-30) REVERT: I 49 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8947 (tp) REVERT: I 92 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7365 (pt) REVERT: I 192 MET cc_start: 0.8851 (mtp) cc_final: 0.8526 (mmm) REVERT: I 283 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8141 (tmm) REVERT: I 440 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7434 (ppp) REVERT: I 450 GLU cc_start: 0.9453 (OUTLIER) cc_final: 0.9054 (pp20) REVERT: I 546 LYS cc_start: 0.9454 (tptm) cc_final: 0.9254 (mtmm) REVERT: I 705 MET cc_start: 0.8838 (mmm) cc_final: 0.8615 (mmm) REVERT: I 745 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: J 15 ASP cc_start: 0.9368 (OUTLIER) cc_final: 0.9028 (p0) REVERT: J 195 ASN cc_start: 0.9445 (OUTLIER) cc_final: 0.9135 (m-40) REVERT: J 199 GLU cc_start: 0.9542 (mt-10) cc_final: 0.9097 (mm-30) REVERT: J 202 ARG cc_start: 0.9339 (ttp80) cc_final: 0.9111 (ttm110) REVERT: J 214 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8234 (ttpt) REVERT: J 249 MET cc_start: 0.9394 (mmm) cc_final: 0.9041 (tpp) REVERT: J 395 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8319 (mt) REVERT: J 477 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.9055 (mm-40) REVERT: J 511 ASP cc_start: 0.9460 (t0) cc_final: 0.9220 (m-30) REVERT: K 85 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8088 (mt-10) REVERT: K 180 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8839 (mt-10) REVERT: K 195 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8956 (t0) REVERT: K 232 ASP cc_start: 0.9405 (OUTLIER) cc_final: 0.8891 (m-30) REVERT: K 263 PHE cc_start: 0.9478 (m-80) cc_final: 0.9060 (m-80) REVERT: K 283 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9097 (mp0) REVERT: K 307 CYS cc_start: 0.6740 (OUTLIER) cc_final: 0.6480 (p) REVERT: K 343 SER cc_start: 0.9274 (OUTLIER) cc_final: 0.9052 (p) REVERT: K 354 MET cc_start: 0.8924 (tpp) cc_final: 0.8329 (tpp) REVERT: K 422 GLU cc_start: 0.9516 (tt0) cc_final: 0.9301 (tt0) REVERT: K 438 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: K 477 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.9084 (mm-40) REVERT: K 492 MET cc_start: 0.9299 (mtm) cc_final: 0.9087 (mtm) REVERT: L 5 ASN cc_start: 0.8455 (t0) cc_final: 0.8245 (t0) REVERT: L 32 SER cc_start: 0.8476 (m) cc_final: 0.8214 (p) REVERT: L 83 TYR cc_start: 0.7947 (p90) cc_final: 0.7191 (p90) REVERT: L 112 GLU cc_start: 0.8027 (tp30) cc_final: 0.7811 (tp30) REVERT: L 119 TRP cc_start: 0.7357 (m100) cc_final: 0.6863 (m100) REVERT: L 150 ASP cc_start: 0.7455 (p0) cc_final: 0.7137 (m-30) REVERT: L 178 MET cc_start: 0.9087 (mtp) cc_final: 0.8874 (mtt) REVERT: M 1 MET cc_start: 0.8016 (tpt) cc_final: 0.7422 (tpp) REVERT: M 33 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8729 (mt) REVERT: M 51 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8853 (mttp) REVERT: M 52 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8144 (pp20) REVERT: N 65 HIS cc_start: 0.9073 (OUTLIER) cc_final: 0.8216 (m-70) REVERT: N 67 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7710 (pp) REVERT: N 84 GLN cc_start: 0.9415 (OUTLIER) cc_final: 0.9093 (tm-30) REVERT: N 152 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8076 (mp0) REVERT: N 156 MET cc_start: 0.9236 (ttp) cc_final: 0.8853 (ttp) REVERT: N 171 GLU cc_start: 0.9250 (mt-10) cc_final: 0.9048 (tp30) REVERT: N 351 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: N 358 ILE cc_start: 0.8206 (tt) cc_final: 0.7996 (pt) REVERT: N 518 GLU cc_start: 0.9586 (tm-30) cc_final: 0.9240 (tm-30) REVERT: N 531 PHE cc_start: 0.7816 (t80) cc_final: 0.7433 (t80) REVERT: N 611 VAL cc_start: 0.4858 (OUTLIER) cc_final: 0.4608 (m) REVERT: N 613 GLU cc_start: 0.8136 (tp30) cc_final: 0.7041 (mp0) REVERT: N 622 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6699 (m-80) REVERT: N 625 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7245 (tptm) REVERT: N 685 VAL cc_start: 0.7058 (OUTLIER) cc_final: 0.6703 (t) REVERT: N 687 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7341 (ptm) REVERT: O 56 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.4563 (mm-30) REVERT: O 110 GLN cc_start: 0.9059 (tt0) cc_final: 0.8678 (tp40) REVERT: O 149 SER cc_start: 0.9717 (OUTLIER) cc_final: 0.9339 (t) REVERT: O 384 LEU cc_start: 0.8902 (tp) cc_final: 0.8662 (tt) REVERT: O 406 ASP cc_start: 0.8549 (m-30) cc_final: 0.8246 (m-30) REVERT: O 414 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8209 (pt) REVERT: O 464 GLU cc_start: 0.9136 (tt0) cc_final: 0.8895 (pm20) REVERT: O 505 GLN cc_start: 0.9055 (mt0) cc_final: 0.8784 (mp10) REVERT: O 556 GLN cc_start: 0.9183 (tt0) cc_final: 0.8642 (tp40) REVERT: O 562 LYS cc_start: 0.9568 (mttt) cc_final: 0.9338 (mptt) REVERT: O 585 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9175 (mm) REVERT: O 606 GLN cc_start: 0.9338 (tt0) cc_final: 0.9045 (tp-100) REVERT: O 618 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8183 (t80) REVERT: O 685 GLU cc_start: 0.9456 (OUTLIER) cc_final: 0.9227 (pt0) REVERT: P 128 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8892 (mmmm) REVERT: P 149 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.8811 (mp0) REVERT: P 203 TRP cc_start: 0.8555 (t-100) cc_final: 0.8296 (t-100) REVERT: P 229 MET cc_start: 0.7356 (mmm) cc_final: 0.6872 (tpt) REVERT: P 346 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8459 (mt0) REVERT: P 405 LEU cc_start: 0.8870 (mt) cc_final: 0.8564 (tp) REVERT: P 441 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: W 7 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.8924 (p) REVERT: W 10 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9071 (tm-30) REVERT: W 14 ASP cc_start: 0.9375 (OUTLIER) cc_final: 0.9146 (p0) REVERT: W 18 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: W 21 ASN cc_start: 0.8210 (m-40) cc_final: 0.7875 (m110) REVERT: X 76 LYS cc_start: 0.9050 (mttt) cc_final: 0.8691 (ttmm) REVERT: X 91 LYS cc_start: 0.9568 (mttt) cc_final: 0.9190 (tttm) REVERT: X 174 MET cc_start: 0.9370 (tpp) cc_final: 0.8952 (tpt) REVERT: X 347 CYS cc_start: 0.8689 (m) cc_final: 0.8323 (t) REVERT: X 379 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8334 (mmmm) REVERT: X 402 LEU cc_start: 0.8384 (pp) cc_final: 0.7601 (pp) REVERT: X 529 MET cc_start: 0.5104 (mmt) cc_final: 0.4719 (mpp) REVERT: Y 61 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8939 (pp) REVERT: Y 152 ASP cc_start: 0.9338 (OUTLIER) cc_final: 0.8974 (p0) REVERT: Y 173 MET cc_start: 0.8736 (ttp) cc_final: 0.8193 (tpt) REVERT: Y 243 TYR cc_start: 0.8736 (m-80) cc_final: 0.8082 (m-80) REVERT: Y 268 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7942 (ttm-80) REVERT: Y 298 GLN cc_start: 0.8706 (tt0) cc_final: 0.8402 (tt0) REVERT: Y 311 TYR cc_start: 0.9203 (t80) cc_final: 0.8662 (t80) REVERT: Y 325 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8165 (mm-30) REVERT: Y 429 MET cc_start: 0.8646 (mtm) cc_final: 0.8148 (ptp) REVERT: Y 549 MET cc_start: 0.8332 (mmp) cc_final: 0.7991 (mmt) REVERT: Y 551 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7584 (pptt) outliers start: 657 outliers final: 257 residues processed: 1539 average time/residue: 0.5944 time to fit residues: 1547.2603 Evaluate side-chains 1108 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 764 time to evaluate : 5.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 707 TRP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 871 ARG Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1076 ARG Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1104 LYS Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1124 ASN Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1196 TYR Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1292 GLU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1353 LYS Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1532 ASN Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1597 THR Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1622 VAL Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1627 ASN Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1705 GLN Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1827 GLN Chi-restraints excluded: chain A residue 1829 ARG Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1926 ARG Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1936 LEU Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 536 CYS Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 481 CYS Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 623 CYS Chi-restraints excluded: chain F residue 633 ARG Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 643 MET Chi-restraints excluded: chain F residue 675 ILE Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain H residue 47 CYS Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 536 MET Chi-restraints excluded: chain H residue 553 SER Chi-restraints excluded: chain H residue 565 ASN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 141 LYS Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 272 MET Chi-restraints excluded: chain I residue 273 CYS Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 288 THR Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 440 MET Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 450 GLU Chi-restraints excluded: chain I residue 505 SER Chi-restraints excluded: chain I residue 506 HIS Chi-restraints excluded: chain I residue 522 LEU Chi-restraints excluded: chain I residue 722 VAL Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain J residue 15 ASP Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 163 CYS Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain J residue 510 ARG Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 246 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 307 CYS Chi-restraints excluded: chain K residue 316 ASN Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 352 GLN Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 477 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 27 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 417 LEU Chi-restraints excluded: chain N residue 502 ILE Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 506 VAL Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 547 LEU Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 611 VAL Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 625 LYS Chi-restraints excluded: chain N residue 662 VAL Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 687 MET Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 149 SER Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain O residue 385 VAL Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 488 GLU Chi-restraints excluded: chain O residue 579 MET Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 585 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 616 LEU Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 633 ILE Chi-restraints excluded: chain O residue 651 ILE Chi-restraints excluded: chain O residue 657 ILE Chi-restraints excluded: chain O residue 685 GLU Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain O residue 752 ILE Chi-restraints excluded: chain O residue 753 ASN Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 276 ILE Chi-restraints excluded: chain P residue 300 MET Chi-restraints excluded: chain P residue 326 ILE Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 346 GLN Chi-restraints excluded: chain P residue 441 GLU Chi-restraints excluded: chain P residue 472 LYS Chi-restraints excluded: chain P residue 521 PHE Chi-restraints excluded: chain W residue 2 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 59 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 152 ASP Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 379 LYS Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 388 ARG Chi-restraints excluded: chain X residue 443 THR Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 539 ASP Chi-restraints excluded: chain Y residue 40 HIS Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 94 ARG Chi-restraints excluded: chain Y residue 152 ASP Chi-restraints excluded: chain Y residue 168 THR Chi-restraints excluded: chain Y residue 269 ASP Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 345 SER Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 417 TYR Chi-restraints excluded: chain Y residue 433 VAL Chi-restraints excluded: chain Y residue 501 ASN Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 551 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 400 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 599 optimal weight: 3.9990 chunk 490 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 chunk 721 optimal weight: 6.9990 chunk 779 optimal weight: 4.9990 chunk 642 optimal weight: 1.9990 chunk 715 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 578 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 ASN ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1351 GLN ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN F 90 GLN ** F 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 ASN F 667 GLN ** H 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 517 GLN H 674 HIS ** H 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 301 GLN ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS J 173 HIS ** J 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 ASN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN K 207 ASN K 264 HIS ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 521 HIS ** L 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 HIS ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 GLN O 237 GLN O 241 ASN ** O 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 254 HIS O 342 HIS ** O 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 461 ASN O 526 HIS O 552 GLN P 292 GLN X 40 HIS X 151 GLN ** X 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 198 GLN ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 458 GLN Y 289 ASN Y 296 GLN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 64541 Z= 0.392 Angle : 0.843 19.386 87465 Z= 0.432 Chirality : 0.046 0.329 9859 Planarity : 0.005 0.113 11099 Dihedral : 9.605 133.242 9172 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.60 % Favored : 94.76 % Rotamer: Outliers : 8.15 % Allowed : 21.40 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.75 % Cis-general : 0.39 % Twisted Proline : 0.34 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.09), residues: 7920 helix: 1.24 (0.07), residues: 5440 sheet: -0.05 (0.25), residues: 416 loop : -1.78 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP X 235 HIS 0.020 0.002 HIS L 103 PHE 0.036 0.002 PHE N 331 TYR 0.025 0.002 TYR A1891 ARG 0.012 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 542 poor density : 777 time to evaluate : 5.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 SER cc_start: 0.8275 (m) cc_final: 0.7946 (p) REVERT: A 254 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8210 (t) REVERT: A 273 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7918 (mmm-85) REVERT: A 444 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6594 (p90) REVERT: A 459 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8397 (pm20) REVERT: A 511 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7913 (pp) REVERT: A 636 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8675 (mp10) REVERT: A 866 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8435 (pt) REVERT: A 945 GLU cc_start: 0.8762 (tp30) cc_final: 0.8287 (mt-10) REVERT: A 957 ASP cc_start: 0.9234 (t0) cc_final: 0.8833 (t0) REVERT: A 972 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8185 (tp30) REVERT: A 1088 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8913 (p) REVERT: A 1114 ARG cc_start: 0.7766 (ptp90) cc_final: 0.7515 (ptp90) REVERT: A 1116 THR cc_start: 0.8428 (m) cc_final: 0.8203 (t) REVERT: A 1276 GLU cc_start: 0.9009 (tt0) cc_final: 0.8549 (tt0) REVERT: A 1290 ASP cc_start: 0.6863 (m-30) cc_final: 0.6547 (m-30) REVERT: A 1354 GLU cc_start: 0.6360 (tt0) cc_final: 0.6030 (tm-30) REVERT: A 1456 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.9151 (p) REVERT: A 1623 ASP cc_start: 0.9369 (t0) cc_final: 0.9040 (t0) REVERT: A 1646 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8710 (tm-30) REVERT: A 1705 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: A 1777 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8499 (tm-30) REVERT: A 1785 GLU cc_start: 0.9274 (mp0) cc_final: 0.8826 (pm20) REVERT: A 1810 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8549 (mp0) REVERT: A 1827 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.8913 (mp10) REVERT: A 1926 ARG cc_start: 0.9337 (OUTLIER) cc_final: 0.8786 (mtm110) REVERT: B 2 LYS cc_start: 0.7968 (tptt) cc_final: 0.7581 (tptt) REVERT: B 6 LYS cc_start: 0.8097 (ptmm) cc_final: 0.7885 (mtmm) REVERT: B 14 TRP cc_start: 0.7197 (OUTLIER) cc_final: 0.6093 (p-90) REVERT: B 15 LEU cc_start: 0.3578 (OUTLIER) cc_final: 0.3333 (mt) REVERT: B 27 ARG cc_start: 0.6455 (tpt170) cc_final: 0.5811 (tpm170) REVERT: B 43 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7902 (p0) REVERT: C 119 MET cc_start: 0.9718 (tpt) cc_final: 0.9414 (mmm) REVERT: C 218 MET cc_start: 0.9299 (ttp) cc_final: 0.8801 (mtm) REVERT: C 229 MET cc_start: 0.9281 (mmm) cc_final: 0.9076 (mmm) REVERT: C 244 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9167 (mp) REVERT: C 280 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7673 (m-30) REVERT: C 300 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8736 (mmp) REVERT: C 397 ARG cc_start: 0.9401 (ttt-90) cc_final: 0.9169 (ptt90) REVERT: C 475 LYS cc_start: 0.7899 (tmtt) cc_final: 0.7607 (mmmm) REVERT: C 522 LYS cc_start: 0.9491 (tttt) cc_final: 0.9143 (mmtt) REVERT: D 42 GLN cc_start: 0.9548 (mt0) cc_final: 0.9127 (tm-30) REVERT: D 46 GLU cc_start: 0.9590 (mt-10) cc_final: 0.9315 (pp20) REVERT: E 88 GLU cc_start: 0.9249 (tm-30) cc_final: 0.9028 (tm-30) REVERT: F 163 ASP cc_start: 0.9640 (OUTLIER) cc_final: 0.9432 (t0) REVERT: F 534 GLU cc_start: 0.9379 (mm-30) cc_final: 0.9091 (mp0) REVERT: F 568 GLU cc_start: 0.9452 (pm20) cc_final: 0.9236 (pm20) REVERT: F 584 ASP cc_start: 0.9433 (OUTLIER) cc_final: 0.9093 (p0) REVERT: F 626 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8290 (t0) REVERT: F 636 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.7962 (t0) REVERT: F 741 PHE cc_start: 0.8520 (m-80) cc_final: 0.8251 (m-10) REVERT: G 20 GLU cc_start: 0.9414 (mt-10) cc_final: 0.9112 (mp0) REVERT: H 87 GLU cc_start: 0.9410 (tt0) cc_final: 0.9142 (tp30) REVERT: H 463 MET cc_start: 0.9272 (tpp) cc_final: 0.8887 (tpp) REVERT: H 469 MET cc_start: 0.8710 (ttm) cc_final: 0.8396 (ttp) REVERT: H 516 MET cc_start: 0.8831 (ppp) cc_final: 0.8491 (ppp) REVERT: H 519 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7549 (pp20) REVERT: H 581 ARG cc_start: 0.7773 (mtt180) cc_final: 0.7486 (mtm-85) REVERT: H 602 TYR cc_start: 0.7410 (t80) cc_final: 0.7170 (t80) REVERT: H 727 GLU cc_start: 0.9255 (mt-10) cc_final: 0.9034 (tm-30) REVERT: I 40 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9070 (p) REVERT: I 49 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9050 (tp) REVERT: I 283 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7999 (tmm) REVERT: I 322 MET cc_start: 0.8701 (tmm) cc_final: 0.8335 (ptm) REVERT: I 428 MET cc_start: 0.7893 (ppp) cc_final: 0.7058 (ppp) REVERT: I 450 GLU cc_start: 0.9514 (OUTLIER) cc_final: 0.9148 (pp20) REVERT: I 519 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6622 (mtp-110) REVERT: I 529 MET cc_start: 0.9214 (ttp) cc_final: 0.8795 (ptm) REVERT: I 546 LYS cc_start: 0.9476 (tptm) cc_final: 0.9265 (mtmm) REVERT: I 705 MET cc_start: 0.8743 (mmm) cc_final: 0.8500 (mmt) REVERT: J 55 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8680 (ttt180) REVERT: J 195 ASN cc_start: 0.9518 (OUTLIER) cc_final: 0.9166 (m-40) REVERT: J 199 GLU cc_start: 0.9569 (mt-10) cc_final: 0.9172 (mm-30) REVERT: J 202 ARG cc_start: 0.9369 (ttp80) cc_final: 0.9160 (ttm110) REVERT: J 214 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8180 (tmmt) REVERT: J 232 ASP cc_start: 0.8978 (t0) cc_final: 0.8429 (t70) REVERT: J 249 MET cc_start: 0.9422 (mmm) cc_final: 0.8858 (tpp) REVERT: J 395 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8546 (mt) REVERT: J 477 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8920 (mm-40) REVERT: J 511 ASP cc_start: 0.9453 (t0) cc_final: 0.9246 (m-30) REVERT: K 232 ASP cc_start: 0.9388 (m-30) cc_final: 0.8949 (m-30) REVERT: K 263 PHE cc_start: 0.9543 (m-80) cc_final: 0.9108 (m-80) REVERT: K 283 GLU cc_start: 0.9452 (mm-30) cc_final: 0.9072 (mp0) REVERT: K 354 MET cc_start: 0.8965 (tpp) cc_final: 0.8585 (tpp) REVERT: K 417 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8758 (pm20) REVERT: K 422 GLU cc_start: 0.9546 (tt0) cc_final: 0.9330 (tt0) REVERT: K 492 MET cc_start: 0.9208 (mtm) cc_final: 0.8957 (mtm) REVERT: L 32 SER cc_start: 0.8454 (m) cc_final: 0.8217 (p) REVERT: L 84 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8598 (ptpp) REVERT: L 112 GLU cc_start: 0.7976 (tp30) cc_final: 0.7726 (tp30) REVERT: L 150 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7011 (m-30) REVERT: M 1 MET cc_start: 0.8172 (tpt) cc_final: 0.7731 (tpp) REVERT: M 22 ASP cc_start: 0.8656 (t0) cc_final: 0.8327 (t0) REVERT: M 51 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9004 (mmtp) REVERT: N 65 HIS cc_start: 0.9130 (OUTLIER) cc_final: 0.8151 (m-70) REVERT: N 67 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.7855 (pp) REVERT: N 84 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.9165 (tm-30) REVERT: N 152 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8168 (mp0) REVERT: N 180 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8366 (t80) REVERT: N 341 ILE cc_start: 0.7214 (mt) cc_final: 0.6902 (mt) REVERT: N 518 GLU cc_start: 0.9572 (tm-30) cc_final: 0.9213 (tm-30) REVERT: N 531 PHE cc_start: 0.7950 (t80) cc_final: 0.7660 (t80) REVERT: N 549 PHE cc_start: 0.8400 (t80) cc_final: 0.7896 (t80) REVERT: N 622 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.6563 (m-80) REVERT: N 632 MET cc_start: 0.8526 (mmm) cc_final: 0.8186 (mmm) REVERT: N 646 MET cc_start: 0.8604 (mpp) cc_final: 0.8223 (mpp) REVERT: N 685 VAL cc_start: 0.7068 (OUTLIER) cc_final: 0.6455 (t) REVERT: N 687 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7298 (ptp) REVERT: O 110 GLN cc_start: 0.9011 (tt0) cc_final: 0.8594 (tp40) REVERT: O 352 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8807 (pt0) REVERT: O 406 ASP cc_start: 0.8415 (m-30) cc_final: 0.8166 (m-30) REVERT: O 414 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8214 (pp) REVERT: O 505 GLN cc_start: 0.9103 (mt0) cc_final: 0.8700 (mp10) REVERT: O 508 MET cc_start: 0.9321 (mtp) cc_final: 0.9069 (mtp) REVERT: O 562 LYS cc_start: 0.9639 (mttt) cc_final: 0.9421 (mptt) REVERT: O 585 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9088 (mm) REVERT: O 616 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9430 (mt) REVERT: O 618 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8292 (t80) REVERT: O 685 GLU cc_start: 0.9458 (OUTLIER) cc_final: 0.9229 (pt0) REVERT: O 732 ARG cc_start: 0.7847 (mmt180) cc_final: 0.7312 (mmm160) REVERT: P 128 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8861 (tppp) REVERT: P 149 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.8947 (mp0) REVERT: P 346 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8438 (mt0) REVERT: P 441 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8506 (mt-10) REVERT: W 10 GLU cc_start: 0.9470 (mm-30) cc_final: 0.8995 (tm-30) REVERT: W 14 ASP cc_start: 0.9367 (OUTLIER) cc_final: 0.8992 (p0) REVERT: W 21 ASN cc_start: 0.8292 (m-40) cc_final: 0.8009 (m110) REVERT: X 44 MET cc_start: 0.8483 (mmm) cc_final: 0.8277 (mmm) REVERT: X 91 LYS cc_start: 0.9639 (mttt) cc_final: 0.9255 (tttm) REVERT: X 92 GLU cc_start: 0.9101 (mp0) cc_final: 0.8740 (pm20) REVERT: X 174 MET cc_start: 0.9451 (tpp) cc_final: 0.9172 (tpp) REVERT: X 340 GLU cc_start: 0.8585 (mp0) cc_final: 0.8364 (mp0) REVERT: X 342 TRP cc_start: 0.8172 (m100) cc_final: 0.7740 (m100) REVERT: X 347 CYS cc_start: 0.8661 (m) cc_final: 0.8435 (t) REVERT: X 386 MET cc_start: 0.7357 (mmt) cc_final: 0.7033 (mmt) REVERT: X 388 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8392 (mtm-85) REVERT: X 458 GLN cc_start: 0.8951 (mt0) cc_final: 0.8561 (tp40) REVERT: Y 61 LEU cc_start: 0.9214 (tt) cc_final: 0.8914 (pp) REVERT: Y 152 ASP cc_start: 0.9369 (OUTLIER) cc_final: 0.9067 (p0) REVERT: Y 173 MET cc_start: 0.8741 (ttp) cc_final: 0.8529 (tpp) REVERT: Y 243 TYR cc_start: 0.8735 (m-80) cc_final: 0.8152 (m-80) REVERT: Y 268 ARG cc_start: 0.8169 (ttm170) cc_final: 0.7822 (ttm-80) REVERT: Y 298 GLN cc_start: 0.8620 (tt0) cc_final: 0.8385 (tt0) REVERT: Y 429 MET cc_start: 0.8843 (mtm) cc_final: 0.8440 (ptp) REVERT: Y 515 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6711 (tt) REVERT: Y 551 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7810 (pptt) outliers start: 542 outliers final: 291 residues processed: 1214 average time/residue: 0.5773 time to fit residues: 1202.1912 Evaluate side-chains 1021 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 670 time to evaluate : 6.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 TRP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 988 CYS Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1060 HIS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1104 LYS Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1124 ASN Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1190 THR Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1522 SER Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1597 THR Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1646 GLN Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1705 GLN Chi-restraints excluded: chain A residue 1749 SER Chi-restraints excluded: chain A residue 1778 CYS Chi-restraints excluded: chain A residue 1780 THR Chi-restraints excluded: chain A residue 1818 LEU Chi-restraints excluded: chain A residue 1827 GLN Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1887 CYS Chi-restraints excluded: chain A residue 1926 ARG Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 481 CYS Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 584 ASP Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 623 CYS Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 643 MET Chi-restraints excluded: chain F residue 675 ILE Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 536 MET Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 565 ASN Chi-restraints excluded: chain H residue 596 VAL Chi-restraints excluded: chain H residue 623 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 141 LYS Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 273 CYS Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 310 TRP Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 373 LYS Chi-restraints excluded: chain I residue 450 GLU Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 505 SER Chi-restraints excluded: chain I residue 519 ARG Chi-restraints excluded: chain I residue 717 MET Chi-restraints excluded: chain I residue 722 VAL Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 343 SER Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 439 VAL Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 246 ASP Chi-restraints excluded: chain K residue 316 ASN Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 352 GLN Chi-restraints excluded: chain K residue 417 GLU Chi-restraints excluded: chain K residue 458 LEU Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 27 GLU Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 154 HIS Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 180 PHE Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 256 VAL Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 417 LEU Chi-restraints excluded: chain N residue 433 ASP Chi-restraints excluded: chain N residue 500 ASP Chi-restraints excluded: chain N residue 502 ILE Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 547 LEU Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 594 VAL Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 626 TYR Chi-restraints excluded: chain N residue 662 VAL Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 687 MET Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 218 GLN Chi-restraints excluded: chain O residue 224 LYS Chi-restraints excluded: chain O residue 257 SER Chi-restraints excluded: chain O residue 299 SER Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 488 GLU Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 558 SER Chi-restraints excluded: chain O residue 579 MET Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 585 LEU Chi-restraints excluded: chain O residue 598 THR Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 616 LEU Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 657 ILE Chi-restraints excluded: chain O residue 658 LEU Chi-restraints excluded: chain O residue 685 GLU Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 706 CYS Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain O residue 752 ILE Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 276 ILE Chi-restraints excluded: chain P residue 300 MET Chi-restraints excluded: chain P residue 326 ILE Chi-restraints excluded: chain P residue 334 CYS Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 346 GLN Chi-restraints excluded: chain P residue 441 GLU Chi-restraints excluded: chain P residue 521 PHE Chi-restraints excluded: chain W residue 2 LEU Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 59 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 145 CYS Chi-restraints excluded: chain X residue 152 ASP Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 388 ARG Chi-restraints excluded: chain X residue 443 THR Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain Y residue 40 HIS Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 94 ARG Chi-restraints excluded: chain Y residue 152 ASP Chi-restraints excluded: chain Y residue 269 ASP Chi-restraints excluded: chain Y residue 345 SER Chi-restraints excluded: chain Y residue 417 TYR Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 520 VAL Chi-restraints excluded: chain Y residue 551 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 712 optimal weight: 5.9990 chunk 542 optimal weight: 9.9990 chunk 374 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 344 optimal weight: 3.9990 chunk 484 optimal weight: 5.9990 chunk 724 optimal weight: 0.8980 chunk 766 optimal weight: 10.0000 chunk 378 optimal weight: 5.9990 chunk 686 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 ASN ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 ASN A1591 HIS ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 HIS ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN C 390 HIS C 427 GLN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 634 HIS F 667 GLN F 679 GLN H 103 HIS ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 257 HIS I 696 GLN J 271 HIS ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 489 HIS L 55 GLN L 103 HIS ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 266 HIS ** N 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 663 GLN N 722 GLN O 219 GLN ** O 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 461 ASN O 741 HIS W 21 ASN X 66 ASN X 151 GLN ** X 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 501 ASN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 64541 Z= 0.375 Angle : 0.793 21.247 87465 Z= 0.406 Chirality : 0.044 0.308 9859 Planarity : 0.005 0.098 11099 Dihedral : 8.705 140.257 9062 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.63 % Favored : 94.77 % Rotamer: Outliers : 7.55 % Allowed : 22.22 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.75 % Cis-general : 0.38 % Twisted Proline : 0.34 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 7920 helix: 1.23 (0.07), residues: 5452 sheet: -0.12 (0.25), residues: 422 loop : -1.79 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP X 342 HIS 0.025 0.002 HIS N 154 PHE 0.049 0.002 PHE A 830 TYR 0.033 0.002 TYR Y 311 ARG 0.011 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 502 poor density : 688 time to evaluate : 5.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 SER cc_start: 0.8317 (m) cc_final: 0.7987 (p) REVERT: A 254 SER cc_start: 0.8710 (OUTLIER) cc_final: 0.8298 (t) REVERT: A 273 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8028 (mmm-85) REVERT: A 459 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8342 (pm20) REVERT: A 511 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.8006 (pp) REVERT: A 636 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8718 (mp10) REVERT: A 707 TRP cc_start: 0.8262 (OUTLIER) cc_final: 0.6974 (t60) REVERT: A 945 GLU cc_start: 0.8716 (tp30) cc_final: 0.8324 (mt-10) REVERT: A 957 ASP cc_start: 0.9182 (t0) cc_final: 0.8801 (t0) REVERT: A 972 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8175 (tp30) REVERT: A 1088 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8936 (p) REVERT: A 1279 ARG cc_start: 0.7014 (ptm160) cc_final: 0.6640 (ptm160) REVERT: A 1290 ASP cc_start: 0.6957 (m-30) cc_final: 0.6492 (t0) REVERT: A 1354 GLU cc_start: 0.6413 (tt0) cc_final: 0.6059 (tm-30) REVERT: A 1456 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.9187 (p) REVERT: A 1623 ASP cc_start: 0.9286 (t0) cc_final: 0.8984 (t0) REVERT: A 1646 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8663 (tm-30) REVERT: A 1705 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7418 (mp10) REVERT: A 1777 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8469 (tm-30) REVERT: A 1785 GLU cc_start: 0.9316 (mp0) cc_final: 0.8839 (pm20) REVERT: A 1810 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8569 (mp0) REVERT: A 1827 GLN cc_start: 0.9382 (OUTLIER) cc_final: 0.8891 (mp10) REVERT: A 1926 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.8736 (mtm110) REVERT: B 2 LYS cc_start: 0.7811 (tptt) cc_final: 0.7575 (tptt) REVERT: B 6 LYS cc_start: 0.8310 (ptmm) cc_final: 0.8027 (mtmm) REVERT: B 14 TRP cc_start: 0.7086 (OUTLIER) cc_final: 0.6055 (p-90) REVERT: B 27 ARG cc_start: 0.6488 (tpt170) cc_final: 0.5822 (tpm170) REVERT: B 43 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8112 (p0) REVERT: C 119 MET cc_start: 0.9725 (tpt) cc_final: 0.9430 (mmm) REVERT: C 218 MET cc_start: 0.9347 (ttp) cc_final: 0.9124 (mtm) REVERT: C 229 MET cc_start: 0.9499 (mmm) cc_final: 0.9190 (mmm) REVERT: C 280 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7787 (m-30) REVERT: C 397 ARG cc_start: 0.9414 (ttt-90) cc_final: 0.9187 (ptt90) REVERT: C 522 LYS cc_start: 0.9492 (tttt) cc_final: 0.9138 (mmtt) REVERT: C 541 ASP cc_start: 0.8573 (m-30) cc_final: 0.8191 (t0) REVERT: C 556 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7776 (mm) REVERT: D 42 GLN cc_start: 0.9539 (mt0) cc_final: 0.9109 (tm-30) REVERT: D 46 GLU cc_start: 0.9601 (mt-10) cc_final: 0.9273 (pp20) REVERT: F 29 GLU cc_start: 0.9679 (mt-10) cc_final: 0.9468 (mt-10) REVERT: F 534 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9081 (mp0) REVERT: F 568 GLU cc_start: 0.9501 (pm20) cc_final: 0.9260 (pm20) REVERT: F 584 ASP cc_start: 0.9318 (OUTLIER) cc_final: 0.9048 (p0) REVERT: F 626 ASN cc_start: 0.9412 (OUTLIER) cc_final: 0.8877 (t0) REVERT: F 636 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.7925 (t0) REVERT: F 741 PHE cc_start: 0.8551 (m-80) cc_final: 0.8257 (m-10) REVERT: G 10 GLU cc_start: 0.8192 (pm20) cc_final: 0.7745 (pm20) REVERT: G 20 GLU cc_start: 0.9444 (mt-10) cc_final: 0.9133 (mp0) REVERT: H 87 GLU cc_start: 0.9390 (tt0) cc_final: 0.9116 (tp30) REVERT: H 469 MET cc_start: 0.8792 (ttm) cc_final: 0.8564 (ttp) REVERT: I 40 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.9129 (p) REVERT: I 192 MET cc_start: 0.9000 (mtp) cc_final: 0.8411 (mmm) REVERT: I 283 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7994 (tmm) REVERT: I 450 GLU cc_start: 0.9483 (OUTLIER) cc_final: 0.9127 (pp20) REVERT: I 454 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8347 (tp30) REVERT: I 519 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6495 (mtp-110) REVERT: I 529 MET cc_start: 0.9215 (ttp) cc_final: 0.8793 (ptm) REVERT: I 546 LYS cc_start: 0.9445 (tptm) cc_final: 0.9164 (mtmm) REVERT: J 55 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8827 (mtp180) REVERT: J 195 ASN cc_start: 0.9591 (OUTLIER) cc_final: 0.9295 (m-40) REVERT: J 199 GLU cc_start: 0.9584 (mt-10) cc_final: 0.9230 (mm-30) REVERT: J 202 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.9107 (ptp-110) REVERT: J 214 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8377 (ttpp) REVERT: J 249 MET cc_start: 0.9353 (mmm) cc_final: 0.8787 (tpp) REVERT: J 349 GLU cc_start: 0.8991 (mp0) cc_final: 0.8682 (mp0) REVERT: J 395 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8559 (mt) REVERT: J 477 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8733 (mm-40) REVERT: K 232 ASP cc_start: 0.9351 (m-30) cc_final: 0.8931 (m-30) REVERT: K 283 GLU cc_start: 0.9467 (mm-30) cc_final: 0.9135 (mp0) REVERT: K 368 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.8033 (p-80) REVERT: K 422 GLU cc_start: 0.9537 (tt0) cc_final: 0.9319 (tt0) REVERT: K 492 MET cc_start: 0.9157 (mtm) cc_final: 0.8921 (mtm) REVERT: L 84 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8543 (ptpp) REVERT: L 112 GLU cc_start: 0.7929 (tp30) cc_final: 0.7679 (tp30) REVERT: L 150 ASP cc_start: 0.7506 (p0) cc_final: 0.7189 (m-30) REVERT: M 1 MET cc_start: 0.8194 (tpt) cc_final: 0.7788 (tpp) REVERT: M 22 ASP cc_start: 0.8846 (t0) cc_final: 0.8408 (t0) REVERT: M 51 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8948 (mttp) REVERT: N 65 HIS cc_start: 0.9125 (OUTLIER) cc_final: 0.8157 (m-70) REVERT: N 67 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.7941 (pp) REVERT: N 84 GLN cc_start: 0.9441 (OUTLIER) cc_final: 0.9165 (tm-30) REVERT: N 152 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8079 (mp0) REVERT: N 156 MET cc_start: 0.9140 (ttp) cc_final: 0.8901 (ttp) REVERT: N 180 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8546 (t80) REVERT: N 299 TRP cc_start: 0.8587 (t60) cc_final: 0.8168 (t60) REVERT: N 518 GLU cc_start: 0.9579 (OUTLIER) cc_final: 0.9225 (tm-30) REVERT: N 531 PHE cc_start: 0.7977 (t80) cc_final: 0.7670 (t80) REVERT: N 557 CYS cc_start: 0.9137 (m) cc_final: 0.8898 (p) REVERT: N 622 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6820 (m-80) REVERT: N 646 MET cc_start: 0.8502 (mpp) cc_final: 0.8138 (mpp) REVERT: N 687 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7193 (ptp) REVERT: O 56 GLU cc_start: 0.5872 (OUTLIER) cc_final: 0.5406 (mm-30) REVERT: O 110 GLN cc_start: 0.8959 (tt0) cc_final: 0.8549 (tp40) REVERT: O 352 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8756 (pt0) REVERT: O 406 ASP cc_start: 0.8318 (m-30) cc_final: 0.8098 (m-30) REVERT: O 505 GLN cc_start: 0.9144 (mt0) cc_final: 0.8727 (mp10) REVERT: O 508 MET cc_start: 0.9310 (mtp) cc_final: 0.8968 (mtp) REVERT: O 562 LYS cc_start: 0.9611 (mttt) cc_final: 0.9404 (mptt) REVERT: O 593 ARG cc_start: 0.8922 (mtm180) cc_final: 0.8623 (mtp85) REVERT: O 618 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8218 (t80) REVERT: O 685 GLU cc_start: 0.9474 (OUTLIER) cc_final: 0.9254 (pt0) REVERT: O 732 ARG cc_start: 0.7966 (mmt180) cc_final: 0.7504 (mmm160) REVERT: P 346 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8471 (mt0) REVERT: W 10 GLU cc_start: 0.9478 (mm-30) cc_final: 0.9091 (tp30) REVERT: W 14 ASP cc_start: 0.9330 (OUTLIER) cc_final: 0.8832 (p0) REVERT: W 21 ASN cc_start: 0.8236 (m-40) cc_final: 0.7977 (m-40) REVERT: X 44 MET cc_start: 0.8559 (mmm) cc_final: 0.8182 (mmm) REVERT: X 91 LYS cc_start: 0.9683 (mttt) cc_final: 0.9307 (tttm) REVERT: X 174 MET cc_start: 0.9434 (tpp) cc_final: 0.9102 (tpp) REVERT: X 342 TRP cc_start: 0.8055 (m100) cc_final: 0.7711 (m100) REVERT: X 347 CYS cc_start: 0.8688 (m) cc_final: 0.8466 (t) REVERT: X 458 GLN cc_start: 0.8916 (mt0) cc_final: 0.8554 (tp40) REVERT: X 529 MET cc_start: 0.5920 (mpp) cc_final: 0.5684 (mpp) REVERT: Y 61 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8951 (pp) REVERT: Y 102 MET cc_start: 0.9189 (mmm) cc_final: 0.8853 (ptp) REVERT: Y 152 ASP cc_start: 0.9357 (OUTLIER) cc_final: 0.8982 (p0) REVERT: Y 173 MET cc_start: 0.8971 (ttp) cc_final: 0.8605 (tpp) REVERT: Y 243 TYR cc_start: 0.8728 (m-80) cc_final: 0.8123 (m-80) REVERT: Y 268 ARG cc_start: 0.8180 (ttm170) cc_final: 0.7742 (ttm-80) REVERT: Y 386 MET cc_start: 0.7289 (mmm) cc_final: 0.7086 (mmm) REVERT: Y 429 MET cc_start: 0.8876 (mtm) cc_final: 0.8465 (ptp) REVERT: Y 515 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6675 (tt) REVERT: Y 551 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7984 (pptt) outliers start: 502 outliers final: 298 residues processed: 1103 average time/residue: 0.5800 time to fit residues: 1100.1745 Evaluate side-chains 985 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 349 poor density : 636 time to evaluate : 5.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 TRP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 707 TRP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 988 CYS Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1190 THR Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1359 ASN Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1597 THR Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1646 GLN Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1705 GLN Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1778 CYS Chi-restraints excluded: chain A residue 1780 THR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1827 GLN Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1856 LEU Chi-restraints excluded: chain A residue 1887 CYS Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1926 ARG Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 481 CYS Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 489 SER Chi-restraints excluded: chain F residue 584 ASP Chi-restraints excluded: chain F residue 623 CYS Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 643 MET Chi-restraints excluded: chain F residue 675 ILE Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 753 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 536 MET Chi-restraints excluded: chain H residue 565 ASN Chi-restraints excluded: chain H residue 596 VAL Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 141 LYS Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 273 CYS Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 288 THR Chi-restraints excluded: chain I residue 310 TRP Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 450 GLU Chi-restraints excluded: chain I residue 453 THR Chi-restraints excluded: chain I residue 454 GLU Chi-restraints excluded: chain I residue 505 SER Chi-restraints excluded: chain I residue 519 ARG Chi-restraints excluded: chain I residue 717 MET Chi-restraints excluded: chain I residue 722 VAL Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain J residue 8 LYS Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 343 SER Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 246 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 316 ASN Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 352 GLN Chi-restraints excluded: chain K residue 368 HIS Chi-restraints excluded: chain K residue 458 LEU Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 27 GLU Chi-restraints excluded: chain M residue 28 ASP Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 180 PHE Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 256 VAL Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 518 GLU Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 527 LEU Chi-restraints excluded: chain N residue 547 LEU Chi-restraints excluded: chain N residue 548 ARG Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 594 VAL Chi-restraints excluded: chain N residue 598 SER Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 662 VAL Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 687 MET Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 149 SER Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 219 GLN Chi-restraints excluded: chain O residue 224 LYS Chi-restraints excluded: chain O residue 249 ASP Chi-restraints excluded: chain O residue 257 SER Chi-restraints excluded: chain O residue 299 SER Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 488 GLU Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 579 MET Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 633 ILE Chi-restraints excluded: chain O residue 657 ILE Chi-restraints excluded: chain O residue 658 LEU Chi-restraints excluded: chain O residue 685 GLU Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain O residue 752 ILE Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 300 MET Chi-restraints excluded: chain P residue 334 CYS Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 346 GLN Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 447 ASN Chi-restraints excluded: chain P residue 521 PHE Chi-restraints excluded: chain W residue 2 LEU Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 59 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 145 CYS Chi-restraints excluded: chain X residue 152 ASP Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 158 ILE Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 443 THR Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 539 ASP Chi-restraints excluded: chain Y residue 40 HIS Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 94 ARG Chi-restraints excluded: chain Y residue 152 ASP Chi-restraints excluded: chain Y residue 229 THR Chi-restraints excluded: chain Y residue 233 LEU Chi-restraints excluded: chain Y residue 269 ASP Chi-restraints excluded: chain Y residue 345 SER Chi-restraints excluded: chain Y residue 417 TYR Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 551 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 638 optimal weight: 0.8980 chunk 435 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 570 optimal weight: 0.4980 chunk 316 optimal weight: 9.9990 chunk 654 optimal weight: 4.9990 chunk 529 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 391 optimal weight: 0.0570 chunk 688 optimal weight: 10.0000 chunk 193 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 ASN ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 HIS A1599 ASN ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 ASN F 667 GLN ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 ASN L 103 HIS ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 HIS ** N 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 571 ASN ** N 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 247 ASN O 693 ASN P 518 GLN X 166 GLN ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 64541 Z= 0.212 Angle : 0.742 19.902 87465 Z= 0.371 Chirality : 0.042 0.313 9859 Planarity : 0.005 0.080 11099 Dihedral : 8.173 144.106 9006 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.63 % Favored : 94.81 % Rotamer: Outliers : 6.21 % Allowed : 23.39 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.75 % Cis-general : 0.38 % Twisted Proline : 0.34 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.09), residues: 7920 helix: 1.34 (0.07), residues: 5461 sheet: -0.02 (0.25), residues: 422 loop : -1.71 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP X 235 HIS 0.009 0.001 HIS Y 395 PHE 0.033 0.002 PHE K 164 TYR 0.044 0.001 TYR N 626 ARG 0.007 0.001 ARG Y 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 413 poor density : 765 time to evaluate : 5.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.9262 (p0) cc_final: 0.8696 (t70) REVERT: A 114 TYR cc_start: 0.9108 (t80) cc_final: 0.8737 (t80) REVERT: A 157 SER cc_start: 0.8510 (m) cc_final: 0.8233 (p) REVERT: A 218 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8953 (m-30) REVERT: A 220 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9013 (mt) REVERT: A 254 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8332 (t) REVERT: A 273 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7669 (mmm-85) REVERT: A 459 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8189 (pm20) REVERT: A 608 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8271 (p) REVERT: A 611 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8661 (mm-30) REVERT: A 707 TRP cc_start: 0.8188 (OUTLIER) cc_final: 0.7242 (t60) REVERT: A 831 MET cc_start: 0.8218 (mmp) cc_final: 0.7974 (mmp) REVERT: A 945 GLU cc_start: 0.8701 (tp30) cc_final: 0.8409 (mt-10) REVERT: A 957 ASP cc_start: 0.9079 (t0) cc_final: 0.8489 (t0) REVERT: A 972 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8341 (tp30) REVERT: A 1019 MET cc_start: 0.8496 (mtp) cc_final: 0.7711 (mtp) REVERT: A 1088 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8960 (p) REVERT: A 1107 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7160 (mt) REVERT: A 1203 MET cc_start: 0.5992 (mmp) cc_final: 0.5693 (mmp) REVERT: A 1279 ARG cc_start: 0.7162 (ptm160) cc_final: 0.6748 (ptm160) REVERT: A 1290 ASP cc_start: 0.7022 (m-30) cc_final: 0.6615 (t0) REVERT: A 1354 GLU cc_start: 0.6553 (tt0) cc_final: 0.6249 (tm-30) REVERT: A 1456 THR cc_start: 0.9510 (OUTLIER) cc_final: 0.9210 (p) REVERT: A 1527 MET cc_start: 0.9576 (mmm) cc_final: 0.9255 (mmp) REVERT: A 1600 ARG cc_start: 0.7061 (tmm-80) cc_final: 0.6675 (ptm-80) REVERT: A 1623 ASP cc_start: 0.9246 (t0) cc_final: 0.8964 (t0) REVERT: A 1705 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: A 1777 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8483 (tm-30) REVERT: A 1810 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8651 (mp0) REVERT: A 1872 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9180 (mm) REVERT: A 1926 ARG cc_start: 0.9243 (mpp-170) cc_final: 0.8489 (ttp80) REVERT: B 6 LYS cc_start: 0.8393 (ptmm) cc_final: 0.8125 (mtmm) REVERT: B 14 TRP cc_start: 0.6877 (OUTLIER) cc_final: 0.5932 (p-90) REVERT: B 27 ARG cc_start: 0.6466 (tpt170) cc_final: 0.5873 (tpm170) REVERT: B 43 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7917 (p0) REVERT: C 119 MET cc_start: 0.9731 (tpt) cc_final: 0.9443 (mmm) REVERT: C 229 MET cc_start: 0.9407 (mmm) cc_final: 0.9126 (mmm) REVERT: C 475 LYS cc_start: 0.7652 (tmtt) cc_final: 0.7443 (mmmm) REVERT: C 522 LYS cc_start: 0.9485 (tttt) cc_final: 0.9128 (mmtt) REVERT: C 541 ASP cc_start: 0.8695 (m-30) cc_final: 0.8222 (t0) REVERT: C 556 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7731 (mm) REVERT: D 27 GLU cc_start: 0.6456 (tp30) cc_final: 0.6163 (tp30) REVERT: D 42 GLN cc_start: 0.9501 (mt0) cc_final: 0.9066 (tm-30) REVERT: D 46 GLU cc_start: 0.9570 (mt-10) cc_final: 0.9173 (pp20) REVERT: E 78 ARG cc_start: 0.8330 (mtt90) cc_final: 0.8065 (mtm-85) REVERT: E 80 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8084 (pp20) REVERT: E 81 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8487 (mtpp) REVERT: F 584 ASP cc_start: 0.9361 (OUTLIER) cc_final: 0.9103 (p0) REVERT: F 626 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8604 (t0) REVERT: F 636 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8181 (t0) REVERT: F 741 PHE cc_start: 0.8551 (m-80) cc_final: 0.8241 (m-10) REVERT: G 20 GLU cc_start: 0.9443 (mt-10) cc_final: 0.9189 (mp0) REVERT: H 87 GLU cc_start: 0.9401 (tt0) cc_final: 0.9087 (tp30) REVERT: H 127 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.9027 (mmtm) REVERT: H 463 MET cc_start: 0.9264 (tpp) cc_final: 0.9009 (tpp) REVERT: H 469 MET cc_start: 0.8835 (ttm) cc_final: 0.8495 (ttp) REVERT: I 40 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9152 (p) REVERT: I 90 ILE cc_start: 0.8993 (mt) cc_final: 0.8765 (mm) REVERT: I 192 MET cc_start: 0.8950 (mtp) cc_final: 0.8500 (mmm) REVERT: I 283 MET cc_start: 0.8549 (ttp) cc_final: 0.8093 (tmm) REVERT: I 322 MET cc_start: 0.8799 (tmm) cc_final: 0.8449 (ptm) REVERT: I 450 GLU cc_start: 0.9466 (OUTLIER) cc_final: 0.9115 (pp20) REVERT: I 454 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8259 (tp30) REVERT: I 519 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.6375 (mtp-110) REVERT: I 529 MET cc_start: 0.9149 (ttp) cc_final: 0.8693 (ptm) REVERT: I 705 MET cc_start: 0.8743 (mmm) cc_final: 0.8332 (mmm) REVERT: J 20 GLN cc_start: 0.9497 (OUTLIER) cc_final: 0.9205 (mp10) REVERT: J 199 GLU cc_start: 0.9590 (mt-10) cc_final: 0.9292 (mm-30) REVERT: J 249 MET cc_start: 0.9336 (mmm) cc_final: 0.8763 (tpp) REVERT: J 343 SER cc_start: 0.9428 (OUTLIER) cc_final: 0.9202 (p) REVERT: J 349 GLU cc_start: 0.8970 (mp0) cc_final: 0.8643 (mp0) REVERT: J 376 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8911 (mm) REVERT: J 395 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8536 (mt) REVERT: J 511 ASP cc_start: 0.9424 (t0) cc_final: 0.9150 (m-30) REVERT: K 232 ASP cc_start: 0.9334 (m-30) cc_final: 0.8894 (m-30) REVERT: K 258 MET cc_start: 0.8366 (mmt) cc_final: 0.8058 (mmt) REVERT: K 283 GLU cc_start: 0.9464 (mm-30) cc_final: 0.9158 (mp0) REVERT: K 354 MET cc_start: 0.8868 (tpp) cc_final: 0.8565 (tpp) REVERT: K 492 MET cc_start: 0.9175 (mtm) cc_final: 0.8897 (mtm) REVERT: L 32 SER cc_start: 0.8430 (m) cc_final: 0.8175 (p) REVERT: L 112 GLU cc_start: 0.7983 (tp30) cc_final: 0.7739 (tp30) REVERT: L 150 ASP cc_start: 0.7482 (p0) cc_final: 0.7136 (m-30) REVERT: M 17 ASP cc_start: 0.8219 (t70) cc_final: 0.7176 (t70) REVERT: M 21 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8962 (mp0) REVERT: M 22 ASP cc_start: 0.8768 (t0) cc_final: 0.8425 (t0) REVERT: M 51 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8986 (mttp) REVERT: M 59 ASP cc_start: 0.8233 (m-30) cc_final: 0.7972 (m-30) REVERT: N 65 HIS cc_start: 0.9053 (OUTLIER) cc_final: 0.7933 (m90) REVERT: N 67 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8014 (pp) REVERT: N 84 GLN cc_start: 0.9435 (OUTLIER) cc_final: 0.9182 (tm-30) REVERT: N 152 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8045 (mp0) REVERT: N 185 MET cc_start: 0.8369 (mmm) cc_final: 0.7775 (tpt) REVERT: N 237 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8657 (mm) REVERT: N 253 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8650 (tt) REVERT: N 531 PHE cc_start: 0.7950 (t80) cc_final: 0.7650 (t80) REVERT: N 557 CYS cc_start: 0.9102 (m) cc_final: 0.8893 (p) REVERT: N 622 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.5460 (m-80) REVERT: N 646 MET cc_start: 0.8643 (mpp) cc_final: 0.8225 (mpp) REVERT: N 685 VAL cc_start: 0.6621 (OUTLIER) cc_final: 0.5946 (t) REVERT: N 687 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7364 (ptp) REVERT: N 688 PRO cc_start: 0.8875 (Cg_endo) cc_final: 0.8669 (Cg_exo) REVERT: O 56 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.4474 (mm-30) REVERT: O 110 GLN cc_start: 0.8920 (tt0) cc_final: 0.8502 (tp40) REVERT: O 352 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8778 (pt0) REVERT: O 406 ASP cc_start: 0.8253 (m-30) cc_final: 0.8012 (m-30) REVERT: O 414 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8188 (pp) REVERT: O 505 GLN cc_start: 0.8919 (mt0) cc_final: 0.8660 (mp10) REVERT: O 508 MET cc_start: 0.9375 (mtp) cc_final: 0.9000 (mtp) REVERT: O 562 LYS cc_start: 0.9590 (mttt) cc_final: 0.9376 (mptt) REVERT: O 593 ARG cc_start: 0.8709 (mtm180) cc_final: 0.8401 (mtp180) REVERT: O 618 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.8215 (t80) REVERT: O 732 ARG cc_start: 0.7884 (mmt180) cc_final: 0.7669 (mmp-170) REVERT: P 120 TYR cc_start: 0.7877 (t80) cc_final: 0.7531 (t80) REVERT: P 149 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8758 (mp0) REVERT: W 10 GLU cc_start: 0.9467 (mm-30) cc_final: 0.8962 (tp30) REVERT: W 12 LYS cc_start: 0.7773 (mmmm) cc_final: 0.7386 (mtmm) REVERT: W 14 ASP cc_start: 0.9316 (OUTLIER) cc_final: 0.8825 (p0) REVERT: W 21 ASN cc_start: 0.8135 (m-40) cc_final: 0.7870 (m-40) REVERT: X 44 MET cc_start: 0.8625 (mmm) cc_final: 0.8260 (mmm) REVERT: X 91 LYS cc_start: 0.9686 (mttt) cc_final: 0.9308 (tttm) REVERT: X 174 MET cc_start: 0.9441 (tpp) cc_final: 0.9106 (tpp) REVERT: X 204 ASP cc_start: 0.9253 (OUTLIER) cc_final: 0.9038 (m-30) REVERT: X 340 GLU cc_start: 0.8445 (mp0) cc_final: 0.8140 (mp0) REVERT: X 447 LEU cc_start: 0.9237 (mp) cc_final: 0.9007 (tp) REVERT: X 458 GLN cc_start: 0.8889 (mt0) cc_final: 0.8522 (tp40) REVERT: X 529 MET cc_start: 0.5969 (mpp) cc_final: 0.5631 (mpp) REVERT: Y 61 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9005 (pp) REVERT: Y 152 ASP cc_start: 0.9315 (OUTLIER) cc_final: 0.8982 (p0) REVERT: Y 173 MET cc_start: 0.8880 (ttp) cc_final: 0.8566 (tpp) REVERT: Y 243 TYR cc_start: 0.8658 (m-80) cc_final: 0.8046 (m-80) REVERT: Y 268 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7804 (ttm-80) REVERT: Y 323 ASP cc_start: 0.8825 (t0) cc_final: 0.8532 (t0) REVERT: Y 429 MET cc_start: 0.8857 (mtm) cc_final: 0.8467 (ptp) REVERT: Y 515 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6612 (tt) REVERT: Y 549 MET cc_start: 0.8472 (mmt) cc_final: 0.8181 (mmp) REVERT: Y 551 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7971 (pptt) outliers start: 413 outliers final: 233 residues processed: 1102 average time/residue: 0.5793 time to fit residues: 1104.1102 Evaluate side-chains 936 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 655 time to evaluate : 5.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 TRP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 707 TRP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 988 CYS Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1190 THR Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1359 ASN Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1591 HIS Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1705 GLN Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1778 CYS Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1818 LEU Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1872 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 489 SER Chi-restraints excluded: chain F residue 584 ASP Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 643 MET Chi-restraints excluded: chain F residue 675 ILE Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 127 LYS Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 553 SER Chi-restraints excluded: chain H residue 565 ASN Chi-restraints excluded: chain H residue 596 VAL Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 141 LYS Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 310 TRP Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 373 LYS Chi-restraints excluded: chain I residue 450 GLU Chi-restraints excluded: chain I residue 453 THR Chi-restraints excluded: chain I residue 454 GLU Chi-restraints excluded: chain I residue 455 HIS Chi-restraints excluded: chain I residue 519 ARG Chi-restraints excluded: chain I residue 717 MET Chi-restraints excluded: chain I residue 722 VAL Chi-restraints excluded: chain J residue 8 LYS Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 343 SER Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 510 ARG Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 352 GLN Chi-restraints excluded: chain K residue 473 VAL Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 28 ASP Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 154 HIS Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 253 LEU Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 396 ILE Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 518 GLU Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 547 LEU Chi-restraints excluded: chain N residue 554 MET Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 687 MET Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 249 ASP Chi-restraints excluded: chain O residue 299 SER Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 488 GLU Chi-restraints excluded: chain O residue 579 MET Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 633 ILE Chi-restraints excluded: chain O residue 657 ILE Chi-restraints excluded: chain O residue 658 LEU Chi-restraints excluded: chain O residue 685 GLU Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 706 CYS Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 210 CYS Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 521 PHE Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 145 CYS Chi-restraints excluded: chain X residue 152 ASP Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 204 ASP Chi-restraints excluded: chain X residue 290 SER Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 443 THR Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain Y residue 40 HIS Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 94 ARG Chi-restraints excluded: chain Y residue 152 ASP Chi-restraints excluded: chain Y residue 269 ASP Chi-restraints excluded: chain Y residue 345 SER Chi-restraints excluded: chain Y residue 417 TYR Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 551 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 257 optimal weight: 5.9990 chunk 690 optimal weight: 30.0000 chunk 151 optimal weight: 0.0060 chunk 450 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 767 optimal weight: 8.9990 chunk 636 optimal weight: 5.9990 chunk 355 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 253 optimal weight: 0.4980 chunk 402 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN A 473 ASN ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** F 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 ASN F 626 ASN F 667 GLN ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 GLN I 405 GLN J 18 GLN ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 ASN ** K 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 HIS ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 HIS ** N 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 628 GLN ** N 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 GLN O 461 ASN ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 531 GLN ** Y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 333 ASN ** Y 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 64541 Z= 0.202 Angle : 0.731 21.286 87465 Z= 0.365 Chirality : 0.041 0.319 9859 Planarity : 0.004 0.091 11099 Dihedral : 7.598 146.348 8943 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.57 % Favored : 94.85 % Rotamer: Outliers : 5.59 % Allowed : 24.37 % Favored : 70.03 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.75 % Cis-general : 0.38 % Twisted Proline : 0.34 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.09), residues: 7920 helix: 1.37 (0.07), residues: 5471 sheet: 0.02 (0.25), residues: 428 loop : -1.70 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP Y 235 HIS 0.036 0.001 HIS A1591 PHE 0.029 0.002 PHE P 233 TYR 0.024 0.001 TYR N 626 ARG 0.006 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 730 time to evaluate : 5.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TYR cc_start: 0.9075 (t80) cc_final: 0.8759 (t80) REVERT: A 157 SER cc_start: 0.8576 (m) cc_final: 0.8246 (p) REVERT: A 218 ASP cc_start: 0.9237 (OUTLIER) cc_final: 0.8992 (m-30) REVERT: A 273 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7556 (mmm-85) REVERT: A 459 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8203 (pm20) REVERT: A 511 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7702 (pp) REVERT: A 608 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8236 (p) REVERT: A 707 TRP cc_start: 0.8140 (OUTLIER) cc_final: 0.7255 (t60) REVERT: A 831 MET cc_start: 0.8177 (mmp) cc_final: 0.7854 (mmp) REVERT: A 862 TYR cc_start: 0.5058 (OUTLIER) cc_final: 0.4240 (p90) REVERT: A 945 GLU cc_start: 0.8680 (tp30) cc_final: 0.8393 (mt-10) REVERT: A 957 ASP cc_start: 0.9036 (t0) cc_final: 0.8673 (t0) REVERT: A 972 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8469 (tp30) REVERT: A 1019 MET cc_start: 0.8313 (mtp) cc_final: 0.7461 (mtp) REVERT: A 1088 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8945 (p) REVERT: A 1107 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7223 (mt) REVERT: A 1203 MET cc_start: 0.6002 (mmp) cc_final: 0.5757 (mmt) REVERT: A 1279 ARG cc_start: 0.7232 (ptm160) cc_final: 0.6854 (ptm160) REVERT: A 1290 ASP cc_start: 0.7057 (m-30) cc_final: 0.6675 (t0) REVERT: A 1325 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8665 (mt) REVERT: A 1354 GLU cc_start: 0.6623 (tt0) cc_final: 0.6305 (tm-30) REVERT: A 1385 ASP cc_start: 0.9764 (m-30) cc_final: 0.9558 (p0) REVERT: A 1456 THR cc_start: 0.9503 (OUTLIER) cc_final: 0.9201 (p) REVERT: A 1527 MET cc_start: 0.9542 (mmm) cc_final: 0.9144 (mmp) REVERT: A 1599 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.6820 (m-40) REVERT: A 1623 ASP cc_start: 0.9258 (t0) cc_final: 0.8992 (t0) REVERT: A 1705 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7344 (mp10) REVERT: A 1777 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8460 (tm-30) REVERT: A 1785 GLU cc_start: 0.9257 (mp0) cc_final: 0.8765 (pm20) REVERT: A 1807 GLU cc_start: 0.9481 (mm-30) cc_final: 0.8606 (mp0) REVERT: A 1810 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8647 (mp0) REVERT: A 1872 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9196 (mm) REVERT: A 1926 ARG cc_start: 0.9296 (mpp-170) cc_final: 0.8790 (mtm110) REVERT: B 2 LYS cc_start: 0.8332 (tptt) cc_final: 0.8030 (tptp) REVERT: B 6 LYS cc_start: 0.8375 (ptmm) cc_final: 0.8126 (mtmt) REVERT: B 14 TRP cc_start: 0.7094 (OUTLIER) cc_final: 0.6165 (p-90) REVERT: C 119 MET cc_start: 0.9730 (tpt) cc_final: 0.9492 (mmm) REVERT: C 124 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8924 (mm) REVERT: C 201 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8708 (tp) REVERT: C 218 MET cc_start: 0.9309 (ttp) cc_final: 0.9059 (mtm) REVERT: C 229 MET cc_start: 0.9348 (mmm) cc_final: 0.9029 (mmm) REVERT: C 280 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: C 475 LYS cc_start: 0.7645 (tmtt) cc_final: 0.7433 (mmmm) REVERT: C 498 TYR cc_start: 0.8694 (t80) cc_final: 0.8470 (m-80) REVERT: C 522 LYS cc_start: 0.9460 (tttt) cc_final: 0.9091 (mmtt) REVERT: C 541 ASP cc_start: 0.8697 (m-30) cc_final: 0.8234 (t0) REVERT: C 556 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7699 (mm) REVERT: D 27 GLU cc_start: 0.6411 (tp30) cc_final: 0.6193 (tp30) REVERT: D 42 GLN cc_start: 0.9491 (mt0) cc_final: 0.9062 (tm-30) REVERT: D 46 GLU cc_start: 0.9561 (mt-10) cc_final: 0.9139 (pp20) REVERT: E 80 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8110 (pp20) REVERT: E 81 LYS cc_start: 0.8726 (mmmm) cc_final: 0.8404 (mtpp) REVERT: F 580 GLN cc_start: 0.9426 (tp40) cc_final: 0.9157 (mp10) REVERT: F 584 ASP cc_start: 0.9392 (OUTLIER) cc_final: 0.9159 (p0) REVERT: F 741 PHE cc_start: 0.8605 (m-80) cc_final: 0.8289 (m-10) REVERT: G 10 GLU cc_start: 0.8088 (pm20) cc_final: 0.7844 (pm20) REVERT: G 20 GLU cc_start: 0.9526 (mt-10) cc_final: 0.9233 (mp0) REVERT: H 38 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: H 87 GLU cc_start: 0.9397 (tt0) cc_final: 0.9071 (tp30) REVERT: H 469 MET cc_start: 0.8886 (ttm) cc_final: 0.8475 (ttp) REVERT: H 536 MET cc_start: 0.6794 (mmp) cc_final: 0.6578 (mmm) REVERT: I 40 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.9155 (p) REVERT: I 90 ILE cc_start: 0.8981 (mt) cc_final: 0.8764 (mm) REVERT: I 192 MET cc_start: 0.8940 (mtp) cc_final: 0.8477 (mmm) REVERT: I 283 MET cc_start: 0.8592 (ttp) cc_final: 0.8009 (tmm) REVERT: I 310 TRP cc_start: 0.3683 (OUTLIER) cc_final: 0.3035 (m100) REVERT: I 450 GLU cc_start: 0.9442 (OUTLIER) cc_final: 0.9131 (pp20) REVERT: I 454 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8207 (tp30) REVERT: I 519 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6541 (mtp-110) REVERT: I 529 MET cc_start: 0.9119 (ttp) cc_final: 0.8612 (ptm) REVERT: I 705 MET cc_start: 0.8760 (mmm) cc_final: 0.8382 (mmm) REVERT: I 745 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7942 (pt0) REVERT: J 20 GLN cc_start: 0.9541 (OUTLIER) cc_final: 0.9249 (mp10) REVERT: J 199 GLU cc_start: 0.9586 (mt-10) cc_final: 0.9266 (mm-30) REVERT: J 202 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.9091 (ptp-110) REVERT: J 249 MET cc_start: 0.9341 (mmm) cc_final: 0.8797 (tpp) REVERT: J 395 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8445 (mt) REVERT: J 511 ASP cc_start: 0.9439 (t0) cc_final: 0.9171 (m-30) REVERT: K 63 ARG cc_start: 0.9391 (OUTLIER) cc_final: 0.8776 (mpp80) REVERT: K 141 ASP cc_start: 0.9441 (OUTLIER) cc_final: 0.9037 (m-30) REVERT: K 232 ASP cc_start: 0.9343 (m-30) cc_final: 0.8901 (m-30) REVERT: K 283 GLU cc_start: 0.9481 (mm-30) cc_final: 0.9188 (mp0) REVERT: K 354 MET cc_start: 0.8874 (tpp) cc_final: 0.8587 (tpp) REVERT: K 364 MET cc_start: 0.8075 (mtm) cc_final: 0.7780 (mpp) REVERT: K 417 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: K 492 MET cc_start: 0.9196 (mtm) cc_final: 0.8906 (mtm) REVERT: L 32 SER cc_start: 0.8443 (m) cc_final: 0.7847 (p) REVERT: L 67 GLN cc_start: 0.8542 (mt0) cc_final: 0.8082 (mp10) REVERT: L 112 GLU cc_start: 0.7936 (tp30) cc_final: 0.7685 (tp30) REVERT: L 150 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7434 (m-30) REVERT: M 1 MET cc_start: 0.8287 (tpt) cc_final: 0.8001 (tpp) REVERT: M 22 ASP cc_start: 0.8838 (t0) cc_final: 0.8295 (t0) REVERT: M 51 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9071 (mttp) REVERT: M 54 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8706 (mm-30) REVERT: M 59 ASP cc_start: 0.8242 (m-30) cc_final: 0.7947 (m-30) REVERT: N 65 HIS cc_start: 0.9022 (OUTLIER) cc_final: 0.7826 (m90) REVERT: N 67 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8055 (pp) REVERT: N 152 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7892 (mp0) REVERT: N 237 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8655 (mm) REVERT: N 253 LEU cc_start: 0.8833 (tt) cc_final: 0.8610 (tt) REVERT: N 351 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: N 518 GLU cc_start: 0.9558 (OUTLIER) cc_final: 0.9208 (tm-30) REVERT: N 531 PHE cc_start: 0.7933 (t80) cc_final: 0.7634 (t80) REVERT: N 646 MET cc_start: 0.8737 (mpp) cc_final: 0.8254 (mpp) REVERT: N 685 VAL cc_start: 0.6737 (OUTLIER) cc_final: 0.6102 (t) REVERT: O 110 GLN cc_start: 0.8877 (tt0) cc_final: 0.8452 (tp40) REVERT: O 139 MET cc_start: 0.8913 (mmt) cc_final: 0.8609 (mmm) REVERT: O 352 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8777 (pt0) REVERT: O 406 ASP cc_start: 0.8267 (m-30) cc_final: 0.8037 (m-30) REVERT: O 414 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8205 (pp) REVERT: O 505 GLN cc_start: 0.8798 (mt0) cc_final: 0.8598 (mp10) REVERT: O 508 MET cc_start: 0.9367 (mtp) cc_final: 0.9080 (mtp) REVERT: O 562 LYS cc_start: 0.9548 (mttt) cc_final: 0.9327 (mptt) REVERT: O 593 ARG cc_start: 0.8651 (mtm180) cc_final: 0.8415 (mtp180) REVERT: O 618 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.8166 (t80) REVERT: O 685 GLU cc_start: 0.9423 (OUTLIER) cc_final: 0.9173 (pt0) REVERT: P 120 TYR cc_start: 0.7849 (t80) cc_final: 0.7576 (t80) REVERT: P 149 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8748 (mp0) REVERT: P 300 MET cc_start: 0.8892 (mmt) cc_final: 0.8682 (mmp) REVERT: W 10 GLU cc_start: 0.9437 (mm-30) cc_final: 0.8940 (tp30) REVERT: W 12 LYS cc_start: 0.7914 (mmmm) cc_final: 0.7534 (mtmm) REVERT: W 14 ASP cc_start: 0.9288 (OUTLIER) cc_final: 0.8744 (p0) REVERT: X 44 MET cc_start: 0.8560 (mmm) cc_final: 0.7959 (mmm) REVERT: X 91 LYS cc_start: 0.9681 (mttt) cc_final: 0.9267 (tttm) REVERT: X 174 MET cc_start: 0.9452 (tpp) cc_final: 0.9208 (tpp) REVERT: X 204 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8697 (m-30) REVERT: X 282 PHE cc_start: 0.8921 (t80) cc_final: 0.8682 (t80) REVERT: X 359 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8362 (tt) REVERT: X 360 TYR cc_start: 0.8589 (m-80) cc_final: 0.8181 (m-10) REVERT: X 388 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8244 (mtm-85) REVERT: X 447 LEU cc_start: 0.9195 (mp) cc_final: 0.8905 (tp) REVERT: X 458 GLN cc_start: 0.8904 (mt0) cc_final: 0.8552 (tp40) REVERT: X 529 MET cc_start: 0.6000 (mpp) cc_final: 0.5681 (mpp) REVERT: Y 61 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8963 (pp) REVERT: Y 102 MET cc_start: 0.9185 (mpp) cc_final: 0.8984 (ptp) REVERT: Y 152 ASP cc_start: 0.9314 (OUTLIER) cc_final: 0.9010 (p0) REVERT: Y 173 MET cc_start: 0.8976 (ttp) cc_final: 0.8588 (tpp) REVERT: Y 243 TYR cc_start: 0.8715 (m-80) cc_final: 0.7990 (m-80) REVERT: Y 268 ARG cc_start: 0.8088 (ttm170) cc_final: 0.7796 (ttm-80) REVERT: Y 323 ASP cc_start: 0.8857 (t0) cc_final: 0.8554 (t0) REVERT: Y 429 MET cc_start: 0.8830 (mtm) cc_final: 0.8440 (ptp) REVERT: Y 515 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6597 (tt) REVERT: Y 549 MET cc_start: 0.8512 (mmt) cc_final: 0.8222 (mmp) REVERT: Y 551 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7983 (pptt) outliers start: 372 outliers final: 218 residues processed: 1031 average time/residue: 0.5850 time to fit residues: 1049.3728 Evaluate side-chains 945 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 672 time to evaluate : 5.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 TRP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 707 TRP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 988 CYS Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1190 THR Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1359 ASN Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1591 HIS Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1705 GLN Chi-restraints excluded: chain A residue 1778 CYS Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1872 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 489 SER Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 584 ASP Chi-restraints excluded: chain F residue 643 MET Chi-restraints excluded: chain F residue 675 ILE Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 563 ASP Chi-restraints excluded: chain H residue 596 VAL Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 288 THR Chi-restraints excluded: chain I residue 310 TRP Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 373 LYS Chi-restraints excluded: chain I residue 450 GLU Chi-restraints excluded: chain I residue 453 THR Chi-restraints excluded: chain I residue 454 GLU Chi-restraints excluded: chain I residue 455 HIS Chi-restraints excluded: chain I residue 519 ARG Chi-restraints excluded: chain I residue 571 LYS Chi-restraints excluded: chain I residue 717 MET Chi-restraints excluded: chain I residue 722 VAL Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 316 ASN Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 352 GLN Chi-restraints excluded: chain K residue 417 GLU Chi-restraints excluded: chain K residue 473 VAL Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 28 ASP Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 518 GLU Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 547 LEU Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 249 ASP Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 488 GLU Chi-restraints excluded: chain O residue 579 MET Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 633 ILE Chi-restraints excluded: chain O residue 657 ILE Chi-restraints excluded: chain O residue 658 LEU Chi-restraints excluded: chain O residue 685 GLU Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 710 ILE Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 210 CYS Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 521 PHE Chi-restraints excluded: chain W residue 2 LEU Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 145 CYS Chi-restraints excluded: chain X residue 152 ASP Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 204 ASP Chi-restraints excluded: chain X residue 290 SER Chi-restraints excluded: chain X residue 359 LEU Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 388 ARG Chi-restraints excluded: chain X residue 443 THR Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain Y residue 40 HIS Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 94 ARG Chi-restraints excluded: chain Y residue 152 ASP Chi-restraints excluded: chain Y residue 269 ASP Chi-restraints excluded: chain Y residue 345 SER Chi-restraints excluded: chain Y residue 417 TYR Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 551 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 739 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 437 optimal weight: 6.9990 chunk 560 optimal weight: 5.9990 chunk 434 optimal weight: 9.9990 chunk 645 optimal weight: 0.9980 chunk 428 optimal weight: 8.9990 chunk 764 optimal weight: 20.0000 chunk 478 optimal weight: 1.9990 chunk 465 optimal weight: 5.9990 chunk 352 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 HIS A1599 ASN ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1881 GLN ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 HIS ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 ASN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 ASN L 103 HIS ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 GLN N 154 HIS ** N 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 673 GLN ** N 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 GLN O 424 GLN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 64541 Z= 0.348 Angle : 0.764 19.681 87465 Z= 0.386 Chirality : 0.043 0.327 9859 Planarity : 0.005 0.060 11099 Dihedral : 7.325 150.081 8916 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.98 % Favored : 94.43 % Rotamer: Outliers : 5.74 % Allowed : 24.72 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.75 % Cis-general : 0.38 % Twisted Proline : 0.34 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.10), residues: 7920 helix: 1.38 (0.07), residues: 5479 sheet: -0.18 (0.25), residues: 438 loop : -1.73 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP X 342 HIS 0.018 0.001 HIS A1591 PHE 0.036 0.002 PHE K 164 TYR 0.023 0.002 TYR A1891 ARG 0.009 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 382 poor density : 640 time to evaluate : 5.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TYR cc_start: 0.9140 (t80) cc_final: 0.8779 (t80) REVERT: A 157 SER cc_start: 0.8573 (m) cc_final: 0.8251 (p) REVERT: A 218 ASP cc_start: 0.9286 (OUTLIER) cc_final: 0.9039 (m-30) REVERT: A 273 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7668 (mmm-85) REVERT: A 407 LEU cc_start: 0.7883 (tp) cc_final: 0.7660 (tp) REVERT: A 459 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8279 (pm20) REVERT: A 707 TRP cc_start: 0.8233 (OUTLIER) cc_final: 0.6988 (t60) REVERT: A 831 MET cc_start: 0.8203 (mmp) cc_final: 0.7907 (mmp) REVERT: A 862 TYR cc_start: 0.5003 (OUTLIER) cc_final: 0.3987 (p90) REVERT: A 945 GLU cc_start: 0.8792 (tp30) cc_final: 0.8393 (mt-10) REVERT: A 972 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8196 (tp30) REVERT: A 1088 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8916 (p) REVERT: A 1107 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7322 (mt) REVERT: A 1203 MET cc_start: 0.5987 (mmp) cc_final: 0.5739 (mmt) REVERT: A 1290 ASP cc_start: 0.7339 (m-30) cc_final: 0.6935 (m-30) REVERT: A 1354 GLU cc_start: 0.6313 (tt0) cc_final: 0.5984 (tm-30) REVERT: A 1456 THR cc_start: 0.9521 (OUTLIER) cc_final: 0.9236 (p) REVERT: A 1600 ARG cc_start: 0.6807 (ttm-80) cc_final: 0.6456 (ptm160) REVERT: A 1623 ASP cc_start: 0.9321 (t0) cc_final: 0.8975 (t0) REVERT: A 1646 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8641 (tm-30) REVERT: A 1705 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7474 (mp10) REVERT: A 1777 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8404 (tm-30) REVERT: A 1810 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8699 (mp0) REVERT: A 1926 ARG cc_start: 0.9377 (mpp-170) cc_final: 0.8854 (mtm110) REVERT: B 2 LYS cc_start: 0.8042 (tptt) cc_final: 0.7809 (tptp) REVERT: B 6 LYS cc_start: 0.8466 (ptmm) cc_final: 0.8188 (mtmt) REVERT: B 14 TRP cc_start: 0.6973 (OUTLIER) cc_final: 0.6135 (p-90) REVERT: C 124 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8858 (mm) REVERT: C 229 MET cc_start: 0.9477 (mmm) cc_final: 0.9035 (mmm) REVERT: C 522 LYS cc_start: 0.9450 (tttt) cc_final: 0.9097 (mmtt) REVERT: C 541 ASP cc_start: 0.8769 (m-30) cc_final: 0.8306 (t0) REVERT: C 556 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7756 (mm) REVERT: D 42 GLN cc_start: 0.9502 (mt0) cc_final: 0.9073 (tm-30) REVERT: D 46 GLU cc_start: 0.9581 (mt-10) cc_final: 0.9183 (pp20) REVERT: E 80 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8288 (pp20) REVERT: E 81 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8518 (mmmm) REVERT: F 494 HIS cc_start: 0.7894 (OUTLIER) cc_final: 0.7525 (p-80) REVERT: F 741 PHE cc_start: 0.8625 (m-80) cc_final: 0.8334 (m-10) REVERT: G 20 GLU cc_start: 0.9505 (mt-10) cc_final: 0.9211 (mp0) REVERT: H 38 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: H 87 GLU cc_start: 0.9363 (tt0) cc_final: 0.9071 (tp30) REVERT: H 469 MET cc_start: 0.8950 (ttm) cc_final: 0.8725 (ttp) REVERT: I 283 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7894 (tmm) REVERT: I 322 MET cc_start: 0.8663 (tmm) cc_final: 0.8313 (ptm) REVERT: I 365 GLU cc_start: 0.9648 (mm-30) cc_final: 0.9346 (mp0) REVERT: I 450 GLU cc_start: 0.9525 (OUTLIER) cc_final: 0.9216 (pp20) REVERT: I 519 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6540 (mtp-110) REVERT: I 529 MET cc_start: 0.9157 (ttp) cc_final: 0.8725 (ptm) REVERT: I 548 MET cc_start: 0.8652 (mmp) cc_final: 0.8350 (tpt) REVERT: I 598 MET cc_start: 0.8531 (tmm) cc_final: 0.8272 (tmm) REVERT: I 705 MET cc_start: 0.8755 (mmm) cc_final: 0.8335 (mmm) REVERT: J 199 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9378 (mm-30) REVERT: J 202 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.9051 (ptp-110) REVERT: J 249 MET cc_start: 0.9355 (mmm) cc_final: 0.8783 (tpp) REVERT: J 372 LEU cc_start: 0.9144 (tp) cc_final: 0.8736 (tp) REVERT: J 395 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8731 (mt) REVERT: J 511 ASP cc_start: 0.9445 (t0) cc_final: 0.9167 (m-30) REVERT: K 232 ASP cc_start: 0.9346 (m-30) cc_final: 0.8919 (m-30) REVERT: K 283 GLU cc_start: 0.9481 (mm-30) cc_final: 0.9164 (mp0) REVERT: K 358 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8885 (m-80) REVERT: K 417 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8714 (pm20) REVERT: K 492 MET cc_start: 0.9152 (mtm) cc_final: 0.8877 (mtm) REVERT: L 102 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8401 (m-10) REVERT: M 22 ASP cc_start: 0.8886 (t0) cc_final: 0.8496 (t0) REVERT: M 51 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9039 (mttp) REVERT: M 54 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8690 (mm-30) REVERT: N 65 HIS cc_start: 0.9007 (OUTLIER) cc_final: 0.7808 (m90) REVERT: N 67 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8064 (pp) REVERT: N 253 LEU cc_start: 0.8831 (tt) cc_final: 0.8590 (tt) REVERT: N 518 GLU cc_start: 0.9588 (OUTLIER) cc_final: 0.9251 (tm-30) REVERT: N 531 PHE cc_start: 0.7989 (t80) cc_final: 0.7746 (t80) REVERT: N 555 HIS cc_start: 0.9003 (t-90) cc_final: 0.8619 (m-70) REVERT: N 646 MET cc_start: 0.8694 (mpp) cc_final: 0.8272 (mpp) REVERT: O 110 GLN cc_start: 0.8921 (tt0) cc_final: 0.8514 (tp40) REVERT: O 139 MET cc_start: 0.8955 (mmt) cc_final: 0.8645 (mmm) REVERT: O 150 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8771 (mt0) REVERT: O 352 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8809 (pt0) REVERT: O 406 ASP cc_start: 0.8261 (m-30) cc_final: 0.8051 (m-30) REVERT: O 505 GLN cc_start: 0.9056 (mt0) cc_final: 0.8613 (mp10) REVERT: O 508 MET cc_start: 0.9409 (mtp) cc_final: 0.9129 (mtp) REVERT: O 562 LYS cc_start: 0.9627 (mttt) cc_final: 0.9423 (mtmm) REVERT: O 593 ARG cc_start: 0.8834 (mtm180) cc_final: 0.8584 (mtp180) REVERT: O 618 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.8195 (t80) REVERT: O 664 MET cc_start: 0.9416 (mmm) cc_final: 0.9139 (mmm) REVERT: O 732 ARG cc_start: 0.7764 (mmt180) cc_final: 0.7234 (mmp-170) REVERT: P 149 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8800 (mp0) REVERT: W 10 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9194 (mm-30) REVERT: W 12 LYS cc_start: 0.7917 (mmmm) cc_final: 0.7541 (mtmm) REVERT: X 44 MET cc_start: 0.8516 (mmm) cc_final: 0.8096 (mmm) REVERT: X 174 MET cc_start: 0.9466 (tpp) cc_final: 0.9200 (tpp) REVERT: X 204 ASP cc_start: 0.9290 (OUTLIER) cc_final: 0.9053 (m-30) REVERT: X 282 PHE cc_start: 0.8966 (t80) cc_final: 0.8757 (t80) REVERT: X 417 TYR cc_start: 0.9183 (m-80) cc_final: 0.8920 (m-10) REVERT: X 447 LEU cc_start: 0.9238 (mp) cc_final: 0.9026 (tp) REVERT: X 458 GLN cc_start: 0.8849 (mt0) cc_final: 0.8490 (tp40) REVERT: Y 61 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8955 (pp) REVERT: Y 102 MET cc_start: 0.9185 (mpp) cc_final: 0.8977 (ptp) REVERT: Y 152 ASP cc_start: 0.9295 (OUTLIER) cc_final: 0.8945 (p0) REVERT: Y 173 MET cc_start: 0.9016 (ttp) cc_final: 0.8659 (tpp) REVERT: Y 243 TYR cc_start: 0.8675 (m-80) cc_final: 0.8060 (m-80) REVERT: Y 308 MET cc_start: 0.8987 (mmp) cc_final: 0.8770 (mmp) REVERT: Y 323 ASP cc_start: 0.8954 (t0) cc_final: 0.8630 (t0) REVERT: Y 429 MET cc_start: 0.8888 (mtm) cc_final: 0.8535 (ptp) REVERT: Y 515 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6941 (tt) outliers start: 382 outliers final: 261 residues processed: 950 average time/residue: 0.5802 time to fit residues: 961.7512 Evaluate side-chains 909 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 612 time to evaluate : 5.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 707 TRP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 988 CYS Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1359 ASN Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1591 HIS Chi-restraints excluded: chain A residue 1599 ASN Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1646 GLN Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1705 GLN Chi-restraints excluded: chain A residue 1778 CYS Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1818 LEU Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 489 SER Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain F residue 675 ILE Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 565 ASN Chi-restraints excluded: chain H residue 596 VAL Chi-restraints excluded: chain H residue 643 MET Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 288 THR Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 373 LYS Chi-restraints excluded: chain I residue 450 GLU Chi-restraints excluded: chain I residue 453 THR Chi-restraints excluded: chain I residue 519 ARG Chi-restraints excluded: chain I residue 717 MET Chi-restraints excluded: chain I residue 722 VAL Chi-restraints excluded: chain I residue 730 VAL Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 316 ASN Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 352 GLN Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 417 GLU Chi-restraints excluded: chain K residue 473 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 28 ASP Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 326 CYS Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 518 GLU Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 547 LEU Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 596 LEU Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 150 GLN Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 219 GLN Chi-restraints excluded: chain O residue 249 ASP Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 488 GLU Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 579 MET Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 594 SER Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 633 ILE Chi-restraints excluded: chain O residue 657 ILE Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 706 CYS Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 210 CYS Chi-restraints excluded: chain P residue 323 LEU Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 447 ASN Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 521 PHE Chi-restraints excluded: chain W residue 2 LEU Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 145 CYS Chi-restraints excluded: chain X residue 152 ASP Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 204 ASP Chi-restraints excluded: chain X residue 290 SER Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 388 ARG Chi-restraints excluded: chain X residue 443 THR Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain X residue 494 ASP Chi-restraints excluded: chain Y residue 40 HIS Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 94 ARG Chi-restraints excluded: chain Y residue 152 ASP Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 233 LEU Chi-restraints excluded: chain Y residue 269 ASP Chi-restraints excluded: chain Y residue 306 LYS Chi-restraints excluded: chain Y residue 345 SER Chi-restraints excluded: chain Y residue 417 TYR Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 515 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 472 optimal weight: 1.9990 chunk 305 optimal weight: 0.7980 chunk 456 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 chunk 485 optimal weight: 6.9990 chunk 520 optimal weight: 2.9990 chunk 377 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 600 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 HIS A1602 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 455 GLN ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 GLN I 523 HIS ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 HIS ** N 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 424 GLN ** P 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 64541 Z= 0.233 Angle : 0.735 19.217 87465 Z= 0.365 Chirality : 0.041 0.333 9859 Planarity : 0.004 0.060 11099 Dihedral : 7.113 152.993 8902 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.81 % Favored : 94.62 % Rotamer: Outliers : 4.90 % Allowed : 25.00 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.75 % Cis-general : 0.38 % Twisted Proline : 0.34 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.10), residues: 7920 helix: 1.43 (0.07), residues: 5470 sheet: -0.13 (0.25), residues: 433 loop : -1.72 (0.14), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP X 342 HIS 0.021 0.001 HIS A1591 PHE 0.027 0.002 PHE N 331 TYR 0.021 0.001 TYR A1891 ARG 0.007 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 661 time to evaluate : 5.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TYR cc_start: 0.9131 (t80) cc_final: 0.8761 (t80) REVERT: A 157 SER cc_start: 0.8692 (m) cc_final: 0.8347 (p) REVERT: A 191 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8461 (tmm-80) REVERT: A 218 ASP cc_start: 0.9278 (OUTLIER) cc_final: 0.9020 (m-30) REVERT: A 273 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7607 (mmm-85) REVERT: A 407 LEU cc_start: 0.7953 (tp) cc_final: 0.7701 (tp) REVERT: A 483 GLU cc_start: 0.9477 (mt-10) cc_final: 0.9122 (mp0) REVERT: A 511 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7803 (pp) REVERT: A 707 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7147 (t60) REVERT: A 831 MET cc_start: 0.8337 (mmp) cc_final: 0.8030 (mmp) REVERT: A 862 TYR cc_start: 0.5079 (OUTLIER) cc_final: 0.4225 (p90) REVERT: A 945 GLU cc_start: 0.8739 (tp30) cc_final: 0.8341 (mt-10) REVERT: A 957 ASP cc_start: 0.9138 (t0) cc_final: 0.8759 (t0) REVERT: A 972 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8467 (tp30) REVERT: A 1088 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8883 (p) REVERT: A 1107 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7394 (mt) REVERT: A 1203 MET cc_start: 0.5955 (mmp) cc_final: 0.5732 (mmt) REVERT: A 1354 GLU cc_start: 0.6485 (tt0) cc_final: 0.6169 (tm-30) REVERT: A 1456 THR cc_start: 0.9501 (OUTLIER) cc_final: 0.9229 (p) REVERT: A 1527 MET cc_start: 0.9547 (mmm) cc_final: 0.9149 (mmp) REVERT: A 1623 ASP cc_start: 0.9306 (t0) cc_final: 0.9017 (t0) REVERT: A 1705 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7450 (mp10) REVERT: A 1777 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8381 (tm-30) REVERT: A 1810 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8670 (mp0) REVERT: A 1926 ARG cc_start: 0.9376 (mpp-170) cc_final: 0.8897 (mtm110) REVERT: B 2 LYS cc_start: 0.8052 (tptt) cc_final: 0.7781 (tptp) REVERT: B 6 LYS cc_start: 0.8467 (ptmm) cc_final: 0.8199 (mtmt) REVERT: B 14 TRP cc_start: 0.7178 (OUTLIER) cc_final: 0.6274 (p-90) REVERT: B 27 ARG cc_start: 0.6262 (tpt170) cc_final: 0.5758 (tpm170) REVERT: C 119 MET cc_start: 0.9720 (tpt) cc_final: 0.9465 (mmm) REVERT: C 124 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9030 (mm) REVERT: C 218 MET cc_start: 0.9180 (mtm) cc_final: 0.8878 (mtm) REVERT: C 229 MET cc_start: 0.9422 (mmm) cc_final: 0.9051 (mmm) REVERT: C 417 TYR cc_start: 0.9082 (t80) cc_final: 0.8538 (t80) REVERT: C 541 ASP cc_start: 0.8735 (m-30) cc_final: 0.8233 (t0) REVERT: C 556 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7794 (mm) REVERT: D 42 GLN cc_start: 0.9478 (mt0) cc_final: 0.9031 (tm-30) REVERT: D 46 GLU cc_start: 0.9558 (mt-10) cc_final: 0.9141 (pp20) REVERT: E 80 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8222 (pp20) REVERT: E 81 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8526 (mmmm) REVERT: F 463 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7544 (tpp) REVERT: F 494 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7537 (p-80) REVERT: F 680 HIS cc_start: 0.8992 (OUTLIER) cc_final: 0.8730 (t70) REVERT: F 741 PHE cc_start: 0.8629 (m-80) cc_final: 0.8323 (m-10) REVERT: G 20 GLU cc_start: 0.9524 (mt-10) cc_final: 0.9231 (mp0) REVERT: H 38 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: H 87 GLU cc_start: 0.9362 (tt0) cc_final: 0.9099 (tp30) REVERT: I 192 MET cc_start: 0.9029 (mtp) cc_final: 0.8402 (mmm) REVERT: I 283 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7900 (tmm) REVERT: I 310 TRP cc_start: 0.3899 (OUTLIER) cc_final: 0.3497 (m100) REVERT: I 322 MET cc_start: 0.8651 (tmm) cc_final: 0.8410 (ptm) REVERT: I 450 GLU cc_start: 0.9531 (OUTLIER) cc_final: 0.9208 (pp20) REVERT: I 519 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6505 (mtp-110) REVERT: I 529 MET cc_start: 0.9107 (ttp) cc_final: 0.8764 (ptm) REVERT: I 548 MET cc_start: 0.8634 (mmp) cc_final: 0.8323 (tpt) REVERT: I 598 MET cc_start: 0.8626 (tmm) cc_final: 0.8412 (tmm) REVERT: I 705 MET cc_start: 0.8805 (mmm) cc_final: 0.8384 (mmm) REVERT: J 20 GLN cc_start: 0.9526 (OUTLIER) cc_final: 0.9232 (mp10) REVERT: J 199 GLU cc_start: 0.9633 (mt-10) cc_final: 0.9379 (mm-30) REVERT: J 202 ARG cc_start: 0.9311 (OUTLIER) cc_final: 0.9081 (ptp-110) REVERT: J 249 MET cc_start: 0.9348 (mmm) cc_final: 0.8756 (tpp) REVERT: J 395 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8721 (mt) REVERT: J 489 HIS cc_start: 0.8661 (OUTLIER) cc_final: 0.8434 (t-90) REVERT: J 511 ASP cc_start: 0.9470 (t0) cc_final: 0.9182 (m-30) REVERT: K 63 ARG cc_start: 0.9477 (OUTLIER) cc_final: 0.8883 (mpp80) REVERT: K 232 ASP cc_start: 0.9343 (m-30) cc_final: 0.8941 (m-30) REVERT: K 283 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9180 (mp0) REVERT: K 358 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.8538 (m-80) REVERT: K 417 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8694 (pm20) REVERT: K 492 MET cc_start: 0.9145 (mtm) cc_final: 0.8868 (mtm) REVERT: L 32 SER cc_start: 0.8457 (m) cc_final: 0.7991 (p) REVERT: L 67 GLN cc_start: 0.8533 (mt0) cc_final: 0.8250 (mp10) REVERT: L 102 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8392 (m-10) REVERT: M 4 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8163 (mt-10) REVERT: M 21 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8941 (mp0) REVERT: M 22 ASP cc_start: 0.8877 (t0) cc_final: 0.8451 (t0) REVERT: M 51 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9000 (mmmt) REVERT: M 54 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8446 (mm-30) REVERT: N 65 HIS cc_start: 0.8893 (OUTLIER) cc_final: 0.7765 (m90) REVERT: N 67 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8089 (pp) REVERT: N 253 LEU cc_start: 0.8813 (tt) cc_final: 0.8564 (tt) REVERT: N 518 GLU cc_start: 0.9589 (OUTLIER) cc_final: 0.9247 (tm-30) REVERT: N 531 PHE cc_start: 0.8018 (t80) cc_final: 0.7801 (t80) REVERT: N 555 HIS cc_start: 0.9000 (t-90) cc_final: 0.8676 (m-70) REVERT: N 646 MET cc_start: 0.8680 (mpp) cc_final: 0.8220 (mpp) REVERT: O 352 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8790 (pt0) REVERT: O 394 THR cc_start: 0.7392 (OUTLIER) cc_final: 0.6770 (p) REVERT: O 406 ASP cc_start: 0.8279 (m-30) cc_final: 0.8075 (m-30) REVERT: O 414 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.7969 (pp) REVERT: O 505 GLN cc_start: 0.8861 (mt0) cc_final: 0.8612 (mp10) REVERT: O 508 MET cc_start: 0.9425 (mtp) cc_final: 0.9107 (mtp) REVERT: O 562 LYS cc_start: 0.9599 (mttt) cc_final: 0.9394 (mtmm) REVERT: O 593 ARG cc_start: 0.8771 (mtm180) cc_final: 0.8481 (mtp180) REVERT: O 618 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.8230 (t80) REVERT: O 664 MET cc_start: 0.9347 (mmm) cc_final: 0.9099 (mmm) REVERT: P 149 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8810 (mp0) REVERT: W 10 GLU cc_start: 0.9371 (mm-30) cc_final: 0.8680 (mp0) REVERT: W 12 LYS cc_start: 0.8091 (mmmm) cc_final: 0.7754 (mtmm) REVERT: W 14 ASP cc_start: 0.9331 (OUTLIER) cc_final: 0.8852 (p0) REVERT: W 21 ASN cc_start: 0.7215 (m-40) cc_final: 0.7004 (m-40) REVERT: X 44 MET cc_start: 0.8527 (mmm) cc_final: 0.7947 (mmm) REVERT: X 174 MET cc_start: 0.9455 (tpp) cc_final: 0.9220 (tpp) REVERT: X 204 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8745 (m-30) REVERT: X 282 PHE cc_start: 0.8991 (t80) cc_final: 0.8787 (t80) REVERT: X 301 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7479 (t0) REVERT: X 360 TYR cc_start: 0.8709 (m-80) cc_final: 0.8414 (m-10) REVERT: X 417 TYR cc_start: 0.9197 (m-80) cc_final: 0.8907 (m-80) REVERT: X 447 LEU cc_start: 0.9193 (mp) cc_final: 0.8962 (tp) REVERT: X 458 GLN cc_start: 0.8829 (mt0) cc_final: 0.8468 (tp40) REVERT: Y 61 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8917 (pp) REVERT: Y 152 ASP cc_start: 0.9329 (OUTLIER) cc_final: 0.8910 (p0) REVERT: Y 173 MET cc_start: 0.9014 (ttp) cc_final: 0.8654 (tpp) REVERT: Y 243 TYR cc_start: 0.8647 (m-80) cc_final: 0.8000 (m-80) REVERT: Y 268 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7817 (ttm-80) REVERT: Y 308 MET cc_start: 0.8701 (mmp) cc_final: 0.8436 (mmp) REVERT: Y 323 ASP cc_start: 0.8966 (t0) cc_final: 0.8644 (t0) REVERT: Y 429 MET cc_start: 0.8880 (mtm) cc_final: 0.8480 (ptp) REVERT: Y 515 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6976 (tt) outliers start: 326 outliers final: 222 residues processed: 925 average time/residue: 0.5918 time to fit residues: 957.0440 Evaluate side-chains 900 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 633 time to evaluate : 5.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 TRP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 707 TRP Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 988 CYS Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1024 MET Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1244 ASP Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1359 ASN Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1591 HIS Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1705 GLN Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 1778 CYS Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 463 MET Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 489 SER Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 584 ASP Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain F residue 675 ILE Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 565 ASN Chi-restraints excluded: chain H residue 643 MET Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 310 TRP Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 373 LYS Chi-restraints excluded: chain I residue 450 GLU Chi-restraints excluded: chain I residue 453 THR Chi-restraints excluded: chain I residue 519 ARG Chi-restraints excluded: chain I residue 730 VAL Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 489 HIS Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 316 ASN Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 352 GLN Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 417 GLU Chi-restraints excluded: chain K residue 473 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain M residue 28 ASP Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 154 HIS Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 326 CYS Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 518 GLU Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 547 LEU Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 596 LEU Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 218 GLN Chi-restraints excluded: chain O residue 249 ASP Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 488 GLU Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 579 MET Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 594 SER Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 633 ILE Chi-restraints excluded: chain O residue 657 ILE Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 706 CYS Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 208 GLU Chi-restraints excluded: chain P residue 210 CYS Chi-restraints excluded: chain P residue 323 LEU Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 521 PHE Chi-restraints excluded: chain W residue 2 LEU Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 145 CYS Chi-restraints excluded: chain X residue 152 ASP Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 158 ILE Chi-restraints excluded: chain X residue 204 ASP Chi-restraints excluded: chain X residue 290 SER Chi-restraints excluded: chain X residue 301 ASP Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 443 THR Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain X residue 494 ASP Chi-restraints excluded: chain Y residue 40 HIS Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 94 ARG Chi-restraints excluded: chain Y residue 152 ASP Chi-restraints excluded: chain Y residue 269 ASP Chi-restraints excluded: chain Y residue 345 SER Chi-restraints excluded: chain Y residue 373 VAL Chi-restraints excluded: chain Y residue 417 TYR Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 515 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 695 optimal weight: 5.9990 chunk 732 optimal weight: 6.9990 chunk 668 optimal weight: 0.9980 chunk 712 optimal weight: 5.9990 chunk 428 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 559 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 643 optimal weight: 7.9990 chunk 673 optimal weight: 0.6980 chunk 709 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 ASN ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 HIS A1599 ASN ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 455 GLN ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 ASN ** K 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 HIS ** N 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 GLN O 461 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 289 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 64541 Z= 0.226 Angle : 0.736 18.423 87465 Z= 0.364 Chirality : 0.042 0.397 9859 Planarity : 0.004 0.075 11099 Dihedral : 6.994 154.652 8893 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.94 % Favored : 94.53 % Rotamer: Outliers : 4.93 % Allowed : 25.00 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.75 % Cis-general : 0.36 % Twisted Proline : 0.34 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.10), residues: 7920 helix: 1.41 (0.07), residues: 5472 sheet: -0.10 (0.25), residues: 433 loop : -1.74 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP X 342 HIS 0.027 0.001 HIS A1591 PHE 0.039 0.002 PHE K 164 TYR 0.023 0.001 TYR A1294 ARG 0.010 0.000 ARG Y 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 655 time to evaluate : 5.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TYR cc_start: 0.9126 (t80) cc_final: 0.8762 (t80) REVERT: A 157 SER cc_start: 0.8697 (m) cc_final: 0.8349 (p) REVERT: A 191 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8593 (tmm-80) REVERT: A 218 ASP cc_start: 0.9276 (OUTLIER) cc_final: 0.9013 (m-30) REVERT: A 273 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7613 (mmm-85) REVERT: A 407 LEU cc_start: 0.7966 (tp) cc_final: 0.7703 (tp) REVERT: A 483 GLU cc_start: 0.9510 (mt-10) cc_final: 0.9156 (mp0) REVERT: A 707 TRP cc_start: 0.8233 (OUTLIER) cc_final: 0.7145 (t60) REVERT: A 831 MET cc_start: 0.8468 (mmp) cc_final: 0.8141 (mmp) REVERT: A 862 TYR cc_start: 0.5048 (OUTLIER) cc_final: 0.4269 (p90) REVERT: A 945 GLU cc_start: 0.8777 (tp30) cc_final: 0.8394 (mt-10) REVERT: A 957 ASP cc_start: 0.9116 (t0) cc_final: 0.8734 (t0) REVERT: A 972 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8519 (tp30) REVERT: A 1088 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8864 (p) REVERT: A 1107 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7370 (mt) REVERT: A 1203 MET cc_start: 0.5942 (mmp) cc_final: 0.5708 (mmt) REVERT: A 1276 GLU cc_start: 0.8281 (tp30) cc_final: 0.7720 (tp30) REVERT: A 1354 GLU cc_start: 0.6522 (tt0) cc_final: 0.6207 (tm-30) REVERT: A 1456 THR cc_start: 0.9505 (OUTLIER) cc_final: 0.9237 (p) REVERT: A 1513 GLU cc_start: 0.9448 (OUTLIER) cc_final: 0.9240 (tp30) REVERT: A 1527 MET cc_start: 0.9545 (mmm) cc_final: 0.9133 (mmp) REVERT: A 1623 ASP cc_start: 0.9308 (t0) cc_final: 0.9015 (t0) REVERT: A 1705 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: A 1777 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8370 (tm-30) REVERT: A 1810 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8678 (mp0) REVERT: A 1926 ARG cc_start: 0.9378 (OUTLIER) cc_final: 0.8888 (mtm110) REVERT: B 2 LYS cc_start: 0.8153 (tptt) cc_final: 0.7892 (tptp) REVERT: B 6 LYS cc_start: 0.8478 (ptmm) cc_final: 0.8203 (mtmt) REVERT: B 14 TRP cc_start: 0.7171 (OUTLIER) cc_final: 0.6270 (p-90) REVERT: C 119 MET cc_start: 0.9720 (OUTLIER) cc_final: 0.9465 (mmm) REVERT: C 124 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9153 (mm) REVERT: C 133 GLU cc_start: 0.9157 (tp30) cc_final: 0.8931 (mm-30) REVERT: C 218 MET cc_start: 0.9172 (mtm) cc_final: 0.8785 (mtm) REVERT: C 229 MET cc_start: 0.9438 (mmm) cc_final: 0.9027 (mmm) REVERT: C 417 TYR cc_start: 0.9088 (t80) cc_final: 0.8735 (t80) REVERT: C 522 LYS cc_start: 0.9448 (tppt) cc_final: 0.9123 (mmtt) REVERT: C 541 ASP cc_start: 0.8774 (m-30) cc_final: 0.8288 (t0) REVERT: D 42 GLN cc_start: 0.9472 (mt0) cc_final: 0.9030 (tm-30) REVERT: D 46 GLU cc_start: 0.9550 (mt-10) cc_final: 0.9154 (pp20) REVERT: E 80 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8211 (pp20) REVERT: E 81 LYS cc_start: 0.8826 (mmmm) cc_final: 0.8513 (mmmm) REVERT: F 463 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7477 (tpp) REVERT: F 494 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7624 (p-80) REVERT: F 680 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8761 (t70) REVERT: F 741 PHE cc_start: 0.8636 (m-80) cc_final: 0.8331 (m-10) REVERT: G 20 GLU cc_start: 0.9516 (mt-10) cc_final: 0.9236 (mp0) REVERT: H 38 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: H 87 GLU cc_start: 0.9356 (tt0) cc_final: 0.9088 (tp30) REVERT: I 121 GLU cc_start: 0.8786 (mp0) cc_final: 0.8525 (mm-30) REVERT: I 192 MET cc_start: 0.9046 (mtp) cc_final: 0.8422 (mmm) REVERT: I 283 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7877 (tmm) REVERT: I 310 TRP cc_start: 0.3881 (OUTLIER) cc_final: 0.3421 (m100) REVERT: I 365 GLU cc_start: 0.9625 (mm-30) cc_final: 0.9359 (mp0) REVERT: I 450 GLU cc_start: 0.9530 (OUTLIER) cc_final: 0.9187 (pp20) REVERT: I 454 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: I 519 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6448 (mtp-110) REVERT: I 529 MET cc_start: 0.9085 (ttp) cc_final: 0.8738 (ptm) REVERT: I 548 MET cc_start: 0.8619 (mmp) cc_final: 0.8280 (tpt) REVERT: I 705 MET cc_start: 0.8802 (mmm) cc_final: 0.8379 (mmm) REVERT: J 20 GLN cc_start: 0.9524 (OUTLIER) cc_final: 0.9245 (mp10) REVERT: J 199 GLU cc_start: 0.9628 (mt-10) cc_final: 0.9376 (mm-30) REVERT: J 202 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.9073 (ptp-110) REVERT: J 249 MET cc_start: 0.9349 (mmm) cc_final: 0.8755 (tpp) REVERT: J 330 GLU cc_start: 0.9499 (tm-30) cc_final: 0.8936 (tm-30) REVERT: J 395 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8757 (mt) REVERT: J 489 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.8471 (t-90) REVERT: J 511 ASP cc_start: 0.9465 (t0) cc_final: 0.9181 (m-30) REVERT: K 63 ARG cc_start: 0.9488 (OUTLIER) cc_final: 0.8917 (mpp80) REVERT: K 232 ASP cc_start: 0.9343 (m-30) cc_final: 0.8934 (m-30) REVERT: K 283 GLU cc_start: 0.9480 (mm-30) cc_final: 0.9184 (mp0) REVERT: K 417 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8699 (pm20) REVERT: K 492 MET cc_start: 0.9152 (mtm) cc_final: 0.8860 (mtm) REVERT: L 32 SER cc_start: 0.8457 (m) cc_final: 0.7953 (p) REVERT: L 67 GLN cc_start: 0.8468 (mt0) cc_final: 0.8203 (mp10) REVERT: L 102 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8449 (m-10) REVERT: M 1 MET cc_start: 0.8076 (tpt) cc_final: 0.7874 (tpp) REVERT: M 21 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8881 (mp0) REVERT: M 22 ASP cc_start: 0.8885 (t0) cc_final: 0.8442 (t0) REVERT: M 51 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8978 (mmmt) REVERT: M 54 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8629 (mm-30) REVERT: N 65 HIS cc_start: 0.8818 (OUTLIER) cc_final: 0.7674 (m90) REVERT: N 67 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8170 (pp) REVERT: N 185 MET cc_start: 0.8117 (mmp) cc_final: 0.7873 (tpt) REVERT: N 253 LEU cc_start: 0.8812 (tt) cc_final: 0.8563 (tt) REVERT: N 518 GLU cc_start: 0.9599 (OUTLIER) cc_final: 0.9274 (tm-30) REVERT: N 531 PHE cc_start: 0.7885 (t80) cc_final: 0.7683 (t80) REVERT: N 555 HIS cc_start: 0.8949 (t-90) cc_final: 0.8642 (m-70) REVERT: N 646 MET cc_start: 0.8679 (mpp) cc_final: 0.8225 (mpp) REVERT: O 139 MET cc_start: 0.8896 (mmt) cc_final: 0.8678 (mmm) REVERT: O 352 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8787 (pt0) REVERT: O 394 THR cc_start: 0.7206 (OUTLIER) cc_final: 0.6613 (p) REVERT: O 406 ASP cc_start: 0.8269 (m-30) cc_final: 0.8062 (m-30) REVERT: O 505 GLN cc_start: 0.8859 (mt0) cc_final: 0.8631 (mp10) REVERT: O 508 MET cc_start: 0.9430 (mtp) cc_final: 0.9112 (mtp) REVERT: O 562 LYS cc_start: 0.9606 (mttt) cc_final: 0.9402 (mtmm) REVERT: O 593 ARG cc_start: 0.8758 (mtm180) cc_final: 0.8436 (mtp180) REVERT: O 618 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.8221 (t80) REVERT: P 149 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8834 (mp0) REVERT: P 300 MET cc_start: 0.9123 (mmp) cc_final: 0.8863 (mmt) REVERT: W 10 GLU cc_start: 0.9385 (mm-30) cc_final: 0.8817 (mp0) REVERT: W 12 LYS cc_start: 0.8207 (mmmm) cc_final: 0.7859 (mtmm) REVERT: W 14 ASP cc_start: 0.9315 (OUTLIER) cc_final: 0.8823 (p0) REVERT: X 174 MET cc_start: 0.9446 (tpp) cc_final: 0.9226 (tpp) REVERT: X 204 ASP cc_start: 0.9217 (OUTLIER) cc_final: 0.8999 (m-30) REVERT: X 301 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7487 (t0) REVERT: X 360 TYR cc_start: 0.8720 (m-80) cc_final: 0.8497 (m-10) REVERT: X 417 TYR cc_start: 0.8975 (m-80) cc_final: 0.8768 (m-80) REVERT: X 447 LEU cc_start: 0.9182 (mp) cc_final: 0.8954 (tp) REVERT: X 458 GLN cc_start: 0.8773 (mt0) cc_final: 0.8400 (tp40) REVERT: Y 61 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8913 (pp) REVERT: Y 152 ASP cc_start: 0.9349 (OUTLIER) cc_final: 0.8955 (p0) REVERT: Y 173 MET cc_start: 0.9016 (ttp) cc_final: 0.8661 (tpp) REVERT: Y 243 TYR cc_start: 0.8693 (m-80) cc_final: 0.7979 (m-80) REVERT: Y 268 ARG cc_start: 0.8101 (ttm170) cc_final: 0.7809 (ttm-80) REVERT: Y 308 MET cc_start: 0.8924 (mmp) cc_final: 0.8650 (mmp) REVERT: Y 323 ASP cc_start: 0.8967 (t0) cc_final: 0.8638 (t0) REVERT: Y 429 MET cc_start: 0.8831 (mtm) cc_final: 0.8321 (ptt) REVERT: Y 515 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7119 (tt) outliers start: 328 outliers final: 238 residues processed: 916 average time/residue: 0.5792 time to fit residues: 926.3594 Evaluate side-chains 916 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 633 time to evaluate : 5.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 TRP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 707 TRP Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 988 CYS Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1244 ASP Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1359 ASN Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1513 GLU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1591 HIS Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1705 GLN Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 1778 CYS Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1887 CYS Chi-restraints excluded: chain A residue 1926 ARG Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 463 MET Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 489 SER Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 584 ASP Chi-restraints excluded: chain F residue 675 ILE Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 565 ASN Chi-restraints excluded: chain H residue 596 VAL Chi-restraints excluded: chain H residue 643 MET Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 310 TRP Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 373 LYS Chi-restraints excluded: chain I residue 450 GLU Chi-restraints excluded: chain I residue 453 THR Chi-restraints excluded: chain I residue 454 GLU Chi-restraints excluded: chain I residue 455 HIS Chi-restraints excluded: chain I residue 519 ARG Chi-restraints excluded: chain I residue 717 MET Chi-restraints excluded: chain I residue 730 VAL Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 489 HIS Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 316 ASN Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 352 GLN Chi-restraints excluded: chain K residue 417 GLU Chi-restraints excluded: chain K residue 473 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain M residue 28 ASP Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 326 CYS Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 518 GLU Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 547 LEU Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 596 LEU Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 150 GLN Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 249 ASP Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 488 GLU Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 579 MET Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 594 SER Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 633 ILE Chi-restraints excluded: chain O residue 657 ILE Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 706 CYS Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 208 GLU Chi-restraints excluded: chain P residue 210 CYS Chi-restraints excluded: chain P residue 323 LEU Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 418 CYS Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 521 PHE Chi-restraints excluded: chain W residue 2 LEU Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 145 CYS Chi-restraints excluded: chain X residue 152 ASP Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 158 ILE Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 204 ASP Chi-restraints excluded: chain X residue 238 VAL Chi-restraints excluded: chain X residue 290 SER Chi-restraints excluded: chain X residue 301 ASP Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 388 ARG Chi-restraints excluded: chain X residue 443 THR Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain X residue 494 ASP Chi-restraints excluded: chain Y residue 40 HIS Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 94 ARG Chi-restraints excluded: chain Y residue 152 ASP Chi-restraints excluded: chain Y residue 269 ASP Chi-restraints excluded: chain Y residue 345 SER Chi-restraints excluded: chain Y residue 373 VAL Chi-restraints excluded: chain Y residue 417 TYR Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 467 optimal weight: 0.9980 chunk 753 optimal weight: 5.9990 chunk 459 optimal weight: 10.0000 chunk 357 optimal weight: 0.6980 chunk 523 optimal weight: 9.9990 chunk 790 optimal weight: 8.9990 chunk 727 optimal weight: 4.9990 chunk 629 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 485 optimal weight: 6.9990 chunk 385 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 HIS ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 455 GLN ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 HIS ** N 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 GLN O 552 GLN ** O 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 21 ASN ** Y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 64541 Z= 0.255 Angle : 0.748 18.114 87465 Z= 0.370 Chirality : 0.042 0.357 9859 Planarity : 0.004 0.076 11099 Dihedral : 6.951 156.050 8892 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.86 % Favored : 94.62 % Rotamer: Outliers : 4.68 % Allowed : 25.44 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.75 % Cis-general : 0.36 % Twisted Proline : 0.34 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.10), residues: 7920 helix: 1.40 (0.07), residues: 5473 sheet: -0.08 (0.25), residues: 432 loop : -1.74 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP X 342 HIS 0.024 0.001 HIS A1591 PHE 0.031 0.002 PHE Y 282 TYR 0.018 0.001 TYR C 417 ARG 0.009 0.000 ARG P 458 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15840 Ramachandran restraints generated. 7920 Oldfield, 0 Emsley, 7920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 638 time to evaluate : 5.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TYR cc_start: 0.9128 (t80) cc_final: 0.8758 (t80) REVERT: A 157 SER cc_start: 0.8775 (m) cc_final: 0.8435 (p) REVERT: A 218 ASP cc_start: 0.9281 (OUTLIER) cc_final: 0.9012 (m-30) REVERT: A 273 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7910 (mmm-85) REVERT: A 407 LEU cc_start: 0.7958 (tp) cc_final: 0.7681 (tp) REVERT: A 483 GLU cc_start: 0.9512 (mt-10) cc_final: 0.9202 (mp0) REVERT: A 707 TRP cc_start: 0.8239 (OUTLIER) cc_final: 0.7144 (t60) REVERT: A 831 MET cc_start: 0.8389 (mmp) cc_final: 0.8076 (mmp) REVERT: A 862 TYR cc_start: 0.5109 (OUTLIER) cc_final: 0.4110 (p90) REVERT: A 945 GLU cc_start: 0.8781 (tp30) cc_final: 0.8403 (mt-10) REVERT: A 957 ASP cc_start: 0.9138 (t0) cc_final: 0.8750 (t0) REVERT: A 972 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8566 (tp30) REVERT: A 1088 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8874 (p) REVERT: A 1107 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7342 (mt) REVERT: A 1203 MET cc_start: 0.5926 (mmp) cc_final: 0.5689 (mmt) REVERT: A 1276 GLU cc_start: 0.8149 (tp30) cc_final: 0.7839 (tp30) REVERT: A 1354 GLU cc_start: 0.6524 (tt0) cc_final: 0.6217 (tm-30) REVERT: A 1456 THR cc_start: 0.9507 (OUTLIER) cc_final: 0.9240 (p) REVERT: A 1527 MET cc_start: 0.9545 (mmm) cc_final: 0.9146 (mmp) REVERT: A 1623 ASP cc_start: 0.9326 (t0) cc_final: 0.9027 (t0) REVERT: A 1624 VAL cc_start: 0.9541 (OUTLIER) cc_final: 0.9338 (t) REVERT: A 1705 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7409 (mp10) REVERT: A 1777 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8329 (tm-30) REVERT: A 1810 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8696 (mp0) REVERT: A 1840 MET cc_start: 0.9428 (mtt) cc_final: 0.9146 (ttm) REVERT: A 1926 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.8839 (ttp80) REVERT: B 2 LYS cc_start: 0.8184 (tptt) cc_final: 0.7911 (tptp) REVERT: B 6 LYS cc_start: 0.8569 (ptmm) cc_final: 0.8361 (mtmt) REVERT: B 14 TRP cc_start: 0.7127 (OUTLIER) cc_final: 0.6235 (p-90) REVERT: B 27 ARG cc_start: 0.6193 (tpt170) cc_final: 0.5747 (tpm170) REVERT: C 119 MET cc_start: 0.9718 (OUTLIER) cc_final: 0.9464 (mmm) REVERT: C 124 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9134 (mm) REVERT: C 133 GLU cc_start: 0.9155 (tp30) cc_final: 0.8936 (mm-30) REVERT: C 218 MET cc_start: 0.9220 (mtm) cc_final: 0.8820 (mtm) REVERT: C 229 MET cc_start: 0.9499 (mmm) cc_final: 0.9132 (mmm) REVERT: C 417 TYR cc_start: 0.9123 (t80) cc_final: 0.8811 (t80) REVERT: C 522 LYS cc_start: 0.9449 (tppt) cc_final: 0.9109 (mmtt) REVERT: C 541 ASP cc_start: 0.8741 (m-30) cc_final: 0.8266 (t0) REVERT: D 42 GLN cc_start: 0.9477 (mt0) cc_final: 0.9048 (tm-30) REVERT: D 46 GLU cc_start: 0.9521 (mt-10) cc_final: 0.9089 (pp20) REVERT: E 80 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8231 (pp20) REVERT: E 81 LYS cc_start: 0.8811 (mmmm) cc_final: 0.8489 (mmmm) REVERT: F 463 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7477 (tpp) REVERT: F 494 HIS cc_start: 0.7963 (OUTLIER) cc_final: 0.7607 (p-80) REVERT: F 600 TYR cc_start: 0.7691 (t80) cc_final: 0.7480 (t80) REVERT: F 741 PHE cc_start: 0.8649 (m-80) cc_final: 0.8349 (m-10) REVERT: G 20 GLU cc_start: 0.9557 (mt-10) cc_final: 0.9293 (mp0) REVERT: H 38 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: H 87 GLU cc_start: 0.9353 (tt0) cc_final: 0.9124 (tp30) REVERT: H 536 MET cc_start: 0.6489 (mmp) cc_final: 0.6254 (mmp) REVERT: I 121 GLU cc_start: 0.8783 (mp0) cc_final: 0.8510 (mm-30) REVERT: I 192 MET cc_start: 0.9059 (mtp) cc_final: 0.8424 (mmm) REVERT: I 283 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7916 (tmm) REVERT: I 310 TRP cc_start: 0.3888 (OUTLIER) cc_final: 0.3397 (m100) REVERT: I 365 GLU cc_start: 0.9629 (mm-30) cc_final: 0.9339 (mp0) REVERT: I 450 GLU cc_start: 0.9544 (OUTLIER) cc_final: 0.9231 (pp20) REVERT: I 519 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6523 (mtp-110) REVERT: I 529 MET cc_start: 0.9081 (ttp) cc_final: 0.8834 (ptm) REVERT: I 548 MET cc_start: 0.8659 (mmp) cc_final: 0.8311 (tpt) REVERT: I 705 MET cc_start: 0.8739 (mmm) cc_final: 0.8293 (mmm) REVERT: J 20 GLN cc_start: 0.9528 (OUTLIER) cc_final: 0.9253 (mp10) REVERT: J 199 GLU cc_start: 0.9650 (mt-10) cc_final: 0.9355 (mm-30) REVERT: J 202 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.9115 (ptp-110) REVERT: J 249 MET cc_start: 0.9359 (mmm) cc_final: 0.8758 (tpp) REVERT: J 330 GLU cc_start: 0.9500 (tm-30) cc_final: 0.8935 (tm-30) REVERT: J 395 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8772 (mt) REVERT: J 489 HIS cc_start: 0.8708 (OUTLIER) cc_final: 0.8437 (t-90) REVERT: J 511 ASP cc_start: 0.9462 (t0) cc_final: 0.9180 (m-30) REVERT: K 63 ARG cc_start: 0.9442 (OUTLIER) cc_final: 0.8885 (mpp80) REVERT: K 232 ASP cc_start: 0.9348 (m-30) cc_final: 0.8944 (m-30) REVERT: K 283 GLU cc_start: 0.9481 (mm-30) cc_final: 0.9184 (mp0) REVERT: K 417 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8702 (pm20) REVERT: K 492 MET cc_start: 0.9155 (mtm) cc_final: 0.8865 (mtm) REVERT: L 17 GLU cc_start: 0.8359 (pt0) cc_final: 0.7998 (mm-30) REVERT: L 32 SER cc_start: 0.8465 (m) cc_final: 0.7988 (p) REVERT: L 67 GLN cc_start: 0.8487 (mt0) cc_final: 0.8220 (mp10) REVERT: L 102 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8497 (m-10) REVERT: M 4 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8698 (tm-30) REVERT: M 21 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8941 (mm-30) REVERT: M 22 ASP cc_start: 0.8927 (t0) cc_final: 0.8487 (t0) REVERT: M 51 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8967 (mmmt) REVERT: M 54 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8640 (mm-30) REVERT: N 65 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.7710 (m90) REVERT: N 67 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8174 (pp) REVERT: N 154 HIS cc_start: 0.8788 (OUTLIER) cc_final: 0.8580 (m90) REVERT: N 185 MET cc_start: 0.8106 (mmp) cc_final: 0.7855 (tpt) REVERT: N 253 LEU cc_start: 0.8808 (tt) cc_final: 0.8560 (tt) REVERT: N 518 GLU cc_start: 0.9602 (OUTLIER) cc_final: 0.9271 (tm-30) REVERT: N 555 HIS cc_start: 0.8936 (t-90) cc_final: 0.8663 (m-70) REVERT: N 646 MET cc_start: 0.8677 (mpp) cc_final: 0.8374 (mpp) REVERT: O 100 MET cc_start: 0.9075 (ttp) cc_final: 0.8683 (tpp) REVERT: O 139 MET cc_start: 0.8912 (mmt) cc_final: 0.8679 (mmm) REVERT: O 352 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8794 (pt0) REVERT: O 406 ASP cc_start: 0.8252 (m-30) cc_final: 0.8039 (m-30) REVERT: O 505 GLN cc_start: 0.8874 (mt0) cc_final: 0.8639 (mp10) REVERT: O 508 MET cc_start: 0.9432 (mtp) cc_final: 0.9109 (mtp) REVERT: O 562 LYS cc_start: 0.9629 (mttt) cc_final: 0.9415 (mtmm) REVERT: O 618 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.8239 (t80) REVERT: O 685 GLU cc_start: 0.9438 (OUTLIER) cc_final: 0.9173 (pt0) REVERT: P 149 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8801 (mp0) REVERT: P 300 MET cc_start: 0.9136 (mmp) cc_final: 0.8881 (mmt) REVERT: P 378 MET cc_start: 0.8515 (ttm) cc_final: 0.8306 (ttm) REVERT: W 10 GLU cc_start: 0.9375 (mm-30) cc_final: 0.9073 (mm-30) REVERT: W 12 LYS cc_start: 0.8358 (mmmm) cc_final: 0.8128 (mtmm) REVERT: X 44 MET cc_start: 0.8360 (mmm) cc_final: 0.8096 (mmm) REVERT: X 174 MET cc_start: 0.9419 (tpp) cc_final: 0.9110 (tpp) REVERT: X 204 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.9037 (m-30) REVERT: X 308 MET cc_start: 0.7897 (mtt) cc_final: 0.7463 (mmt) REVERT: X 417 TYR cc_start: 0.8993 (m-80) cc_final: 0.8773 (m-80) REVERT: X 429 MET cc_start: 0.8896 (tpp) cc_final: 0.8474 (tpp) REVERT: X 447 LEU cc_start: 0.9177 (mp) cc_final: 0.8957 (tp) REVERT: X 458 GLN cc_start: 0.8760 (mt0) cc_final: 0.8393 (tp40) REVERT: Y 61 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8927 (pp) REVERT: Y 104 LEU cc_start: 0.9424 (pt) cc_final: 0.9129 (tp) REVERT: Y 152 ASP cc_start: 0.9351 (OUTLIER) cc_final: 0.9003 (p0) REVERT: Y 173 MET cc_start: 0.9028 (ttp) cc_final: 0.8701 (tpp) REVERT: Y 243 TYR cc_start: 0.8686 (m-80) cc_final: 0.7978 (m-80) REVERT: Y 268 ARG cc_start: 0.8158 (ttm170) cc_final: 0.7864 (ttm-80) REVERT: Y 308 MET cc_start: 0.8940 (mmp) cc_final: 0.8688 (mmp) REVERT: Y 323 ASP cc_start: 0.8970 (t0) cc_final: 0.8643 (t0) REVERT: Y 429 MET cc_start: 0.8832 (mtm) cc_final: 0.8337 (ptt) REVERT: Y 515 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7078 (tt) outliers start: 311 outliers final: 238 residues processed: 883 average time/residue: 0.5597 time to fit residues: 864.1774 Evaluate side-chains 901 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 622 time to evaluate : 5.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 TRP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 707 TRP Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 988 CYS Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1244 ASP Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1359 ASN Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1591 HIS Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1705 GLN Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 1778 CYS Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1887 CYS Chi-restraints excluded: chain A residue 1926 ARG Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 463 MET Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 489 SER Chi-restraints excluded: chain F residue 494 HIS Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 584 ASP Chi-restraints excluded: chain F residue 675 ILE Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 565 ASN Chi-restraints excluded: chain H residue 596 VAL Chi-restraints excluded: chain H residue 643 MET Chi-restraints excluded: chain H residue 729 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 310 TRP Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain I residue 341 TYR Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 373 LYS Chi-restraints excluded: chain I residue 450 GLU Chi-restraints excluded: chain I residue 453 THR Chi-restraints excluded: chain I residue 455 HIS Chi-restraints excluded: chain I residue 519 ARG Chi-restraints excluded: chain I residue 717 MET Chi-restraints excluded: chain I residue 730 VAL Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 489 HIS Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 316 ASN Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 352 GLN Chi-restraints excluded: chain K residue 417 GLU Chi-restraints excluded: chain K residue 473 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 28 ASP Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 154 HIS Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 326 CYS Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 518 GLU Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 547 LEU Chi-restraints excluded: chain N residue 596 LEU Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 150 GLN Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 219 GLN Chi-restraints excluded: chain O residue 249 ASP Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 488 GLU Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 579 MET Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 594 SER Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 633 ILE Chi-restraints excluded: chain O residue 657 ILE Chi-restraints excluded: chain O residue 685 GLU Chi-restraints excluded: chain O residue 706 CYS Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 208 GLU Chi-restraints excluded: chain P residue 210 CYS Chi-restraints excluded: chain P residue 323 LEU Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 418 CYS Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 521 PHE Chi-restraints excluded: chain W residue 2 LEU Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 145 CYS Chi-restraints excluded: chain X residue 152 ASP Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 158 ILE Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 204 ASP Chi-restraints excluded: chain X residue 238 VAL Chi-restraints excluded: chain X residue 290 SER Chi-restraints excluded: chain X residue 383 LEU Chi-restraints excluded: chain X residue 388 ARG Chi-restraints excluded: chain X residue 443 THR Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain X residue 494 ASP Chi-restraints excluded: chain Y residue 40 HIS Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 152 ASP Chi-restraints excluded: chain Y residue 269 ASP Chi-restraints excluded: chain Y residue 345 SER Chi-restraints excluded: chain Y residue 373 VAL Chi-restraints excluded: chain Y residue 417 TYR Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 499 optimal weight: 8.9990 chunk 670 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 chunk 580 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 630 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 647 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 455 GLN ** H 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.081243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.061261 restraints weight = 269967.255| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 4.16 r_work: 0.3096 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 64541 Z= 0.281 Angle : 0.819 59.164 87465 Z= 0.431 Chirality : 0.042 0.687 9859 Planarity : 0.005 0.220 11099 Dihedral : 6.827 156.081 8881 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.90 % Favored : 94.60 % Rotamer: Outliers : 4.45 % Allowed : 25.53 % Favored : 70.02 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.75 % Cis-general : 0.36 % Twisted Proline : 0.34 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.10), residues: 7920 helix: 1.40 (0.07), residues: 5473 sheet: -0.08 (0.25), residues: 432 loop : -1.74 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP X 342 HIS 0.380 0.002 HIS N 154 PHE 0.051 0.002 PHE B 30 TYR 0.059 0.001 TYR X 360 ARG 0.008 0.000 ARG O 593 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19062.68 seconds wall clock time: 334 minutes 12.74 seconds (20052.74 seconds total)