Starting phenix.real_space_refine (version: dev) on Mon Dec 19 00:21:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g05_3388/12_2022/5g05_3388.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g05_3388/12_2022/5g05_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_3388/12_2022/5g05_3388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g05_3388/12_2022/5g05_3388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g05_3388/12_2022/5g05_3388.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g05_3388/12_2022/5g05_3388.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 25.81, per 1000 atoms: 0.41 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: 20.15 Conformation dependent library (CDL) restraints added in 6.9 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: 2.55 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: 22.01 Time building geometry restraints manager: 22.04 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 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. 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: 0.850 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: 0.030 Extract box with map and model: 8.820 Check model and map are aligned: 0.710 Convert atoms to be neutral: 0.400 Process input model: 134.120 Find NCS groups from input model: 2.950 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 1.813 31.876 87465 Z= 1.169 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 : 56.80 Ramachandran Plot: Outliers : 1.83 % Allowed : 4.54 % Favored : 93.63 % Rotamer Outliers : 17.76 % 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 *********************** 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 : 5.665 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 outliers start: 1181 outliers final: 386 residues processed: 2303 average time/residue: 0.6200 time to fit residues: 2356.7376 Evaluate side-chains 1190 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 804 time to evaluate : 5.716 Switching outliers to nearest non-outliers 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 outliers start: 386 outliers final: 14 residues processed: 386 average time/residue: 0.5109 time to fit residues: 360.6481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 669 optimal weight: 1.9990 chunk 601 optimal weight: 1.9990 chunk 333 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 405 optimal weight: 1.9990 chunk 321 optimal weight: 6.9990 chunk 621 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 377 optimal weight: 10.0000 chunk 462 optimal weight: 5.9990 chunk 720 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 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 ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 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 ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1595 HIS ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1627 ASN A1705 GLN A1727 ASN A1861 GLN ** A1899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 ASN B 53 HIS 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 488 GLN C 518 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 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 ASN F 667 GLN F 702 ASN H 90 GLN H 103 HIS H 545 HIS H 634 HIS H 648 GLN ** H 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 345 GLN I 362 HIS I 523 HIS J 16 GLN J 38 GLN J 54 HIS J 87 GLN ** 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 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 503 HIS K 45 GLN K 58 HIS K 207 ASN K 271 HIS L 28 GLN ** L 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 GLN ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 34 ASN N 65 HIS 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 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 671 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 424 GLN O 449 ASN O 462 ASN O 565 GLN ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 247 HIS X 298 GLN X 337 GLN X 338 HIS X 490 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: 104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 64541 Z= 0.332 Angle : 0.972 28.308 87465 Z= 0.488 Chirality : 0.050 0.416 9859 Planarity : 0.006 0.158 11099 Dihedral : 5.562 48.497 8712 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.77 % Allowed : 4.08 % Favored : 95.15 % Rotamer Outliers : 5.83 % 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: 1.23 (0.07), residues: 5385 sheet: 0.04 (0.25), residues: 416 loop : -1.93 (0.13), residues: 2119 *********************** 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 1352 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 964 time to evaluate : 5.752 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 outliers start: 388 outliers final: 121 residues processed: 1272 average time/residue: 0.5697 time to fit residues: 1250.0936 Evaluate side-chains 800 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 679 time to evaluate : 5.740 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 121 outliers final: 1 residues processed: 121 average time/residue: 0.4696 time to fit residues: 114.3564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 400 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 599 optimal weight: 2.9990 chunk 490 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 721 optimal weight: 9.9990 chunk 779 optimal weight: 3.9990 chunk 642 optimal weight: 9.9990 chunk 715 optimal weight: 9.9990 chunk 245 optimal weight: 0.9990 chunk 578 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 242 HIS ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 HIS C 552 GLN ** 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 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 ASN F 636 ASN F 667 GLN F 679 GLN H 517 GLN ** H 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS J 173 HIS J 271 HIS J 279 ASN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN K 264 HIS K 521 HIS L 103 HIS ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN N 154 HIS ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 555 HIS ** N 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 663 GLN ** 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 461 ASN O 552 GLN O 565 GLN O 680 GLN ** O 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 722 HIS X 40 HIS X 66 ASN X 151 GLN ** X 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 289 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 64541 Z= 0.380 Angle : 0.856 29.265 87465 Z= 0.430 Chirality : 0.046 0.301 9859 Planarity : 0.005 0.113 11099 Dihedral : 5.315 59.321 8712 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.71 % Favored : 94.65 % Rotamer Outliers : 4.19 % 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: 0.58 (0.09), residues: 7920 helix: 1.25 (0.07), residues: 5436 sheet: -0.21 (0.24), residues: 427 loop : -1.81 (0.13), residues: 2057 *********************** 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 1027 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 748 time to evaluate : 5.627 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 outliers start: 279 outliers final: 120 residues processed: 973 average time/residue: 0.5475 time to fit residues: 928.0563 Evaluate side-chains 762 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 642 time to evaluate : 5.736 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 0 residues processed: 120 average time/residue: 0.4631 time to fit residues: 110.4358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 712 optimal weight: 3.9990 chunk 542 optimal weight: 9.9990 chunk 374 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 344 optimal weight: 1.9990 chunk 484 optimal weight: 6.9990 chunk 724 optimal weight: 0.7980 chunk 766 optimal weight: 6.9990 chunk 378 optimal weight: 9.9990 chunk 686 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 HIS ** A1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1599 ASN ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 HIS ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN ** 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 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 667 GLN H 495 HIS H 657 HIS ** H 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 257 HIS I 401 ASN I 455 HIS I 696 GLN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN N 266 HIS ** 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** N 663 GLN N 722 GLN O 219 GLN ** O 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 424 GLN O 441 GLN ** O 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 461 ASN ** O 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 184 GLN X 289 ASN X 531 GLN Y 151 GLN Y 289 ASN Y 298 GLN Y 369 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 64541 Z= 0.295 Angle : 0.793 28.687 87465 Z= 0.393 Chirality : 0.043 0.308 9859 Planarity : 0.005 0.096 11099 Dihedral : 5.171 52.610 8712 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.55 % Favored : 94.86 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.75 % Cis-general : 0.40 % Twisted Proline : 0.68 % Twisted General : 0.00 % 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: 0.63 (0.09), residues: 7920 helix: 1.27 (0.07), residues: 5444 sheet: -0.07 (0.25), residues: 421 loop : -1.79 (0.13), residues: 2055 *********************** 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 918 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 707 time to evaluate : 5.724 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 outliers start: 211 outliers final: 79 residues processed: 880 average time/residue: 0.5416 time to fit residues: 836.2768 Evaluate side-chains 688 residues out of total 7037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 609 time to evaluate : 5.645 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 0 residues processed: 79 average time/residue: 0.4509 time to fit residues: 74.3290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.5089 > 50: distance: 42 - 57: 27.007 distance: 46 - 64: 34.521 distance: 51 - 72: 32.600 distance: 55 - 57: 30.528 distance: 57 - 58: 40.703 distance: 58 - 59: 55.352 distance: 58 - 61: 57.356 distance: 59 - 64: 41.040 distance: 61 - 62: 55.357 distance: 64 - 65: 39.704 distance: 66 - 67: 40.964 distance: 66 - 72: 50.217 distance: 68 - 69: 41.138 distance: 69 - 70: 31.445 distance: 69 - 71: 33.725 distance: 72 - 73: 7.786 distance: 73 - 74: 40.156 distance: 73 - 76: 39.297 distance: 74 - 75: 56.541 distance: 76 - 77: 41.212 distance: 77 - 78: 31.190 distance: 77 - 79: 19.254 distance: 78 - 80: 39.953 distance: 79 - 81: 23.255 distance: 81 - 82: 40.625 distance: 85 - 86: 40.418 distance: 85 - 94: 69.299 distance: 87 - 88: 39.185 distance: 88 - 89: 40.937 distance: 88 - 90: 41.599 distance: 90 - 92: 10.034 distance: 91 - 93: 39.679 distance: 92 - 93: 40.039 distance: 94 - 95: 41.234 distance: 95 - 96: 39.715 distance: 95 - 98: 40.744 distance: 96 - 99: 41.214 distance: 99 - 100: 68.413 distance: 100 - 101: 40.612 distance: 100 - 103: 3.257 distance: 101 - 102: 34.014 distance: 101 - 104: 39.791 distance: 104 - 105: 35.179 distance: 104 - 110: 39.713 distance: 105 - 106: 43.559 distance: 105 - 108: 36.447 distance: 106 - 107: 17.824 distance: 106 - 111: 46.635 distance: 108 - 109: 44.590 distance: 109 - 110: 19.960 distance: 111 - 112: 38.568 distance: 112 - 113: 40.593 distance: 112 - 115: 38.863 distance: 113 - 114: 40.753 distance: 115 - 116: 57.363 distance: 116 - 117: 39.029 distance: 118 - 119: 28.907 distance: 119 - 120: 49.214 distance: 119 - 121: 40.990 distance: 122 - 123: 4.791 distance: 123 - 124: 3.299 distance: 123 - 126: 4.075 distance: 124 - 129: 28.262 distance: 125 - 156: 37.889 distance: 126 - 128: 38.960 distance: 129 - 130: 8.600 distance: 130 - 131: 44.978 distance: 130 - 133: 17.527 distance: 131 - 132: 55.815 distance: 131 - 140: 35.566 distance: 132 - 163: 35.452 distance: 133 - 134: 40.964 distance: 134 - 135: 38.873 distance: 136 - 138: 39.141