Starting phenix.real_space_refine on Wed Mar 13 11:30:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ui9_2924/03_2024/4ui9_2924.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ui9_2924/03_2024/4ui9_2924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ui9_2924/03_2024/4ui9_2924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ui9_2924/03_2024/4ui9_2924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ui9_2924/03_2024/4ui9_2924.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ui9_2924/03_2024/4ui9_2924.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 5 6.06 5 S 396 5.16 5 C 42477 2.51 5 N 11404 2.21 5 O 12171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 715": "OE1" <-> "OE2" Residue "K ASP 232": "OD1" <-> "OD2" Residue "K TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 66453 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 10947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1441, 10947 Classifications: {'peptide': 1441} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 79, 'TRANS': 1357} Chain breaks: 20 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 398 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 24, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 241 Chain: "B" Number of atoms: 650 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 84, 645 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, 645 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: 661 Chain: "C" Number of atoms: 4305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4305 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 509} 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: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 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: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3923 Classifications: {'peptide': 498} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 482} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "G" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 214 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3853 Classifications: {'peptide': 483} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 5709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5709 Classifications: {'peptide': 730} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 706} Chain breaks: 3 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 108 Chain: "J" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4047 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 14, 'TRANS': 489} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 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': 6} Link IDs: {'PTRANS': 14, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, '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': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "M" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 493 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain breaks: 1 Chain: "N" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4831 Classifications: {'peptide': 631} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'CIS': 15, 'PCIS': 3, 'PTRANS': 25, 'TRANS': 587} Chain breaks: 9 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 480 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 8, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 200 Chain: "O" Number of atoms: 5396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5396 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 665} Chain breaks: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 4042 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 477} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3003 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 5, 'PTRANS': 12, 'TRANS': 369} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 648 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 88} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "T" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 109 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'TRANS': 18} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 20} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "W" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 213 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3770 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "Y" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3865 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 480} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 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} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11123 SG CYS B 23 134.280 50.930 152.578 1.00370.06 S ATOM 11141 SG CYS B 26 135.517 54.703 151.653 1.00349.21 S ATOM 11386 SG CYS B 59 132.027 55.249 153.440 1.00371.88 S ATOM 11495 SG CYS B 73 129.545 42.933 150.724 1.00451.97 S ATOM 11516 SG CYS B 76 129.219 38.848 149.464 1.00467.29 S Time building chain proxies: 27.52, per 1000 atoms: 0.41 Number of scatterers: 66453 At special positions: 0 Unit cell: (233.92, 193.12, 220.32, 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 5 29.99 S 396 16.00 O 12171 8.00 N 11404 7.00 C 42477 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.53 Conformation dependent library (CDL) restraints added in 9.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 23 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 26 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 59 " pdb="ZN ZN B 101 " - pdb=" ND1 HIS B 56 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" ND1 HIS B 53 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 76 " Number of angles added : 3 16642 Ramachandran restraints generated. 8321 Oldfield, 0 Emsley, 8321 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16200 Finding SS restraints... Secondary structure from input PDB file: 389 helices and 33 sheets defined 68.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.92 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 removed outlier: 4.124A pdb=" N ASP A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 294 removed outlier: 5.750A pdb=" N GLN A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 631 through 647 removed outlier: 4.009A pdb=" N ALA A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 667 removed outlier: 3.598A pdb=" N MET A 667 " --> pdb=" O CYS A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 777 removed outlier: 3.750A pdb=" N ILE A 762 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 798 removed outlier: 3.666A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 810 Processing helix chain 'A' and resid 843 through 854 Processing helix chain 'A' and resid 867 through 882 Processing helix chain 'A' and resid 924 through 937 Processing helix chain 'A' and resid 942 through 946 Processing helix chain 'A' and resid 948 through 965 Proline residue: A 954 - end of helix removed outlier: 3.777A pdb=" N GLN A 965 " --> pdb=" O HIS A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 978 Processing helix chain 'A' and resid 980 through 984 removed outlier: 3.612A pdb=" N LEU A 983 " --> pdb=" O ARG A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1032 through 1041 removed outlier: 3.701A pdb=" N ASP A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1088 removed outlier: 3.773A pdb=" N GLU A1064 " --> pdb=" O HIS A1060 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A1076 " --> pdb=" O GLN A1072 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A1079 " --> pdb=" O GLN A1075 " (cutoff:3.500A) Proline residue: A1081 - end of helix removed outlier: 3.607A pdb=" N MET A1086 " --> pdb=" O VAL A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1146 removed outlier: 3.530A pdb=" N LYS A1146 " --> pdb=" O ALA A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1161 Processing helix chain 'A' and resid 1168 through 1183 removed outlier: 3.543A pdb=" N TYR A1172 " --> pdb=" O LEU A1168 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A1180 " --> pdb=" O LEU A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1188 Processing helix chain 'A' and resid 1189 through 1200 removed outlier: 3.523A pdb=" N ASP A1195 " --> pdb=" O LEU A1191 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A1200 " --> pdb=" O TYR A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1217 Processing helix chain 'A' and resid 1221 through 1232 removed outlier: 3.833A pdb=" N HIS A1231 " --> pdb=" O LEU A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1261 removed outlier: 3.558A pdb=" N ALA A1252 " --> pdb=" O ASN A1248 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A1258 " --> pdb=" O VAL A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1278 removed outlier: 3.531A pdb=" N GLU A1271 " --> pdb=" O ARG A1267 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1307 removed outlier: 3.727A 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: 3.884A 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: 3.722A pdb=" N PHE A1398 " --> pdb=" O TYR A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1415 removed outlier: 3.700A pdb=" N LEU A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 4.198A pdb=" N VAL A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A1429 " --> pdb=" O TRP A1425 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A1430 " --> pdb=" O VAL A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1437 removed outlier: 3.901A pdb=" N ASN A1437 " --> pdb=" O ILE A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1476 Processing helix chain 'A' and resid 1481 through 1500 removed outlier: 3.530A pdb=" N SER A1500 " --> pdb=" O MET A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1508 removed outlier: 3.581A pdb=" N THR A1507 " --> pdb=" O ASN A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1527 removed outlier: 3.545A pdb=" N MET A1527 " --> pdb=" O LEU A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1546 removed outlier: 3.844A 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 1578 through 1588 Processing helix chain 'A' and resid 1603 through 1608 Processing helix chain 'A' and resid 1609 through 1613 removed outlier: 3.947A 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 Processing helix chain 'A' and resid 1747 through 1758 Processing helix chain 'A' and resid 1767 through 1784 removed outlier: 3.667A pdb=" N LEU A1771 " --> pdb=" O LYS A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1806 removed outlier: 4.117A pdb=" N ALA A1792 " --> pdb=" O GLU A1788 " (cutoff:3.500A) Processing helix chain 'A' and resid 1811 through 1825 removed outlier: 3.692A pdb=" N TRP A1815 " --> pdb=" O THR A1811 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A1816 " --> pdb=" O SER A1812 " (cutoff:3.500A) Processing helix chain 'A' and resid 1847 through 1866 Processing helix chain 'A' and resid 1867 through 1876 Processing helix chain 'A' and resid 1881 through 1896 removed outlier: 3.649A pdb=" N SER A1886 " --> pdb=" O GLU A1882 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET A1887 " --> pdb=" O SER A1883 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS A1890 " --> pdb=" O SER A1886 " (cutoff:3.500A) Processing helix chain 'A' and resid 1911 through 1921 removed outlier: 3.640A pdb=" N ALA A1915 " --> pdb=" O SER A1911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1925 through 1935 removed outlier: 3.972A pdb=" N ARG A1929 " --> pdb=" O LYS A1925 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 68 Processing helix chain 'C' and resid 28 through 47 removed outlier: 4.137A pdb=" N LYS C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 62 Processing helix chain 'C' and resid 77 through 97 removed outlier: 4.985A pdb=" N ASP C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ALA C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 111 through 137 removed outlier: 3.692A pdb=" N VAL C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP C 136 " --> pdb=" O ASP C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 removed outlier: 3.849A 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: 3.503A pdb=" N ASP C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.688A 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 262 through 277 Processing helix chain 'C' and resid 278 through 293 removed outlier: 3.508A 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 345 Processing helix chain 'C' and resid 346 through 361 Processing helix chain 'C' and resid 365 through 378 removed outlier: 3.555A pdb=" N THR C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 398 through 412 removed outlier: 3.546A pdb=" N TRP C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 429 removed outlier: 4.165A pdb=" N TYR C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR C 421 " --> pdb=" O TYR C 417 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 447 removed outlier: 3.627A 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 468 through 480 Processing helix chain 'C' and resid 483 through 500 Processing helix chain 'C' and resid 509 through 523 Processing helix chain 'C' and resid 525 through 540 Processing helix chain 'C' and resid 543 through 557 removed outlier: 3.762A pdb=" N ARG C 557 " --> pdb=" O ILE C 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 46 Processing helix chain 'E' and resid 52 through 92 removed outlier: 3.919A pdb=" N GLU E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU E 88 " --> pdb=" O GLY E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 103 Processing helix chain 'F' and resid 6 through 18 Processing helix chain 'F' and resid 20 through 36 Processing helix chain 'F' and resid 37 through 51 Processing helix chain 'F' and resid 53 through 64 Processing helix chain 'F' and resid 68 through 82 Processing helix chain 'F' and resid 84 through 94 removed outlier: 3.585A pdb=" N GLN F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE F 91 " --> pdb=" O GLU F 87 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 113 through 129 Processing helix chain 'F' and resid 130 through 145 removed outlier: 3.707A pdb=" N GLU F 136 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER F 141 " --> pdb=" O CYS F 137 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 158 removed outlier: 3.933A pdb=" N PHE F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 479 removed outlier: 4.229A pdb=" N ALA F 458 " --> pdb=" O LEU F 454 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA F 459 " --> pdb=" O GLN F 455 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY F 461 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU F 462 " --> pdb=" O ALA F 458 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU F 465 " --> pdb=" O GLY F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 490 removed outlier: 3.550A pdb=" N HIS F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) 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 547 Processing helix chain 'F' and resid 548 through 563 Processing helix chain 'F' and resid 566 through 580 removed outlier: 3.655A 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 615 removed outlier: 4.186A pdb=" N TYR F 604 " --> pdb=" O TYR F 600 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR F 605 " --> pdb=" O ALA F 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 631 removed outlier: 3.538A pdb=" N ALA F 622 " --> pdb=" O ASP F 618 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS F 623 " --> pdb=" O LYS F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 648 removed outlier: 3.717A pdb=" N TRP F 638 " --> pdb=" O HIS F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 665 Processing helix chain 'F' and resid 668 through 683 Processing helix chain 'F' and resid 684 through 699 Processing helix chain 'F' and resid 702 through 716 Processing helix chain 'F' and resid 718 through 733 removed outlier: 3.517A pdb=" N GLU F 728 " --> pdb=" O GLN F 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 736 through 751 removed outlier: 3.712A pdb=" N TYR F 740 " --> pdb=" O GLU F 736 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 767 Processing helix chain 'F' and resid 769 through 819 removed outlier: 3.626A pdb=" N LYS F 813 " --> pdb=" O ASN F 778 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 816 " --> pdb=" O ILE F 812 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 25 removed outlier: 3.838A pdb=" N GLU G 18 " --> pdb=" O GLU G 14 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE G 19 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP G 25 " --> pdb=" O ASN G 21 " (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: 3.730A pdb=" N ILE H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 113 through 129 Processing helix chain 'H' and resid 130 through 145 removed outlier: 3.654A pdb=" N GLU H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER H 141 " --> pdb=" O CYS H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 158 removed outlier: 3.903A pdb=" N PHE H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 169 removed outlier: 4.483A pdb=" N THR H 167 " --> pdb=" O ASP H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 479 removed outlier: 3.626A pdb=" N GLY H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU H 462 " --> pdb=" O ALA H 458 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 465 " --> pdb=" O GLY H 461 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 490 removed outlier: 3.527A pdb=" N HIS H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 512 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: 3.633A pdb=" N TRP H 570 " --> pdb=" O SER H 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 597 Processing helix chain 'H' and resid 600 through 615 removed outlier: 4.196A pdb=" N TYR H 604 " --> pdb=" O TYR H 600 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 605 " --> pdb=" O ALA H 601 " (cutoff:3.500A) Processing helix chain 'H' and resid 616 through 631 removed outlier: 3.540A pdb=" N ALA H 622 " --> pdb=" O ASP H 618 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS H 623 " --> pdb=" O LYS H 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 634 through 648 removed outlier: 3.701A pdb=" N TRP H 638 " --> pdb=" O HIS H 634 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 665 Processing helix chain 'H' and resid 668 through 683 Processing helix chain 'H' and resid 684 through 699 Processing helix chain 'H' and resid 702 through 716 removed outlier: 3.640A pdb=" N LYS H 706 " --> pdb=" O ASN H 702 " (cutoff:3.500A) Processing helix chain 'H' and resid 718 through 733 removed outlier: 3.537A pdb=" N GLU H 728 " --> pdb=" O GLN H 724 " (cutoff:3.500A) Processing helix chain 'H' and resid 736 through 751 removed outlier: 3.684A pdb=" N TYR H 740 " --> pdb=" O GLU H 736 " (cutoff:3.500A) Processing helix chain 'H' and resid 752 through 771 Processing helix chain 'I' and resid 49 through 52 Processing helix chain 'I' and resid 132 through 137 removed outlier: 4.167A pdb=" N ASN I 136 " --> pdb=" O GLU I 132 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU I 137 " --> pdb=" O ASP I 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 132 through 137' Processing helix chain 'I' and resid 163 through 170 Processing helix chain 'I' and resid 190 through 192 No H-bonds generated for 'chain 'I' and resid 190 through 192' Processing helix chain 'I' and resid 238 through 244 Processing helix chain 'I' and resid 244 through 294 removed outlier: 3.902A pdb=" N ALA I 275 " --> pdb=" O CYS I 271 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP I 276 " --> pdb=" O MET I 272 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU I 277 " --> pdb=" O CYS I 273 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLU I 278 " --> pdb=" O GLU I 274 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE I 279 " --> pdb=" O ALA I 275 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU I 280 " --> pdb=" O TRP I 276 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET I 281 " --> pdb=" O GLU I 277 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN I 282 " --> pdb=" O GLU I 278 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET I 283 " --> pdb=" O ILE I 279 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP I 284 " --> pdb=" O LEU I 280 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER I 285 " --> pdb=" O MET I 281 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG I 286 " --> pdb=" O GLN I 282 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU I 287 " --> pdb=" O MET I 283 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN I 292 " --> pdb=" O THR I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 310 Processing helix chain 'I' and resid 315 through 325 removed outlier: 3.745A pdb=" N GLN I 324 " --> pdb=" O LEU I 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 351 Processing helix chain 'I' and resid 351 through 372 removed outlier: 3.510A pdb=" N MET I 369 " --> pdb=" O GLU I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 377 Processing helix chain 'I' and resid 382 through 429 removed outlier: 3.512A pdb=" N MET I 428 " --> pdb=" O ALA I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 441 through 456 Processing helix chain 'I' and resid 474 through 481 removed outlier: 4.323A pdb=" N TYR I 478 " --> pdb=" O ARG I 474 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU I 479 " --> pdb=" O VAL I 475 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP I 481 " --> pdb=" O GLN I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 503 Processing helix chain 'I' and resid 505 through 510 removed outlier: 3.833A pdb=" N GLU I 509 " --> pdb=" O SER I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 521 through 548 Proline residue: I 540 - end of helix removed outlier: 3.710A 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 removed outlier: 3.504A pdb=" N TRP J 42 " --> pdb=" O GLN J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 63 removed outlier: 3.836A pdb=" N ARG J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 70 removed outlier: 3.533A pdb=" N GLU J 70 " --> pdb=" O ASP J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 84 Processing helix chain 'J' and resid 87 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: 4.044A pdb=" N PHE J 167 " --> pdb=" O CYS J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 188 Processing helix chain 'J' and resid 194 through 209 removed outlier: 3.522A pdb=" N LYS J 208 " --> pdb=" O LEU J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 245 Processing helix chain 'J' and resid 246 through 261 Processing helix chain 'J' and resid 266 through 278 removed outlier: 4.488A 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: 3.694A pdb=" N GLY J 313 " --> pdb=" O TYR J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 330 Processing helix chain 'J' and resid 333 through 348 removed outlier: 3.793A pdb=" N TRP J 337 " --> pdb=" O TYR J 333 " (cutoff:3.500A) removed outlier: 3.720A 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 381 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: 3.579A pdb=" N ALA J 434 " --> pdb=" O GLU J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 458 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 removed outlier: 3.541A pdb=" N ASP J 500 " --> pdb=" O GLU J 496 " (cutoff:3.500A) Processing helix chain 'J' and resid 512 through 529 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 87 through 93 Processing helix chain 'K' and resid 128 through 144 removed outlier: 3.639A pdb=" N CYS K 133 " --> pdb=" O LYS K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 161 Processing helix chain 'K' and resid 163 through 172 removed outlier: 4.024A pdb=" N PHE K 167 " --> pdb=" O CYS K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 175 No H-bonds generated for 'chain 'K' and resid 173 through 175' Processing helix chain 'K' and resid 178 through 188 Processing helix chain 'K' and resid 194 through 211 removed outlier: 3.665A pdb=" N LYS K 208 " --> pdb=" O LEU K 204 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS K 211 " --> pdb=" O ASN K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 225 removed outlier: 3.574A 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 278 removed outlier: 4.488A 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: 3.971A pdb=" N TRP K 302 " --> pdb=" O ASN K 298 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY K 313 " --> pdb=" O TYR K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 330 Processing helix chain 'K' and resid 334 through 348 removed outlier: 3.632A 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 removed outlier: 3.550A pdb=" N ILE K 397 " --> pdb=" O GLN K 393 " (cutoff:3.500A) 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 458 removed outlier: 4.027A 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: 3.583A pdb=" N LEU K 474 " --> pdb=" O GLN K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 492 Processing helix chain 'K' and resid 494 through 509 removed outlier: 3.535A pdb=" N ASP K 500 " --> pdb=" O GLU K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 512 through 527 Processing helix chain 'L' and resid 12 through 20 removed outlier: 3.555A pdb=" N LEU L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) removed outlier: 3.894A 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: 3.712A 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 182 removed outlier: 4.144A pdb=" N TYR L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER L 182 " --> pdb=" O MET L 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 16 removed outlier: 3.773A pdb=" N ASP M 16 " --> pdb=" O LEU M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 56 Processing helix chain 'N' and resid 15 through 29 Processing helix chain 'N' and resid 53 through 63 Processing helix chain 'N' and resid 79 through 92 removed outlier: 3.886A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) Proline residue: N 89 - end of helix Processing helix chain 'N' and resid 93 through 99 Processing helix chain 'N' and resid 107 through 123 Processing helix chain 'N' and resid 123 through 139 removed outlier: 4.293A pdb=" N SER N 128 " --> pdb=" O PRO N 124 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LEU N 129 " --> pdb=" O TYR N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 162 Processing helix chain 'N' and resid 166 through 191 Processing helix chain 'N' and resid 203 through 215 Processing helix chain 'N' and resid 234 through 250 Processing helix chain 'N' and resid 252 through 278 removed outlier: 4.117A pdb=" N VAL N 256 " --> pdb=" O LEU N 252 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA N 258 " --> pdb=" O GLU N 254 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU N 259 " --> pdb=" O ARG N 255 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG N 276 " --> pdb=" O ARG N 272 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG N 278 " --> pdb=" O GLU N 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 304 removed outlier: 3.537A pdb=" N LYS N 291 " --> pdb=" O ARG N 287 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE N 293 " --> pdb=" O PHE N 289 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU N 300 " --> pdb=" O VAL N 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 349 removed outlier: 3.506A pdb=" N ILE N 335 " --> pdb=" O PHE N 331 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE N 345 " --> pdb=" O ILE N 341 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER N 346 " --> pdb=" O GLU N 342 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 367 Processing helix chain 'N' and resid 370 through 386 Processing helix chain 'N' and resid 395 through 409 removed outlier: 3.563A pdb=" N LEU N 399 " --> pdb=" O ASP N 395 " (cutoff:3.500A) Processing helix chain 'N' and resid 414 through 421 removed outlier: 3.624A pdb=" N VAL N 419 " --> pdb=" O VAL N 415 " (cutoff:3.500A) Processing helix chain 'N' and resid 421 through 432 Processing helix chain 'N' and resid 433 through 442 Processing helix chain 'N' and resid 451 through 458 removed outlier: 4.186A pdb=" N LYS N 458 " --> pdb=" O VAL N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 499 through 510 removed outlier: 3.794A pdb=" N GLY N 510 " --> pdb=" O VAL N 506 " (cutoff:3.500A) Processing helix chain 'N' and resid 512 through 530 Processing helix chain 'N' and resid 536 through 549 Processing helix chain 'N' and resid 554 through 563 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: 4.058A pdb=" N ALA N 617 " --> pdb=" O GLU N 613 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA N 618 " --> pdb=" O ASP N 614 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 642 removed outlier: 3.500A pdb=" N LEU N 641 " --> pdb=" O LYS N 638 " (cutoff:3.500A) Processing helix chain 'N' and resid 660 through 672 removed outlier: 3.674A pdb=" N ASP N 672 " --> pdb=" O LEU N 668 " (cutoff:3.500A) Processing helix chain 'N' and resid 677 through 686 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: 3.575A pdb=" N ARG O 58 " --> pdb=" O LEU O 54 " (cutoff:3.500A) Proline residue: O 66 - end of helix Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'O' and resid 88 through 103 Processing helix chain 'O' and resid 104 through 121 removed outlier: 3.838A pdb=" N MET O 108 " --> pdb=" O GLU O 104 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER O 120 " --> pdb=" O SER O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 146 removed outlier: 3.590A pdb=" N LEU O 146 " --> pdb=" O ALA O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 169 removed outlier: 3.814A pdb=" N LYS O 169 " --> pdb=" O ASP O 165 " (cutoff:3.500A) Processing helix chain 'O' and resid 208 through 226 Processing helix chain 'O' and resid 232 through 247 removed outlier: 3.709A pdb=" N PHE O 246 " --> pdb=" O ASN O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 251 through 265 removed outlier: 3.771A pdb=" N TYR O 255 " --> pdb=" O ALA O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 281 removed outlier: 3.686A pdb=" N SER O 270 " --> pdb=" O ASP O 266 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 314 removed outlier: 4.303A pdb=" N ARG O 301 " --> pdb=" O GLY O 297 " (cutoff:3.500A) removed outlier: 3.887A 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: 3.528A pdb=" N LEU O 340 " --> pdb=" O ASP O 336 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS O 342 " --> pdb=" O VAL O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 357 through 370 removed outlier: 3.922A pdb=" N LEU O 361 " --> pdb=" O SER O 357 " (cutoff:3.500A) Processing helix chain 'O' and resid 373 through 392 Processing helix chain 'O' and resid 394 through 413 removed outlier: 3.571A pdb=" N LEU O 408 " --> pdb=" O ASP O 404 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 432 removed outlier: 3.682A pdb=" N ILE O 418 " --> pdb=" O LEU O 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 434 through 448 Processing helix chain 'O' and resid 462 through 480 removed outlier: 3.859A pdb=" N PHE O 466 " --> pdb=" O ASN O 462 " (cutoff:3.500A) removed outlier: 3.721A 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: 3.559A pdb=" N THR O 533 " --> pdb=" O ASP O 529 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY O 534 " --> pdb=" O SER O 530 " (cutoff:3.500A) removed outlier: 3.705A 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: 3.950A pdb=" N ARG O 593 " --> pdb=" O GLU O 589 " (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 614 removed outlier: 4.310A pdb=" N MET O 603 " --> pdb=" O ILE O 599 " (cutoff:3.500A) Processing helix chain 'O' and resid 616 through 634 removed outlier: 3.510A pdb=" N GLU O 622 " --> pdb=" O TYR O 618 " (cutoff:3.500A) Processing helix chain 'O' and resid 636 through 654 removed outlier: 4.154A pdb=" N MET O 646 " --> pdb=" O SER O 642 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA O 647 " --> pdb=" O LEU O 643 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU O 649 " --> pdb=" O HIS O 645 " (cutoff:3.500A) Proline residue: O 650 - end of helix removed outlier: 3.662A pdb=" N ASP O 654 " --> pdb=" O PRO O 650 " (cutoff:3.500A) Processing helix chain 'O' and resid 657 through 678 removed outlier: 3.517A pdb=" N MET O 664 " --> pdb=" O LYS O 660 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER O 677 " --> pdb=" O ALA O 673 " (cutoff:3.500A) Processing helix chain 'O' and resid 682 through 705 removed outlier: 3.607A pdb=" N ALA O 689 " --> pdb=" O GLU O 685 " (cutoff:3.500A) Processing helix chain 'O' and resid 707 through 725 removed outlier: 4.093A pdb=" N ASP O 712 " --> pdb=" O GLU O 708 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL O 713 " --> pdb=" O ARG O 709 " (cutoff:3.500A) Processing helix chain 'O' and resid 726 through 741 removed outlier: 3.771A pdb=" N ARG O 732 " --> pdb=" O GLN O 728 " (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: 4.970A pdb=" N ASP P 85 " --> pdb=" O ALA P 81 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA P 86 " --> pdb=" O GLN P 82 " (cutoff:3.500A) removed outlier: 4.242A 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: 3.537A pdb=" N GLU P 153 " --> pdb=" O GLU P 149 " (cutoff:3.500A) removed outlier: 3.885A 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 removed outlier: 3.502A pdb=" N ASP P 190 " --> pdb=" O LYS P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 213 removed outlier: 3.715A 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: 3.697A pdb=" N VAL P 266 " --> pdb=" O SER P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 278 through 293 removed outlier: 3.558A 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 345 Processing helix chain 'P' and resid 346 through 361 Processing helix chain 'P' and resid 364 through 378 removed outlier: 3.908A pdb=" N TRP P 368 " --> pdb=" O TYR P 364 " (cutoff:3.500A) removed outlier: 3.630A 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 removed outlier: 3.542A pdb=" N TRP P 402 " --> pdb=" O ASP P 398 " (cutoff:3.500A) Processing helix chain 'P' and resid 415 through 429 Processing helix chain 'P' and resid 432 through 447 removed outlier: 3.566A pdb=" N LEU P 436 " --> pdb=" O ASP P 432 " (cutoff:3.500A) 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: 3.561A pdb=" N ALA P 486 " --> pdb=" O GLU P 482 " (cutoff:3.500A) Processing helix chain 'P' and resid 511 through 523 Processing helix chain 'P' and resid 525 through 538 Processing helix chain 'R' and resid 56 through 63 Processing helix chain 'R' and resid 88 through 100 Processing helix chain 'R' and resid 154 through 163 removed outlier: 3.622A pdb=" N LEU R 160 " --> pdb=" O LYS R 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 358 through 366 Processing helix chain 'S' and resid 423 through 432 Processing helix chain 'U' and resid 6 through 21 Proline residue: U 16 - end of helix removed outlier: 4.067A pdb=" N ALA U 21 " --> pdb=" O PRO U 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 25 removed outlier: 3.803A pdb=" N GLU W 18 " --> pdb=" O ASP W 14 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE W 19 " --> pdb=" O ASP W 15 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP W 25 " --> pdb=" O ASN W 21 " (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 161 removed outlier: 3.667A pdb=" N ALA X 155 " --> pdb=" O GLN X 151 " (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 Processing helix chain 'X' and resid 235 through 249 Processing helix chain 'X' and resid 250 through 264 removed outlier: 3.599A 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: 3.534A pdb=" N VAL X 291 " --> pdb=" O ASN X 287 " (cutoff:3.500A) Processing helix chain 'X' and resid 304 through 319 removed outlier: 3.952A pdb=" N ASP X 309 " --> pdb=" O ILE X 305 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL X 310 " --> pdb=" O LYS X 306 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR X 313 " --> pdb=" O ASP X 309 " (cutoff:3.500A) removed outlier: 3.546A 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: 3.954A pdb=" N TRP X 342 " --> pdb=" O HIS X 338 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE X 350 " --> pdb=" O GLY X 346 " (cutoff:3.500A) removed outlier: 3.985A 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 373 through 387 removed outlier: 3.568A pdb=" N ALA X 382 " --> pdb=" O LEU X 378 " (cutoff:3.500A) Processing helix chain 'X' and resid 388 through 403 removed outlier: 3.878A pdb=" N HIS X 395 " --> pdb=" O GLU X 391 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG X 401 " --> pdb=" O ARG X 397 " (cutoff:3.500A) Processing helix chain 'X' and resid 406 through 421 Processing helix chain 'X' and resid 422 through 438 Processing helix chain 'X' and resid 441 through 454 removed outlier: 3.570A pdb=" N THR X 445 " --> pdb=" O ALA X 441 " (cutoff:3.500A) Processing helix chain 'X' and resid 457 through 472 removed outlier: 3.897A pdb=" N LEU X 464 " --> pdb=" O LYS X 460 " (cutoff:3.500A) Processing helix chain 'X' and resid 475 through 490 Processing helix chain 'X' and resid 491 through 506 removed outlier: 3.607A pdb=" N GLY X 495 " --> pdb=" O LYS X 491 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN X 505 " --> pdb=" O ASN X 501 " (cutoff:3.500A) Processing helix chain 'X' and resid 509 through 523 removed outlier: 3.837A pdb=" N ARG X 513 " --> pdb=" O CYS X 509 " (cutoff:3.500A) removed outlier: 3.514A 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 48 Processing helix chain 'Y' and resid 49 through 67 Processing helix chain 'Y' and resid 72 through 90 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: 3.670A pdb=" N ALA Y 155 " --> pdb=" O GLN Y 151 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE Y 162 " --> pdb=" O ILE Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 168 through 183 Processing helix chain 'Y' and resid 184 through 199 removed outlier: 3.940A 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 Processing helix chain 'Y' and resid 250 through 264 removed outlier: 3.579A 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 removed outlier: 3.532A pdb=" N VAL Y 291 " --> pdb=" O ASN Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 304 through 319 removed outlier: 3.618A pdb=" N MET Y 308 " --> pdb=" O LEU Y 304 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP Y 309 " --> pdb=" O ILE Y 305 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL Y 310 " --> pdb=" O LYS Y 306 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR Y 313 " --> pdb=" O ASP Y 309 " (cutoff:3.500A) removed outlier: 3.551A 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 353 removed outlier: 3.951A pdb=" N TRP Y 342 " --> pdb=" O HIS Y 338 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE Y 350 " --> pdb=" O GLY Y 346 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR Y 351 " --> pdb=" O CYS Y 347 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 369 Processing helix chain 'Y' and resid 372 through 387 removed outlier: 3.710A pdb=" N LEU Y 376 " --> pdb=" O SER Y 372 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA Y 382 " --> pdb=" O LEU Y 378 " (cutoff:3.500A) Processing helix chain 'Y' and resid 388 through 403 removed outlier: 3.875A pdb=" N HIS Y 395 " --> pdb=" O GLU Y 391 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG Y 401 " --> pdb=" O ARG Y 397 " (cutoff:3.500A) Processing helix chain 'Y' and resid 406 through 421 Processing helix chain 'Y' and resid 422 through 438 Processing helix chain 'Y' and resid 441 through 454 removed outlier: 3.592A pdb=" N THR Y 445 " --> pdb=" O ALA Y 441 " (cutoff:3.500A) Processing helix chain 'Y' and resid 457 through 472 removed outlier: 3.916A pdb=" N LEU Y 464 " --> pdb=" O LYS Y 460 " (cutoff:3.500A) Processing helix chain 'Y' and resid 475 through 490 Processing helix chain 'Y' and resid 491 through 506 removed outlier: 3.620A pdb=" N GLY Y 495 " --> pdb=" O LYS Y 491 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN Y 501 " --> pdb=" O ALA Y 497 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN Y 505 " --> pdb=" O ASN Y 501 " (cutoff:3.500A) Processing helix chain 'Y' and resid 509 through 523 removed outlier: 3.843A pdb=" N ARG Y 513 " --> pdb=" O CYS Y 509 " (cutoff:3.500A) removed outlier: 3.532A 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: 3.777A pdb=" N GLY Y 548 " --> pdb=" O LYS Y 544 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET Y 549 " --> pdb=" O SER Y 545 " (cutoff:3.500A) removed outlier: 3.736A 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 19 removed outlier: 6.798A pdb=" N ARG A 594 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP A 589 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A 596 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 587 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 6.630A 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 Processing sheet with id= AC, first strand: chain 'A' and resid 127 through 132 removed outlier: 3.505A pdb=" N LEU A 127 " --> pdb=" O CYS A 152 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 151 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 177 through 180 removed outlier: 6.856A pdb=" N GLU A 190 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL A 180 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 188 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 245 through 250 removed outlier: 6.154A pdb=" N ILE A 246 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR A 259 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 255 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 268 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.978A pdb=" N LYS A 440 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 452 " --> pdb=" O ASN A 473 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN A 473 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N CYS A 454 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A 471 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS A 456 " --> pdb=" O GLY A 469 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 458 " --> pdb=" O ILE A 467 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 478 through 482 removed outlier: 3.764A pdb=" N ASP A 478 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 482 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 487 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU A 497 " --> pdb=" O LYS A 508 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS A 508 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 499 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 1108 through 1111 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: 3.520A pdb=" N THR A1647 " --> pdb=" O TYR A1638 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A1633 " --> pdb=" O VAL A1668 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A1668 " --> pdb=" O LEU A1633 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU A1635 " --> pdb=" O ILE A1666 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE A1666 " --> pdb=" O GLU A1635 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A1637 " --> pdb=" O LYS A1664 " (cutoff:3.500A) removed outlier: 3.657A 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: 5.302A pdb=" N ILE B 5 " --> pdb=" O ASP N 647 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASP N 647 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS B 7 " --> pdb=" O THR N 645 " (cutoff:3.500A) removed outlier: 3.850A 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: 6.902A pdb=" N VAL I 44 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER I 57 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 6.653A 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: 4.179A pdb=" N CYS I 70 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS I 93 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS I 102 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASP I 94 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER I 100 " --> pdb=" O ASP I 94 " (cutoff:3.500A) Processing sheet with id= IC, first strand: chain 'I' and resid 112 through 117 removed outlier: 3.588A pdb=" N TYR I 188 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE I 185 " --> pdb=" O ARG I 197 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG I 197 " --> pdb=" O ILE I 185 " (cutoff:3.500A) removed outlier: 6.483A 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: 5.734A pdb=" N CYS I 205 " --> pdb=" O GLU I 222 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU I 222 " --> pdb=" O CYS I 205 " (cutoff:3.500A) removed outlier: 3.772A 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: 11.922A pdb=" N TYR I 596 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.191A 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: 11.922A pdb=" N TYR I 596 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE I 707 " --> pdb=" O GLY I 621 " (cutoff:3.500A) removed outlier: 4.021A 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: 5.623A pdb=" N CYS I 638 " --> pdb=" O LYS I 654 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LYS I 654 " --> pdb=" O CYS I 638 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR I 648 " --> pdb=" O TYR I 644 " (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: 4.162A 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: 12.044A pdb=" N ILE L 66 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N ALA L 140 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N PHE L 68 " --> pdb=" O GLN L 138 " (cutoff:3.500A) removed outlier: 11.322A pdb=" N GLN L 138 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N ARG L 70 " --> pdb=" O MET L 136 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N MET L 136 " --> pdb=" O ARG L 70 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR L 72 " --> pdb=" O THR L 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR L 132 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE L 94 " --> pdb=" O GLN L 110 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLN L 110 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL L 96 " --> pdb=" O ILE L 108 " (cutoff:3.500A) Processing sheet with id= RA, first strand: chain 'R' and resid 177 through 180 removed outlier: 3.611A pdb=" N LYS R 177 " --> pdb=" O PHE R 469 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR R 466 " --> pdb=" O ALA R 462 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA R 462 " --> pdb=" O THR R 466 " (cutoff:3.500A) Processing sheet with id= RB, first strand: chain 'R' and resid 193 through 195 removed outlier: 6.357A pdb=" N VAL R 209 " --> pdb=" O LEU R 222 " (cutoff:3.500A) Processing sheet with id= RC, first strand: chain 'R' and resid 232 through 237 removed outlier: 6.387A pdb=" N VAL R 253 " --> pdb=" O MET R 266 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N MET R 266 " --> pdb=" O VAL R 253 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE R 255 " --> pdb=" O LEU R 264 " (cutoff:3.500A) Processing sheet with id= RD, first strand: chain 'R' and resid 274 through 280 removed outlier: 4.263A pdb=" N MET R 292 " --> pdb=" O SER R 288 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE R 293 " --> pdb=" O ARG R 307 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG R 307 " --> pdb=" O ILE R 293 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN R 295 " --> pdb=" O SER R 305 " (cutoff:3.500A) Processing sheet with id= RE, first strand: chain 'R' and resid 319 through 321 Processing sheet with id= RF, first strand: chain 'R' and resid 360 through 363 removed outlier: 3.896A pdb=" N ALA R 360 " --> pdb=" O GLY R 374 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE R 382 " --> pdb=" O CYS R 395 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N CYS R 395 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE R 384 " --> pdb=" O LEU R 393 " (cutoff:3.500A) Processing sheet with id= RG, first strand: chain 'R' and resid 402 through 407 removed outlier: 3.608A pdb=" N ASN R 404 " --> pdb=" O THR R 417 " (cutoff:3.500A) Processing sheet with id= SA, first strand: chain 'S' and resid 376 through 377 4225 hydrogen bonds defined for protein. 12546 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: 26.65 Time building geometry restraints manager: 24.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.45: 30077 1.45 - 1.71: 37166 1.71 - 1.98: 586 1.98 - 2.25: 4 2.25 - 2.52: 2 Bond restraints: 67835 Sorted by residual: bond pdb=" C ASP N 563 " pdb=" N MET N 564 " ideal model delta sigma weight residual 1.335 2.519 -1.184 1.31e-02 5.83e+03 8.17e+03 bond pdb=" N PRO R 431 " pdb=" CD PRO R 431 " ideal model delta sigma weight residual 1.473 2.227 -0.754 1.40e-02 5.10e+03 2.90e+03 bond pdb=" N PRO R 392 " pdb=" CD PRO R 392 " ideal model delta sigma weight residual 1.473 2.186 -0.713 1.40e-02 5.10e+03 2.60e+03 bond pdb=" N PRO R 302 " pdb=" CD PRO R 302 " ideal model delta sigma weight residual 1.473 2.160 -0.687 1.40e-02 5.10e+03 2.41e+03 bond pdb=" N PRO R 301 " pdb=" CD PRO R 301 " ideal model delta sigma weight residual 1.473 2.139 -0.666 1.40e-02 5.10e+03 2.26e+03 ... (remaining 67830 not shown) Histogram of bond angle deviations from ideal: 39.44 - 62.77: 1 62.77 - 86.10: 6 86.10 - 109.42: 10463 109.42 - 132.75: 81265 132.75 - 156.07: 156 Bond angle restraints: 91891 Sorted by residual: angle pdb=" O PRO R 431 " pdb=" C PRO R 431 " pdb=" N SER R 432 " ideal model delta sigma weight residual 122.64 39.44 83.20 1.35e+00 5.49e-01 3.80e+03 angle pdb=" O GLN R 310 " pdb=" C GLN R 310 " pdb=" N GLY R 311 " ideal model delta sigma weight residual 122.84 73.03 49.81 1.20e+00 6.94e-01 1.72e+03 angle pdb=" N THR R 434 " pdb=" CA THR R 434 " pdb=" CB THR R 434 " ideal model delta sigma weight residual 110.60 156.07 -45.47 1.52e+00 4.33e-01 8.95e+02 angle pdb=" N VAL R 436 " pdb=" CA VAL R 436 " pdb=" CB VAL R 436 " ideal model delta sigma weight residual 112.34 142.56 -30.22 1.30e+00 5.92e-01 5.40e+02 angle pdb=" C VAL R 436 " pdb=" CA VAL R 436 " pdb=" CB VAL R 436 " ideal model delta sigma weight residual 110.41 85.19 25.22 1.14e+00 7.69e-01 4.89e+02 ... (remaining 91886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.04: 37401 26.04 - 52.08: 2989 52.08 - 78.12: 396 78.12 - 104.16: 39 104.16 - 130.21: 1 Dihedral angle restraints: 40826 sinusoidal: 15845 harmonic: 24981 Sorted by residual: dihedral pdb=" CA GLU N 280 " pdb=" C GLU N 280 " pdb=" N TYR N 281 " pdb=" CA TYR N 281 " ideal model delta harmonic sigma weight residual 180.00 49.79 130.21 0 5.00e+00 4.00e-02 6.78e+02 dihedral pdb=" CA CYS N 394 " pdb=" C CYS N 394 " pdb=" N ASP N 395 " pdb=" CA ASP N 395 " ideal model delta harmonic sigma weight residual 180.00 98.07 81.93 0 5.00e+00 4.00e-02 2.68e+02 dihedral pdb=" N THR R 434 " pdb=" C THR R 434 " pdb=" CA THR R 434 " pdb=" CB THR R 434 " ideal model delta harmonic sigma weight residual 123.40 156.24 -32.84 0 2.50e+00 1.60e-01 1.73e+02 ... (remaining 40823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 9972 0.248 - 0.497: 363 0.497 - 0.745: 21 0.745 - 0.994: 5 0.994 - 1.242: 1 Chirality restraints: 10362 Sorted by residual: chirality pdb=" CA THR R 434 " pdb=" N THR R 434 " pdb=" C THR R 434 " pdb=" CB THR R 434 " both_signs ideal model delta sigma weight residual False 2.53 1.28 1.24 2.00e-01 2.50e+01 3.86e+01 chirality pdb=" CA ASP N 395 " pdb=" N ASP N 395 " pdb=" C ASP N 395 " pdb=" CB ASP N 395 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" CA ASN P 361 " pdb=" N ASN P 361 " pdb=" C ASN P 361 " pdb=" CB ASN P 361 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.01e+01 ... (remaining 10359 not shown) Planarity restraints: 11673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO R 431 " 0.193 2.00e-02 2.50e+03 2.73e-01 7.46e+02 pdb=" C PRO R 431 " -0.457 2.00e-02 2.50e+03 pdb=" O PRO R 431 " 0.226 2.00e-02 2.50e+03 pdb=" N SER R 432 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN R 310 " -0.156 2.00e-02 2.50e+03 2.37e-01 5.62e+02 pdb=" C GLN R 310 " 0.409 2.00e-02 2.50e+03 pdb=" O GLN R 310 " -0.150 2.00e-02 2.50e+03 pdb=" N GLY R 311 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 430 " 0.202 5.00e-02 4.00e+02 2.59e-01 1.07e+02 pdb=" N PRO R 431 " -0.436 5.00e-02 4.00e+02 pdb=" CA PRO R 431 " 0.188 5.00e-02 4.00e+02 pdb=" CD PRO R 431 " 0.046 5.00e-02 4.00e+02 ... (remaining 11670 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.66: 23 1.66 - 2.47: 346 2.47 - 3.28: 77025 3.28 - 4.09: 165360 4.09 - 4.90: 302492 Warning: very small nonbonded interaction distances. Nonbonded interactions: 545246 Sorted by model distance: nonbonded pdb=" CD GLN R 310 " pdb=" CD2 LEU R 338 " model vdw 0.849 3.690 nonbonded pdb=" CE1 TYR X 355 " pdb=" N ASN X 385 " model vdw 0.943 3.420 nonbonded pdb=" CG GLN R 310 " pdb=" CD2 LEU R 338 " model vdw 0.952 3.860 nonbonded pdb=" CZ TYR X 355 " pdb=" N ASN X 385 " model vdw 0.958 3.340 nonbonded pdb=" SD MET R 292 " pdb=" CD2 LEU R 309 " model vdw 1.028 3.820 ... (remaining 545241 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 134 or resid 147 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 r \ esid 498 through 500 or resid 511 through 538)) selection = chain 'P' } ncs_group { reference = (chain 'F' and resid 5 through 767) selection = (chain 'H' and (resid 5 through 455 or (resid 456 through 459 and (name N or nam \ e CA or name C or name O or name CB )) or resid 460 through 771)) } ncs_group { reference = (chain 'G' and (resid 1 through 13 or resid 15 through 25)) selection = (chain 'W' and (resid 1 through 13 or resid 15 through 25)) } ncs_group { reference = (chain 'J' and (resid 2 through 93 or resid 127 through 213 or (resid 214 and (n \ ame N or name CA or name C or name O or name CB )) or resid 215 through 224 or r \ esid 226 through 227 or (resid 228 and (name N or name CA or name C or name O or \ name CB )) or resid 229 through 264 or resid 266 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 224 or resid 226 through 264 or \ resid 266 through 346 or (resid 347 and (name N or name CA or name C or name O o \ r name CB )) or resid 348 through 523 or (resid 524 and (name N or name CA or na \ me C or name O or name CB )) or resid 525 through 527)) } ncs_group { reference = chain 'X' selection = (chain 'Y' and resid 36 through 540) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 6.970 Check model and map are aligned: 0.760 Set scattering table: 0.480 Process input model: 153.250 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 1.184 67835 Z= 1.098 Angle : 1.970 83.198 91891 Z= 1.272 Chirality : 0.111 1.242 10362 Planarity : 0.010 0.273 11673 Dihedral : 17.965 130.206 24626 Min Nonbonded Distance : 0.849 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 1.88 % Allowed : 5.29 % Favored : 92.84 % Rotamer: Outliers : 11.86 % Allowed : 13.54 % Favored : 74.59 % Cbeta Deviations : 1.53 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.28 % Twisted Proline : 1.31 % Twisted General : 0.48 % 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: -1.90 (0.08), residues: 8321 helix: -0.64 (0.06), residues: 5382 sheet: -0.80 (0.21), residues: 574 loop : -2.59 (0.11), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.007 TRP K 302 HIS 0.032 0.004 HIS K 54 PHE 0.058 0.006 PHE P 116 TYR 0.062 0.007 TYR O 161 ARG 0.018 0.002 ARG P 344 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16642 Ramachandran restraints generated. 8321 Oldfield, 0 Emsley, 8321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16642 Ramachandran restraints generated. 8321 Oldfield, 0 Emsley, 8321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1980 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 826 poor density : 1154 time to evaluate : 6.176 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: A 98 ASN cc_start: 0.8984 (OUTLIER) cc_final: 0.8585 (p0) REVERT: A 161 MET cc_start: 0.9743 (OUTLIER) cc_final: 0.9312 (mmt) REVERT: A 218 ASP cc_start: 0.9192 (m-30) cc_final: 0.8865 (m-30) REVERT: A 257 MET cc_start: 0.9663 (tpt) cc_final: 0.9418 (tpp) REVERT: A 449 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8913 (mm-40) REVERT: A 459 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: A 483 GLU cc_start: 0.9687 (tt0) cc_final: 0.9485 (pt0) REVERT: A 487 THR cc_start: 0.9572 (p) cc_final: 0.9250 (t) REVERT: A 488 MET cc_start: 0.9188 (ttp) cc_final: 0.8868 (tmm) REVERT: A 637 MET cc_start: 0.9709 (tpp) cc_final: 0.9445 (tmm) REVERT: A 656 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8658 (tt0) REVERT: A 871 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8544 (ttm-80) REVERT: A 1014 ASP cc_start: 0.9013 (t0) cc_final: 0.8276 (t0) REVERT: A 1016 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.8642 (mtm) REVERT: A 1018 ASP cc_start: 0.9166 (t0) cc_final: 0.8629 (t0) REVERT: A 1060 HIS cc_start: 0.8469 (p-80) cc_final: 0.8192 (t-90) REVERT: A 1081 PRO cc_start: 0.9444 (OUTLIER) cc_final: 0.9225 (Cg_exo) REVERT: A 1089 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9455 (tp) REVERT: A 1136 SER cc_start: 0.9288 (OUTLIER) cc_final: 0.9004 (t) REVERT: A 1165 HIS cc_start: 0.9245 (t70) cc_final: 0.8815 (t-90) REVERT: A 1177 MET cc_start: 0.9693 (OUTLIER) cc_final: 0.9113 (tmm) REVERT: A 1220 MET cc_start: 0.9034 (mtp) cc_final: 0.8824 (mtm) REVERT: A 1279 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.9079 (ttt180) REVERT: A 1296 LEU cc_start: 0.9459 (tp) cc_final: 0.9247 (tt) REVERT: A 1320 ASN cc_start: 0.8851 (t0) cc_final: 0.8227 (t0) REVERT: A 1386 TRP cc_start: 0.9202 (OUTLIER) cc_final: 0.8430 (p90) REVERT: A 1463 TYR cc_start: 0.9321 (m-80) cc_final: 0.9021 (m-10) REVERT: A 1480 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8763 (tm-30) REVERT: A 1513 GLU cc_start: 0.9635 (mm-30) cc_final: 0.9432 (mt-10) REVERT: A 1623 ASP cc_start: 0.9345 (t0) cc_final: 0.9126 (t0) REVERT: A 1646 GLN cc_start: 0.9314 (OUTLIER) cc_final: 0.8775 (tp40) REVERT: A 1665 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8645 (pp30) REVERT: A 1734 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8617 (ttp80) REVERT: A 1780 GLU cc_start: 0.9570 (mt-10) cc_final: 0.9306 (tm-30) REVERT: A 1843 MET cc_start: 0.8846 (mtp) cc_final: 0.8033 (mtm) REVERT: A 1861 GLN cc_start: 0.9655 (OUTLIER) cc_final: 0.9368 (pp30) REVERT: A 1885 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9203 (mt) REVERT: B 1 MET cc_start: 0.7426 (mmm) cc_final: 0.6569 (ttm) REVERT: B 16 TRP cc_start: 0.6519 (OUTLIER) cc_final: 0.4820 (t-100) REVERT: B 34 CYS cc_start: 0.7236 (OUTLIER) cc_final: 0.5886 (p) REVERT: B 71 GLN cc_start: 0.8213 (pt0) cc_final: 0.7782 (pp30) REVERT: B 84 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.5813 (mp0) REVERT: C 133 GLU cc_start: 0.9299 (tt0) cc_final: 0.8987 (tm-30) REVERT: C 161 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8820 (mp) REVERT: C 234 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9291 (tp) REVERT: C 238 TYR cc_start: 0.9212 (m-10) cc_final: 0.8907 (m-80) REVERT: C 244 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9137 (mp) REVERT: C 296 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8847 (tpt-90) REVERT: C 298 GLU cc_start: 0.9385 (tt0) cc_final: 0.8971 (mm-30) REVERT: C 343 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9408 (tt) REVERT: C 377 GLU cc_start: 0.9491 (OUTLIER) cc_final: 0.9135 (mm-30) REVERT: C 419 LEU cc_start: 0.9216 (tp) cc_final: 0.8998 (tt) REVERT: C 423 ARG cc_start: 0.9290 (OUTLIER) cc_final: 0.8889 (mtm-85) REVERT: C 432 ASP cc_start: 0.9245 (OUTLIER) cc_final: 0.8576 (t70) REVERT: C 446 LEU cc_start: 0.9434 (tp) cc_final: 0.9121 (mt) REVERT: C 468 MET cc_start: 0.9340 (tpp) cc_final: 0.9015 (mmm) REVERT: D 11 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8227 (ptt-90) REVERT: D 26 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.9059 (pm20) REVERT: D 29 GLU cc_start: 0.9621 (tt0) cc_final: 0.9245 (tm-30) REVERT: D 31 GLN cc_start: 0.9308 (tt0) cc_final: 0.9086 (tm-30) REVERT: D 33 GLN cc_start: 0.9450 (mt0) cc_final: 0.8822 (mt0) REVERT: D 36 GLN cc_start: 0.9614 (mt0) cc_final: 0.9347 (tm-30) REVERT: E 56 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.9061 (mm-30) REVERT: E 61 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.7656 (t80) REVERT: E 80 GLU cc_start: 0.9593 (tp30) cc_final: 0.9318 (pt0) REVERT: E 89 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9323 (mt) REVERT: E 106 THR cc_start: 0.8725 (p) cc_final: 0.8378 (t) REVERT: F 70 GLN cc_start: 0.9626 (OUTLIER) cc_final: 0.9299 (mp10) REVERT: F 104 ASP cc_start: 0.9602 (OUTLIER) cc_final: 0.9338 (t0) REVERT: F 480 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8486 (t0) REVERT: F 534 GLU cc_start: 0.9629 (tp30) cc_final: 0.9283 (tm-30) REVERT: F 581 ARG cc_start: 0.9137 (mtm180) cc_final: 0.8779 (mtt180) REVERT: F 687 LYS cc_start: 0.9734 (mttt) cc_final: 0.9439 (tptp) REVERT: F 735 LYS cc_start: 0.9283 (mttt) cc_final: 0.8958 (mttp) REVERT: G 5 LYS cc_start: 0.9639 (OUTLIER) cc_final: 0.9391 (mtmm) REVERT: G 9 LEU cc_start: 0.9162 (mt) cc_final: 0.8788 (mt) REVERT: G 17 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9363 (tp30) REVERT: G 21 ASN cc_start: 0.9512 (m-40) cc_final: 0.9032 (m-40) REVERT: H 89 GLU cc_start: 0.9667 (tt0) cc_final: 0.9397 (tm-30) REVERT: H 480 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8729 (t0) REVERT: H 492 PRO cc_start: 0.9526 (OUTLIER) cc_final: 0.9300 (Cg_endo) REVERT: H 496 TYR cc_start: 0.9293 (t80) cc_final: 0.8973 (t80) REVERT: H 514 GLU cc_start: 0.9524 (mt-10) cc_final: 0.9270 (tp30) REVERT: H 516 MET cc_start: 0.9400 (mmm) cc_final: 0.9129 (tmm) REVERT: H 536 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.9012 (mmm) REVERT: H 582 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8678 (tp30) REVERT: H 613 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8974 (mp) REVERT: H 629 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.9105 (ttp80) REVERT: H 643 MET cc_start: 0.9482 (mtp) cc_final: 0.9238 (mmm) REVERT: H 699 ASP cc_start: 0.9145 (m-30) cc_final: 0.8920 (t0) REVERT: H 702 ASN cc_start: 0.9516 (OUTLIER) cc_final: 0.8731 (t0) REVERT: H 758 MET cc_start: 0.9460 (tpp) cc_final: 0.9197 (tpt) REVERT: I 80 LEU cc_start: 0.9588 (tp) cc_final: 0.9351 (tp) REVERT: I 94 ASP cc_start: 0.9496 (t0) cc_final: 0.9210 (p0) REVERT: I 138 LEU cc_start: 0.9347 (tp) cc_final: 0.9115 (tp) REVERT: I 269 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9274 (tp) REVERT: I 283 MET cc_start: 0.8735 (mmm) cc_final: 0.8063 (tmm) REVERT: I 337 ILE cc_start: 0.9574 (OUTLIER) cc_final: 0.9365 (mm) REVERT: I 440 MET cc_start: 0.9399 (mmm) cc_final: 0.9066 (mpp) REVERT: I 473 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.9156 (mt-10) REVERT: I 489 PRO cc_start: 0.8908 (OUTLIER) cc_final: 0.8688 (Cg_endo) REVERT: I 553 CYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8570 (t) REVERT: I 600 ILE cc_start: 0.9158 (mt) cc_final: 0.8505 (mp) REVERT: I 632 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8073 (ttm-80) REVERT: I 747 ASP cc_start: 0.8412 (t0) cc_final: 0.8116 (t0) REVERT: J 148 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9174 (tp) REVERT: J 202 ARG cc_start: 0.9344 (OUTLIER) cc_final: 0.8989 (mtm110) REVERT: J 211 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7827 (mmtp) REVERT: J 239 GLU cc_start: 0.9487 (mt-10) cc_final: 0.9238 (mt-10) REVERT: J 258 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.9215 (mmm) REVERT: J 477 GLN cc_start: 0.9317 (OUTLIER) cc_final: 0.8990 (mm110) REVERT: J 510 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8628 (tpt90) REVERT: J 525 MET cc_start: 0.9451 (OUTLIER) cc_final: 0.9202 (tpp) REVERT: K 88 GLN cc_start: 0.9361 (mt0) cc_final: 0.8894 (tp-100) REVERT: K 164 PHE cc_start: 0.9526 (OUTLIER) cc_final: 0.9302 (t80) REVERT: K 165 GLU cc_start: 0.9467 (mt-10) cc_final: 0.9143 (tp30) REVERT: K 194 CYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8778 (p) REVERT: K 195 ASN cc_start: 0.9545 (OUTLIER) cc_final: 0.9082 (t0) REVERT: K 283 GLU cc_start: 0.9731 (OUTLIER) cc_final: 0.9375 (mp0) REVERT: K 343 SER cc_start: 0.9416 (OUTLIER) cc_final: 0.9138 (t) REVERT: K 349 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9072 (mm-30) REVERT: K 363 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9018 (pp) REVERT: K 393 GLN cc_start: 0.9518 (tp40) cc_final: 0.9183 (mm-40) REVERT: K 492 MET cc_start: 0.9296 (ptt) cc_final: 0.8902 (tmm) REVERT: K 496 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8861 (pm20) REVERT: K 518 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8885 (tpt) REVERT: L 12 ASP cc_start: 0.9381 (OUTLIER) cc_final: 0.8872 (t0) REVERT: L 15 GLN cc_start: 0.9493 (mm-40) cc_final: 0.9247 (mp10) REVERT: L 24 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8905 (tp30) REVERT: L 47 ASP cc_start: 0.9260 (m-30) cc_final: 0.8788 (m-30) REVERT: L 66 ILE cc_start: 0.9446 (mt) cc_final: 0.9220 (mt) REVERT: L 67 GLN cc_start: 0.9638 (OUTLIER) cc_final: 0.9190 (mp10) REVERT: L 101 ASN cc_start: 0.9183 (m110) cc_final: 0.8917 (t0) REVERT: L 115 GLU cc_start: 0.9400 (mt-10) cc_final: 0.9032 (tm-30) REVERT: L 137 ILE cc_start: 0.9261 (mt) cc_final: 0.9058 (tt) REVERT: L 147 ASN cc_start: 0.9416 (m-40) cc_final: 0.8968 (t0) REVERT: L 178 MET cc_start: 0.9616 (mtt) cc_final: 0.9398 (mmt) REVERT: M 7 ARG cc_start: 0.8411 (mtt180) cc_final: 0.7876 (mtp85) REVERT: M 8 ASP cc_start: 0.9292 (t0) cc_final: 0.8783 (t0) REVERT: M 11 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8944 (mp) REVERT: M 27 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8819 (tp30) REVERT: M 28 ASP cc_start: 0.9450 (m-30) cc_final: 0.9031 (p0) REVERT: M 55 MET cc_start: 0.9533 (OUTLIER) cc_final: 0.9314 (mmp) REVERT: M 63 GLN cc_start: 0.9561 (OUTLIER) cc_final: 0.9225 (pm20) REVERT: M 66 HIS cc_start: 0.9150 (t-90) cc_final: 0.8729 (t-90) REVERT: N 74 TRP cc_start: 0.8171 (p-90) cc_final: 0.7965 (p-90) REVERT: N 156 MET cc_start: 0.9531 (mmm) cc_final: 0.9302 (tpp) REVERT: N 170 GLN cc_start: 0.9537 (OUTLIER) cc_final: 0.9271 (tp-100) REVERT: N 259 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9010 (mp0) REVERT: N 273 MET cc_start: 0.9437 (ttm) cc_final: 0.9155 (tpp) REVERT: N 277 CYS cc_start: 0.9612 (m) cc_final: 0.9114 (m) REVERT: N 340 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8511 (mmp80) REVERT: N 373 GLN cc_start: 0.9536 (OUTLIER) cc_final: 0.9169 (tm-30) REVERT: N 392 ASN cc_start: 0.9615 (OUTLIER) cc_final: 0.9411 (t0) REVERT: N 564 MET cc_start: 0.8820 (mmp) cc_final: 0.8352 (ptt) REVERT: N 609 LEU cc_start: 0.4232 (OUTLIER) cc_final: 0.3857 (mt) REVERT: N 622 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7418 (m-80) REVERT: N 623 CYS cc_start: 0.7567 (OUTLIER) cc_final: 0.6652 (p) REVERT: N 639 HIS cc_start: 0.7078 (t70) cc_final: 0.6671 (t70) REVERT: N 670 PHE cc_start: 0.1615 (OUTLIER) cc_final: 0.0648 (m-80) REVERT: N 687 MET cc_start: 0.2902 (mtp) cc_final: 0.2441 (mtm) REVERT: N 696 MET cc_start: 0.8699 (tpp) cc_final: 0.8345 (tmm) REVERT: N 708 GLU cc_start: 0.8569 (tt0) cc_final: 0.8343 (pm20) REVERT: O 104 GLU cc_start: 0.9347 (OUTLIER) cc_final: 0.9076 (mt-10) REVERT: O 166 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8085 (pp20) REVERT: O 207 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8336 (tt) REVERT: O 218 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8909 (pp30) REVERT: O 280 ARG cc_start: 0.9556 (OUTLIER) cc_final: 0.9272 (mmm-85) REVERT: O 287 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8954 (mp0) REVERT: O 318 GLN cc_start: 0.9643 (mm110) cc_final: 0.9311 (mp10) REVERT: O 419 ASP cc_start: 0.9339 (m-30) cc_final: 0.8864 (p0) REVERT: O 440 GLN cc_start: 0.9538 (tm-30) cc_final: 0.9217 (tm-30) REVERT: O 475 GLU cc_start: 0.9779 (tt0) cc_final: 0.9473 (pt0) REVERT: O 491 LYS cc_start: 0.9613 (tttt) cc_final: 0.9390 (tptt) REVERT: O 495 GLU cc_start: 0.9500 (OUTLIER) cc_final: 0.9234 (pt0) REVERT: O 567 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9273 (tp) REVERT: O 573 LYS cc_start: 0.9349 (mmtt) cc_final: 0.9026 (mtmm) REVERT: O 575 LYS cc_start: 0.9313 (tttt) cc_final: 0.9046 (mmmt) REVERT: O 636 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.9189 (pt) REVERT: O 649 GLU cc_start: 0.9701 (OUTLIER) cc_final: 0.9369 (tm-30) REVERT: O 654 ASP cc_start: 0.9614 (OUTLIER) cc_final: 0.9298 (p0) REVERT: O 735 MET cc_start: 0.9696 (OUTLIER) cc_final: 0.9207 (mtt) REVERT: O 753 ASN cc_start: 0.9062 (m-40) cc_final: 0.8636 (p0) REVERT: P 70 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8643 (mp) REVERT: P 89 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9409 (tp) REVERT: P 98 GLU cc_start: 0.9601 (OUTLIER) cc_final: 0.9238 (pm20) REVERT: P 128 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8679 (mmmt) REVERT: P 153 GLU cc_start: 0.9651 (mt-10) cc_final: 0.9407 (mp0) REVERT: P 221 PHE cc_start: 0.9359 (m-80) cc_final: 0.8767 (m-80) REVERT: P 298 GLU cc_start: 0.9678 (tt0) cc_final: 0.9247 (mp0) REVERT: P 325 GLU cc_start: 0.9666 (tp30) cc_final: 0.9189 (tm-30) REVERT: P 423 ARG cc_start: 0.9678 (OUTLIER) cc_final: 0.9477 (tpt-90) REVERT: P 441 GLU cc_start: 0.9742 (OUTLIER) cc_final: 0.9519 (mt-10) REVERT: R 44 HIS cc_start: 0.8630 (OUTLIER) cc_final: 0.8185 (t70) REVERT: R 94 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9081 (tp) REVERT: R 128 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8745 (m-80) REVERT: S 361 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8637 (mp0) REVERT: S 387 TYR cc_start: 0.7585 (t80) cc_final: 0.7346 (t80) REVERT: S 395 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8195 (p) REVERT: S 397 LYS cc_start: 0.8165 (mmtp) cc_final: 0.7934 (mmtt) REVERT: S 408 LYS cc_start: 0.7718 (mmmt) cc_final: 0.7512 (ttpt) REVERT: S 411 CYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7431 (p) REVERT: S 412 ASN cc_start: 0.7865 (m-40) cc_final: 0.6997 (t0) REVERT: S 413 TYR cc_start: 0.6969 (t80) cc_final: 0.6696 (t80) REVERT: W 2 LEU cc_start: 0.9464 (tp) cc_final: 0.9142 (tp) REVERT: W 4 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8765 (ptm160) REVERT: W 13 LEU cc_start: 0.9256 (mt) cc_final: 0.8981 (mp) REVERT: W 17 GLU cc_start: 0.9493 (mt-10) cc_final: 0.8975 (tm-30) REVERT: W 21 ASN cc_start: 0.9012 (m-40) cc_final: 0.8660 (m-40) REVERT: X 92 GLU cc_start: 0.9351 (mt-10) cc_final: 0.9037 (mp0) REVERT: X 106 GLN cc_start: 0.9630 (OUTLIER) cc_final: 0.9420 (tt0) REVERT: X 137 GLU cc_start: 0.9747 (mt-10) cc_final: 0.9331 (tm-30) REVERT: X 253 ARG cc_start: 0.9518 (ttm-80) cc_final: 0.9181 (mmm160) REVERT: X 427 MET cc_start: 0.8984 (tmm) cc_final: 0.8653 (tpp) REVERT: Y 71 PHE cc_start: 0.8685 (m-80) cc_final: 0.8033 (m-80) REVERT: Y 92 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8830 (pt0) REVERT: Y 94 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8846 (mtt-85) REVERT: Y 110 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7431 (tt) REVERT: Y 145 CYS cc_start: 0.9610 (m) cc_final: 0.9396 (m) REVERT: Y 173 MET cc_start: 0.9559 (ttp) cc_final: 0.9315 (tmm) REVERT: Y 193 LYS cc_start: 0.9449 (OUTLIER) cc_final: 0.9184 (mtmm) REVERT: Y 294 PHE cc_start: 0.8636 (t80) cc_final: 0.8205 (t80) REVERT: Y 322 GLU cc_start: 0.9629 (mt-10) cc_final: 0.9365 (pm20) REVERT: Y 415 GLU cc_start: 0.9611 (mt-10) cc_final: 0.9406 (mt-10) REVERT: Y 429 MET cc_start: 0.9605 (mtm) cc_final: 0.9382 (ptp) REVERT: Y 509 CYS cc_start: 0.9055 (t) cc_final: 0.8756 (m) REVERT: Y 541 ASN cc_start: 0.9186 (m110) cc_final: 0.8918 (t0) outliers start: 826 outliers final: 249 residues processed: 1824 average time/residue: 0.6974 time to fit residues: 2133.7161 Evaluate side-chains 1090 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 354 poor density : 736 time to evaluate : 6.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 871 ARG Chi-restraints excluded: chain A residue 1016 MET Chi-restraints excluded: chain A residue 1081 PRO Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1646 GLN Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1665 GLN Chi-restraints excluded: chain A residue 1666 ILE Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1734 ARG Chi-restraints excluded: chain A residue 1747 ASP Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1778 LEU Chi-restraints excluded: chain A residue 1854 THR Chi-restraints excluded: chain A residue 1861 GLN Chi-restraints excluded: chain A residue 1885 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 434 ARG Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 480 ASN Chi-restraints excluded: chain F residue 530 ASN Chi-restraints excluded: chain F residue 540 SER Chi-restraints excluded: chain F residue 549 ASP Chi-restraints excluded: chain F residue 582 GLU Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain H residue 66 CYS Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 492 PRO Chi-restraints excluded: chain H residue 494 HIS Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 536 MET Chi-restraints excluded: chain H residue 540 SER Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain H residue 629 ARG Chi-restraints excluded: chain H residue 702 ASN Chi-restraints excluded: chain H residue 762 TRP Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 75 PRO Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 273 CYS Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 337 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 397 ILE Chi-restraints excluded: chain I residue 423 VAL Chi-restraints excluded: chain I residue 472 VAL Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 489 PRO Chi-restraints excluded: chain I residue 505 SER Chi-restraints excluded: chain I residue 536 CYS Chi-restraints excluded: chain I residue 553 CYS Chi-restraints excluded: chain I residue 571 LYS Chi-restraints excluded: chain I residue 632 ARG Chi-restraints excluded: chain I residue 652 VAL Chi-restraints excluded: chain I residue 736 SER Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 211 LYS Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 258 MET Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 298 ASN Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain J residue 497 ASN Chi-restraints excluded: chain J residue 510 ARG Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 164 PHE Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 359 THR Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 376 LEU Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 496 GLU Chi-restraints excluded: chain K residue 497 ASN Chi-restraints excluded: chain K residue 504 THR Chi-restraints excluded: chain K residue 518 MET Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 67 GLN Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 63 GLN Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 75 PHE Chi-restraints excluded: chain N residue 77 GLU Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 202 GLU Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 256 VAL Chi-restraints excluded: chain N residue 340 ARG Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 373 GLN Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain N residue 392 ASN Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 425 ARG Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 498 SER Chi-restraints excluded: chain N residue 513 ASP Chi-restraints excluded: chain N residue 516 ILE Chi-restraints excluded: chain N residue 609 LEU Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 623 CYS Chi-restraints excluded: chain N residue 625 LYS Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 98 LYS Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 104 GLU Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 218 GLN Chi-restraints excluded: chain O residue 257 SER Chi-restraints excluded: chain O residue 280 ARG Chi-restraints excluded: chain O residue 299 SER Chi-restraints excluded: chain O residue 319 GLN Chi-restraints excluded: chain O residue 329 ARG Chi-restraints excluded: chain O residue 345 SER Chi-restraints excluded: chain O residue 367 LYS Chi-restraints excluded: chain O residue 396 ASN Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 417 LEU Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 431 LEU Chi-restraints excluded: chain O residue 435 SER Chi-restraints excluded: chain O residue 495 GLU Chi-restraints excluded: chain O residue 510 CYS Chi-restraints excluded: chain O residue 533 THR Chi-restraints excluded: chain O residue 567 LEU Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 623 THR Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 632 LEU Chi-restraints excluded: chain O residue 634 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 649 GLU Chi-restraints excluded: chain O residue 654 ASP Chi-restraints excluded: chain O residue 657 ILE Chi-restraints excluded: chain O residue 735 MET Chi-restraints excluded: chain O residue 752 ILE Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 71 GLN Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 97 LYS Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 183 ASP Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 268 GLN Chi-restraints excluded: chain P residue 300 MET Chi-restraints excluded: chain P residue 303 PHE Chi-restraints excluded: chain P residue 321 HIS Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 423 ARG Chi-restraints excluded: chain P residue 441 GLU Chi-restraints excluded: chain P residue 495 GLN Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 57 TRP Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 488 LEU Chi-restraints excluded: chain R residue 492 ILE Chi-restraints excluded: chain S residue 321 PHE Chi-restraints excluded: chain S residue 326 LYS Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain S residue 411 CYS Chi-restraints excluded: chain W residue 4 ARG Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 106 GLN Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain X residue 465 LEU Chi-restraints excluded: chain X residue 506 GLN Chi-restraints excluded: chain Y residue 94 ARG Chi-restraints excluded: chain Y residue 110 LEU Chi-restraints excluded: chain Y residue 193 LYS Chi-restraints excluded: chain Y residue 198 GLN Chi-restraints excluded: chain Y residue 199 CYS Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Y residue 303 TYR Chi-restraints excluded: chain Y residue 366 ILE Chi-restraints excluded: chain Y residue 418 LEU Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 506 GLN Chi-restraints excluded: chain Y residue 551 LYS Chi-restraints excluded: chain Y residue 552 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 707 optimal weight: 7.9990 chunk 635 optimal weight: 0.2980 chunk 352 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 428 optimal weight: 0.9990 chunk 339 optimal weight: 7.9990 chunk 656 optimal weight: 0.9990 chunk 254 optimal weight: 3.9990 chunk 399 optimal weight: 6.9990 chunk 488 optimal weight: 4.9990 chunk 760 optimal weight: 5.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN A 155 GLN A 176 GLN A 179 ASN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN A 266 HIS ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN A 792 GLN A 846 GLN A1165 HIS A1184 HIS ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1247 HIS A1309 HIS A1380 ASN A1453 ASN ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1665 GLN A1798 GLN A1895 HIS ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 HIS B 78 GLN C 107 HIS C 202 HIS C 287 ASN C 299 ASN C 305 ASN C 321 HIS C 347 HIS C 373 HIS C 407 GLN ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN F 14 GLN F 64 HIS F 517 GLN F 595 GLN F 634 HIS F 636 ASN F 657 HIS H 166 GLN H 480 ASN H 517 GLN H 545 HIS H 595 GLN H 599 ASN H 634 HIS H 648 GLN ** H 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 716 ASN H 754 HIS H 759 ASN ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN I 374 GLN ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 455 HIS I 535 GLN J 16 GLN J 38 GLN J 58 HIS J 80 HIS J 271 HIS J 298 ASN J 316 ASN ** J 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 GLN J 382 ASN J 393 GLN J 406 HIS ** J 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 477 GLN K 18 GLN K 38 GLN K 45 GLN K 80 HIS K 264 HIS K 271 HIS K 316 ASN K 352 GLN K 362 GLN L 101 ASN L 146 GLN ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 370 GLN N 392 ASN ** N 517 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 671 GLN O 62 GLN O 91 ASN O 219 GLN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 242 ASN O 247 ASN O 319 GLN O 387 GLN O 424 GLN ** O 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN O 449 ASN O 472 HIS O 539 ASN O 556 GLN O 565 GLN O 671 GLN O 693 ASN O 754 HIS P 71 GLN ** P 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 287 ASN P 299 ASN P 305 ASN P 321 HIS P 347 HIS P 355 GLN P 361 ASN P 485 GLN R 60 ASN ** R 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 GLN R 350 GLN T 6 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 151 GLN X 166 GLN X 337 GLN X 338 HIS ** X 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 471 GLN ** X 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Y 151 GLN Y 296 GLN Y 326 ASN Y 338 HIS Y 471 GLN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 541 ASN Y 550 GLN Total number of N/Q/H flips: 122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 67835 Z= 0.302 Angle : 0.902 26.947 91891 Z= 0.460 Chirality : 0.047 0.421 10362 Planarity : 0.006 0.192 11673 Dihedral : 10.993 106.036 9934 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.87 % Allowed : 4.57 % Favored : 94.57 % Rotamer: Outliers : 7.45 % Allowed : 17.55 % Favored : 75.00 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.35 % Twisted Proline : 0.65 % Twisted General : 0.15 % 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: 0.02 (0.09), residues: 8323 helix: 0.96 (0.07), residues: 5436 sheet: -0.46 (0.20), residues: 587 loop : -2.12 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP N 232 HIS 0.016 0.002 HIS X 395 PHE 0.045 0.002 PHE N 180 TYR 0.085 0.002 TYR X 355 ARG 0.015 0.001 ARG N 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1417 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 519 poor density : 898 time to evaluate : 6.118 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: A 11 MET cc_start: 0.6697 (mmt) cc_final: 0.6455 (mpp) REVERT: A 90 ASP cc_start: 0.9695 (OUTLIER) cc_final: 0.9263 (p0) REVERT: A 170 ILE cc_start: 0.9402 (mt) cc_final: 0.9172 (mm) REVERT: A 449 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8883 (mp10) REVERT: A 483 GLU cc_start: 0.9667 (tt0) cc_final: 0.9426 (pt0) REVERT: A 487 THR cc_start: 0.9579 (p) cc_final: 0.9297 (t) REVERT: A 617 LEU cc_start: 0.9285 (mm) cc_final: 0.8793 (tp) REVERT: A 656 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: A 668 MET cc_start: 0.7888 (mpp) cc_final: 0.7609 (mpp) REVERT: A 871 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8360 (ttm-80) REVERT: A 934 MET cc_start: 0.9750 (ttp) cc_final: 0.9382 (tpp) REVERT: A 945 GLU cc_start: 0.9407 (OUTLIER) cc_final: 0.9137 (mt-10) REVERT: A 1060 HIS cc_start: 0.8211 (p-80) cc_final: 0.7932 (t-90) REVERT: A 1107 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8820 (mt) REVERT: A 1177 MET cc_start: 0.9596 (OUTLIER) cc_final: 0.9337 (tmm) REVERT: A 1203 MET cc_start: 0.9176 (tpp) cc_final: 0.8601 (mmt) REVERT: A 1209 LEU cc_start: 0.9307 (mt) cc_final: 0.9014 (mp) REVERT: A 1225 THR cc_start: 0.9752 (OUTLIER) cc_final: 0.9546 (p) REVERT: A 1242 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6810 (tm-30) REVERT: A 1296 LEU cc_start: 0.9470 (tp) cc_final: 0.9186 (tt) REVERT: A 1320 ASN cc_start: 0.8484 (t0) cc_final: 0.8072 (t0) REVERT: A 1325 LEU cc_start: 0.9552 (mt) cc_final: 0.9347 (mp) REVERT: A 1373 MET cc_start: 0.9621 (mmm) cc_final: 0.9329 (mtp) REVERT: A 1383 ILE cc_start: 0.8807 (mt) cc_final: 0.8565 (mp) REVERT: A 1386 TRP cc_start: 0.8800 (OUTLIER) cc_final: 0.8587 (p-90) REVERT: A 1397 ASP cc_start: 0.9227 (m-30) cc_final: 0.8862 (t70) REVERT: A 1463 TYR cc_start: 0.9172 (m-80) cc_final: 0.8926 (m-10) REVERT: A 1480 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8611 (tm-30) REVERT: A 1496 MET cc_start: 0.9533 (mtp) cc_final: 0.9266 (ptt) REVERT: A 1550 MET cc_start: 0.8109 (tpp) cc_final: 0.7788 (mmt) REVERT: A 1623 ASP cc_start: 0.9328 (t0) cc_final: 0.9074 (t0) REVERT: A 1646 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8615 (tp40) REVERT: A 1656 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8959 (mp) REVERT: A 1665 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8390 (pm20) REVERT: A 1756 TYR cc_start: 0.9048 (m-80) cc_final: 0.8754 (m-80) REVERT: A 1816 GLN cc_start: 0.8961 (mt0) cc_final: 0.8650 (mt0) REVERT: A 1861 GLN cc_start: 0.9639 (OUTLIER) cc_final: 0.9419 (pp30) REVERT: B 1 MET cc_start: 0.7495 (mmm) cc_final: 0.6621 (ttt) REVERT: B 16 TRP cc_start: 0.6508 (OUTLIER) cc_final: 0.5294 (t-100) REVERT: B 43 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6966 (t0) REVERT: B 50 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8675 (pm20) REVERT: B 71 GLN cc_start: 0.8070 (pt0) cc_final: 0.7791 (pp30) REVERT: B 79 GLU cc_start: 0.7103 (pp20) cc_final: 0.6409 (tm-30) REVERT: B 84 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5685 (mp0) REVERT: C 84 MET cc_start: 0.9428 (tpp) cc_final: 0.9200 (tpp) REVERT: C 89 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9337 (tp) REVERT: C 133 GLU cc_start: 0.9233 (tt0) cc_final: 0.8868 (tm-30) REVERT: C 161 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8748 (mp) REVERT: C 168 ASP cc_start: 0.9237 (t70) cc_final: 0.8889 (m-30) REVERT: C 202 HIS cc_start: 0.9491 (OUTLIER) cc_final: 0.8888 (t-90) REVERT: C 218 MET cc_start: 0.9541 (ttp) cc_final: 0.8962 (ptm) REVERT: C 234 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9131 (tp) REVERT: C 238 TYR cc_start: 0.9271 (m-10) cc_final: 0.8939 (m-80) REVERT: C 244 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.8628 (mm) REVERT: C 298 GLU cc_start: 0.9269 (tt0) cc_final: 0.8920 (mm-30) REVERT: C 455 CYS cc_start: 0.9602 (m) cc_final: 0.9208 (m) REVERT: D 29 GLU cc_start: 0.9548 (tt0) cc_final: 0.9308 (tm-30) REVERT: D 31 GLN cc_start: 0.9240 (tt0) cc_final: 0.8865 (tm-30) REVERT: D 35 GLN cc_start: 0.9292 (pp30) cc_final: 0.9048 (pp30) REVERT: D 36 GLN cc_start: 0.9620 (OUTLIER) cc_final: 0.9349 (tm-30) REVERT: D 42 GLN cc_start: 0.9600 (mt0) cc_final: 0.9344 (mp10) REVERT: E 56 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.9015 (mm-30) REVERT: E 86 VAL cc_start: 0.8804 (t) cc_final: 0.8559 (t) REVERT: E 90 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.9046 (mp0) REVERT: E 97 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8625 (tptp) REVERT: F 534 GLU cc_start: 0.9314 (tp30) cc_final: 0.8716 (tm-30) REVERT: F 562 MET cc_start: 0.8560 (ppp) cc_final: 0.8337 (ppp) REVERT: F 568 GLU cc_start: 0.9471 (mt-10) cc_final: 0.9163 (mp0) REVERT: F 735 LYS cc_start: 0.9264 (mttt) cc_final: 0.9014 (mttp) REVERT: F 762 TRP cc_start: 0.9032 (m-10) cc_final: 0.8784 (m-10) REVERT: G 5 LYS cc_start: 0.9618 (OUTLIER) cc_final: 0.9374 (mtmm) REVERT: G 14 GLU cc_start: 0.9460 (mp0) cc_final: 0.9199 (mp0) REVERT: G 17 GLU cc_start: 0.9567 (mt-10) cc_final: 0.9274 (tm-30) REVERT: G 20 GLU cc_start: 0.9662 (mm-30) cc_final: 0.9362 (pt0) REVERT: G 21 ASN cc_start: 0.9410 (m-40) cc_final: 0.8612 (m-40) REVERT: H 47 CYS cc_start: 0.9731 (m) cc_final: 0.9478 (m) REVERT: H 89 GLU cc_start: 0.9696 (tt0) cc_final: 0.9425 (tm-30) REVERT: H 496 TYR cc_start: 0.8963 (t80) cc_final: 0.8442 (t80) REVERT: H 584 ASP cc_start: 0.9279 (OUTLIER) cc_final: 0.9002 (p0) REVERT: H 643 MET cc_start: 0.9336 (mtp) cc_final: 0.9090 (mmm) REVERT: H 762 TRP cc_start: 0.8740 (OUTLIER) cc_final: 0.8427 (t60) REVERT: I 40 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9095 (p) REVERT: I 94 ASP cc_start: 0.9475 (t0) cc_final: 0.9175 (p0) REVERT: I 99 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8871 (mp0) REVERT: I 113 MET cc_start: 0.9099 (ptp) cc_final: 0.8838 (ptt) REVERT: I 116 MET cc_start: 0.8984 (ppp) cc_final: 0.8751 (ppp) REVERT: I 237 GLU cc_start: 0.9527 (tt0) cc_final: 0.9141 (tm-30) REVERT: I 283 MET cc_start: 0.8581 (mmm) cc_final: 0.7806 (tmm) REVERT: I 473 GLU cc_start: 0.9430 (OUTLIER) cc_final: 0.9140 (mt-10) REVERT: I 569 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9009 (mp) REVERT: I 705 MET cc_start: 0.8287 (mmm) cc_final: 0.8065 (mmm) REVERT: I 717 MET cc_start: 0.8379 (tpt) cc_final: 0.8076 (tpt) REVERT: J 180 GLU cc_start: 0.9609 (OUTLIER) cc_final: 0.9389 (mp0) REVERT: J 202 ARG cc_start: 0.9596 (OUTLIER) cc_final: 0.9291 (mtm110) REVERT: J 288 SER cc_start: 0.9481 (m) cc_final: 0.9272 (p) REVERT: J 400 GLU cc_start: 0.9336 (OUTLIER) cc_final: 0.9069 (pm20) REVERT: J 448 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9076 (mm) REVERT: J 477 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8919 (mm110) REVERT: K 194 CYS cc_start: 0.9513 (OUTLIER) cc_final: 0.9196 (t) REVERT: K 277 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9095 (mp0) REVERT: K 283 GLU cc_start: 0.9727 (mm-30) cc_final: 0.9441 (mp0) REVERT: K 354 MET cc_start: 0.9531 (tpp) cc_final: 0.8948 (mpp) REVERT: K 492 MET cc_start: 0.9276 (ptt) cc_final: 0.8930 (tmm) REVERT: L 12 ASP cc_start: 0.9455 (OUTLIER) cc_final: 0.9134 (t0) REVERT: L 63 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.8999 (mt) REVERT: L 66 ILE cc_start: 0.9342 (mt) cc_final: 0.8971 (mt) REVERT: L 67 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.8499 (mp10) REVERT: L 71 LYS cc_start: 0.9128 (tttm) cc_final: 0.8844 (ttmm) REVERT: L 102 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: L 147 ASN cc_start: 0.9318 (m-40) cc_final: 0.8694 (t0) REVERT: L 150 ASP cc_start: 0.8638 (m-30) cc_final: 0.8110 (t0) REVERT: L 151 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8522 (p) REVERT: L 156 ILE cc_start: 0.9629 (mt) cc_final: 0.9260 (mm) REVERT: L 158 ILE cc_start: 0.9304 (tt) cc_final: 0.9004 (mp) REVERT: M 7 ARG cc_start: 0.8387 (mtt180) cc_final: 0.8116 (mtp85) REVERT: M 8 ASP cc_start: 0.9131 (t0) cc_final: 0.8781 (t0) REVERT: M 27 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8551 (tp30) REVERT: M 28 ASP cc_start: 0.9359 (m-30) cc_final: 0.8824 (p0) REVERT: M 63 GLN cc_start: 0.9519 (tp40) cc_final: 0.9079 (pm20) REVERT: M 66 HIS cc_start: 0.9163 (t-90) cc_final: 0.8905 (t70) REVERT: N 170 GLN cc_start: 0.9465 (OUTLIER) cc_final: 0.8956 (tp-100) REVERT: N 181 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9390 (tp) REVERT: N 277 CYS cc_start: 0.9566 (m) cc_final: 0.9304 (p) REVERT: N 361 LEU cc_start: 0.9492 (tp) cc_final: 0.9279 (tp) REVERT: N 373 GLN cc_start: 0.9568 (OUTLIER) cc_final: 0.9197 (tp-100) REVERT: N 622 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.6912 (m-80) REVERT: N 632 MET cc_start: 0.8545 (mpp) cc_final: 0.8156 (mpp) REVERT: N 670 PHE cc_start: 0.2921 (OUTLIER) cc_final: 0.1860 (m-80) REVERT: N 696 MET cc_start: 0.8607 (tpp) cc_final: 0.8348 (tmm) REVERT: O 44 MET cc_start: 0.9314 (ttp) cc_final: 0.9039 (ppp) REVERT: O 104 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.8998 (mm-30) REVERT: O 218 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8664 (pp30) REVERT: O 280 ARG cc_start: 0.9573 (OUTLIER) cc_final: 0.9226 (mmm-85) REVERT: O 287 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8969 (mp0) REVERT: O 419 ASP cc_start: 0.9252 (m-30) cc_final: 0.8879 (p0) REVERT: O 440 GLN cc_start: 0.9324 (tm-30) cc_final: 0.8955 (tm-30) REVERT: O 510 CYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9205 (m) REVERT: O 539 ASN cc_start: 0.9332 (OUTLIER) cc_final: 0.9107 (t0) REVERT: O 636 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8964 (pt) REVERT: O 654 ASP cc_start: 0.9629 (OUTLIER) cc_final: 0.9317 (p0) REVERT: O 660 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8531 (mttp) REVERT: O 680 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7350 (pm20) REVERT: O 735 MET cc_start: 0.9563 (OUTLIER) cc_final: 0.9204 (mtt) REVERT: P 70 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8386 (mp) REVERT: P 128 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8707 (mmmt) REVERT: P 246 GLU cc_start: 0.9537 (tp30) cc_final: 0.9314 (tm-30) REVERT: P 295 TYR cc_start: 0.9523 (m-80) cc_final: 0.9261 (m-80) REVERT: P 298 GLU cc_start: 0.9559 (tt0) cc_final: 0.9309 (mp0) REVERT: P 325 GLU cc_start: 0.9590 (tp30) cc_final: 0.9279 (tm-30) REVERT: P 328 LYS cc_start: 0.9210 (ttmt) cc_final: 0.8984 (tptt) REVERT: P 524 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7353 (mmpt) REVERT: S 361 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8635 (mp0) REVERT: S 362 PHE cc_start: 0.7816 (m-80) cc_final: 0.7403 (m-80) REVERT: S 375 LEU cc_start: 0.8171 (mp) cc_final: 0.7701 (tp) REVERT: S 386 LYS cc_start: 0.7960 (tppt) cc_final: 0.7501 (mmmm) REVERT: S 393 ARG cc_start: 0.8248 (ttt-90) cc_final: 0.8012 (ttt-90) REVERT: S 397 LYS cc_start: 0.8479 (mmtp) cc_final: 0.8179 (mmtt) REVERT: S 411 CYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7787 (p) REVERT: S 412 ASN cc_start: 0.7631 (m-40) cc_final: 0.6802 (t0) REVERT: S 413 TYR cc_start: 0.6401 (t80) cc_final: 0.6179 (t80) REVERT: W 2 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8888 (mp) REVERT: W 9 LEU cc_start: 0.9356 (mt) cc_final: 0.9005 (mt) REVERT: W 17 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8733 (tm-30) REVERT: W 21 ASN cc_start: 0.8955 (m-40) cc_final: 0.8229 (m-40) REVERT: X 92 GLU cc_start: 0.9314 (mt-10) cc_final: 0.9107 (tp30) REVERT: X 137 GLU cc_start: 0.9679 (mt-10) cc_final: 0.9362 (tm-30) REVERT: X 253 ARG cc_start: 0.9573 (ttm-80) cc_final: 0.9236 (mmm160) REVERT: X 360 TYR cc_start: 0.8676 (m-80) cc_final: 0.8334 (m-80) REVERT: X 395 HIS cc_start: 0.8574 (m-70) cc_final: 0.8321 (m90) REVERT: X 427 MET cc_start: 0.8960 (tmm) cc_final: 0.8616 (tpp) REVERT: Y 52 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8874 (m-40) REVERT: Y 71 PHE cc_start: 0.8760 (m-80) cc_final: 0.7770 (m-80) REVERT: Y 94 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8982 (mtt-85) REVERT: Y 173 MET cc_start: 0.9517 (ttp) cc_final: 0.9314 (tmm) REVERT: Y 222 MET cc_start: 0.9330 (mmm) cc_final: 0.9119 (mmm) REVERT: Y 304 LEU cc_start: 0.9210 (mt) cc_final: 0.8922 (mt) REVERT: Y 541 ASN cc_start: 0.9203 (m-40) cc_final: 0.8983 (t0) outliers start: 519 outliers final: 203 residues processed: 1316 average time/residue: 0.6307 time to fit residues: 1423.7201 Evaluate side-chains 964 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 696 time to evaluate : 6.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 871 ARG Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1361 ASP Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1413 LEU Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1646 GLN Chi-restraints excluded: chain A residue 1650 GLU Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1665 GLN Chi-restraints excluded: chain A residue 1666 ILE Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1854 THR Chi-restraints excluded: chain A residue 1861 GLN Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 434 ARG Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 36 GLN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 549 ASP Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 685 SER Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 494 HIS Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 536 MET Chi-restraints excluded: chain H residue 584 ASP Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain H residue 704 LEU Chi-restraints excluded: chain H residue 762 TRP Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 273 CYS Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 569 LEU Chi-restraints excluded: chain I residue 652 VAL Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 343 SER Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 400 GLU Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain J residue 485 ILE Chi-restraints excluded: chain J residue 497 ASN Chi-restraints excluded: chain J residue 500 ASP Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 359 THR Chi-restraints excluded: chain K residue 407 GLU Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 497 ASN Chi-restraints excluded: chain K residue 518 MET Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 67 GLN Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 299 TRP Chi-restraints excluded: chain N residue 373 GLN Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 513 ASP Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 625 LYS Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 104 GLU Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 218 GLN Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 257 SER Chi-restraints excluded: chain O residue 280 ARG Chi-restraints excluded: chain O residue 299 SER Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain O residue 396 ASN Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 417 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 510 CYS Chi-restraints excluded: chain O residue 539 ASN Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 634 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 654 ASP Chi-restraints excluded: chain O residue 660 LYS Chi-restraints excluded: chain O residue 680 GLN Chi-restraints excluded: chain O residue 735 MET Chi-restraints excluded: chain O residue 752 ILE Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 300 MET Chi-restraints excluded: chain P residue 302 THR Chi-restraints excluded: chain P residue 321 HIS Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 382 SER Chi-restraints excluded: chain P residue 435 MET Chi-restraints excluded: chain P residue 441 GLU Chi-restraints excluded: chain P residue 524 LYS Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 57 TRP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 488 LEU Chi-restraints excluded: chain S residue 326 LYS Chi-restraints excluded: chain S residue 389 CYS Chi-restraints excluded: chain S residue 401 CYS Chi-restraints excluded: chain S residue 411 CYS Chi-restraints excluded: chain W residue 2 LEU Chi-restraints excluded: chain W residue 4 ARG Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 329 CYS Chi-restraints excluded: chain X residue 450 VAL Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain X residue 465 LEU Chi-restraints excluded: chain X residue 506 GLN Chi-restraints excluded: chain Y residue 52 ASN Chi-restraints excluded: chain Y residue 94 ARG Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 198 GLN Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 303 TYR Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 506 GLN Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 520 VAL Chi-restraints excluded: chain Y residue 551 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 422 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 633 optimal weight: 7.9990 chunk 518 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 762 optimal weight: 0.0770 chunk 823 optimal weight: 9.9990 chunk 678 optimal weight: 10.0000 chunk 756 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 611 optimal weight: 10.0000 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 125 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN A 619 GLN A 936 ASN A1021 HIS ** A1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN C 202 HIS C 540 ASN ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 545 HIS H 599 ASN H 609 HIS ** H 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 HIS I 257 HIS I 676 ASN J 18 GLN J 264 HIS ** J 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 453 HIS ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 503 HIS K 86 HIS ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN ** N 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 GLN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN O 552 GLN O 556 GLN O 753 ASN P 299 ASN P 339 ASN P 495 GLN ** R 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 242 ASN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 GLN ** X 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 251 ASN Y 326 ASN Y 374 GLN Y 395 HIS Y 458 GLN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 67835 Z= 0.307 Angle : 0.785 18.932 91891 Z= 0.401 Chirality : 0.044 0.279 10362 Planarity : 0.005 0.095 11673 Dihedral : 8.748 98.688 9539 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.35 % Favored : 94.00 % Rotamer: Outliers : 6.49 % Allowed : 19.27 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.36 % Twisted Proline : 0.65 % Twisted General : 0.09 % 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: 0.51 (0.09), residues: 8323 helix: 1.33 (0.07), residues: 5462 sheet: -0.35 (0.21), residues: 571 loop : -1.91 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 641 HIS 0.015 0.001 HIS B 53 PHE 0.026 0.002 PHE N 180 TYR 0.042 0.002 TYR X 355 ARG 0.020 0.001 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 452 poor density : 708 time to evaluate : 6.108 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: A 11 MET cc_start: 0.7023 (mmt) cc_final: 0.6321 (mpp) REVERT: A 90 ASP cc_start: 0.9587 (OUTLIER) cc_final: 0.9303 (p0) REVERT: A 159 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8947 (tt) REVERT: A 161 MET cc_start: 0.9232 (mpp) cc_final: 0.9019 (mmt) REVERT: A 170 ILE cc_start: 0.9323 (mt) cc_final: 0.9032 (mm) REVERT: A 449 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8806 (mp10) REVERT: A 483 GLU cc_start: 0.9635 (tt0) cc_final: 0.9307 (tm-30) REVERT: A 488 MET cc_start: 0.9080 (ppp) cc_final: 0.8649 (tmm) REVERT: A 617 LEU cc_start: 0.9172 (mm) cc_final: 0.8787 (tp) REVERT: A 656 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: A 781 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8759 (mp0) REVERT: A 788 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8577 (tm-30) REVERT: A 871 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8340 (ttp-110) REVERT: A 945 GLU cc_start: 0.9471 (OUTLIER) cc_final: 0.9176 (mt-10) REVERT: A 1073 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9241 (mm) REVERT: A 1075 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8582 (mm110) REVERT: A 1152 GLN cc_start: 0.9674 (pt0) cc_final: 0.9417 (pm20) REVERT: A 1320 ASN cc_start: 0.8512 (t0) cc_final: 0.8184 (t0) REVERT: A 1373 MET cc_start: 0.9646 (mmm) cc_final: 0.9407 (mtp) REVERT: A 1376 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9568 (tt) REVERT: A 1386 TRP cc_start: 0.9040 (OUTLIER) cc_final: 0.8744 (p-90) REVERT: A 1397 ASP cc_start: 0.9252 (m-30) cc_final: 0.8869 (t70) REVERT: A 1463 TYR cc_start: 0.9152 (m-80) cc_final: 0.8908 (m-10) REVERT: A 1623 ASP cc_start: 0.9315 (t0) cc_final: 0.9073 (t0) REVERT: A 1646 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8618 (tp40) REVERT: A 1665 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8380 (pm20) REVERT: A 1861 GLN cc_start: 0.9614 (OUTLIER) cc_final: 0.9335 (pp30) REVERT: B 1 MET cc_start: 0.7113 (mmm) cc_final: 0.6332 (ttt) REVERT: B 16 TRP cc_start: 0.6785 (OUTLIER) cc_final: 0.5736 (t-100) REVERT: B 43 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6919 (t0) REVERT: B 84 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.4470 (mp0) REVERT: C 84 MET cc_start: 0.9402 (tpp) cc_final: 0.9160 (tpp) REVERT: C 133 GLU cc_start: 0.9247 (tt0) cc_final: 0.9035 (pt0) REVERT: C 161 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8763 (mp) REVERT: C 168 ASP cc_start: 0.9223 (t70) cc_final: 0.8895 (m-30) REVERT: C 202 HIS cc_start: 0.9435 (OUTLIER) cc_final: 0.8947 (t70) REVERT: C 234 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9189 (tp) REVERT: C 238 TYR cc_start: 0.9238 (m-10) cc_final: 0.8914 (m-80) REVERT: C 244 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8631 (mm) REVERT: C 257 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.8971 (m) REVERT: C 468 MET cc_start: 0.9020 (mmm) cc_final: 0.8764 (mtm) REVERT: C 476 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8993 (mm) REVERT: C 490 TYR cc_start: 0.9464 (m-80) cc_final: 0.9007 (m-80) REVERT: D 29 GLU cc_start: 0.9564 (tt0) cc_final: 0.9214 (tm-30) REVERT: D 31 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8676 (pp30) REVERT: D 32 GLN cc_start: 0.9413 (tt0) cc_final: 0.9168 (tm-30) REVERT: D 35 GLN cc_start: 0.9300 (pp30) cc_final: 0.8966 (pp30) REVERT: D 36 GLN cc_start: 0.9598 (mt0) cc_final: 0.9319 (tm-30) REVERT: D 42 GLN cc_start: 0.9561 (mt0) cc_final: 0.8899 (tm-30) REVERT: E 56 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8930 (mm-30) REVERT: E 80 GLU cc_start: 0.9543 (tp30) cc_final: 0.9266 (pt0) REVERT: F 128 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8751 (p) REVERT: F 534 GLU cc_start: 0.9226 (tp30) cc_final: 0.8629 (tt0) REVERT: F 568 GLU cc_start: 0.9470 (mt-10) cc_final: 0.9190 (mp0) REVERT: F 735 LYS cc_start: 0.9290 (mttt) cc_final: 0.9005 (mttp) REVERT: G 5 LYS cc_start: 0.9618 (pmtt) cc_final: 0.9401 (mtmm) REVERT: G 20 GLU cc_start: 0.9672 (mm-30) cc_final: 0.9335 (tp30) REVERT: G 21 ASN cc_start: 0.9316 (m-40) cc_final: 0.8997 (m110) REVERT: H 89 GLU cc_start: 0.9715 (tt0) cc_final: 0.9446 (tm-30) REVERT: H 496 TYR cc_start: 0.9045 (t80) cc_final: 0.8815 (t80) REVERT: H 536 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8740 (mmp) REVERT: H 643 MET cc_start: 0.9286 (mtp) cc_final: 0.9054 (mmm) REVERT: H 699 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8593 (t0) REVERT: I 185 ILE cc_start: 0.9755 (OUTLIER) cc_final: 0.9480 (tp) REVERT: I 473 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.9086 (tm-30) REVERT: I 632 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8064 (ttm110) REVERT: I 717 MET cc_start: 0.8319 (tpt) cc_final: 0.7574 (tpt) REVERT: J 47 LEU cc_start: 0.9552 (mt) cc_final: 0.9308 (mt) REVERT: J 202 ARG cc_start: 0.9601 (OUTLIER) cc_final: 0.9327 (mtm110) REVERT: J 400 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.9080 (pm20) REVERT: J 444 TRP cc_start: 0.8552 (m100) cc_final: 0.8281 (m100) REVERT: J 477 GLN cc_start: 0.9441 (OUTLIER) cc_final: 0.9108 (mm110) REVERT: K 8 LYS cc_start: 0.9612 (OUTLIER) cc_final: 0.9300 (pttm) REVERT: K 190 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8102 (tp) REVERT: K 283 GLU cc_start: 0.9714 (mm-30) cc_final: 0.9412 (mp0) REVERT: K 354 MET cc_start: 0.9556 (tpp) cc_final: 0.8963 (mpp) REVERT: K 395 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9488 (pp) REVERT: K 454 VAL cc_start: 0.9395 (OUTLIER) cc_final: 0.9194 (p) REVERT: L 12 ASP cc_start: 0.9448 (OUTLIER) cc_final: 0.9071 (t0) REVERT: L 63 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9073 (mt) REVERT: L 71 LYS cc_start: 0.9080 (tttm) cc_final: 0.8691 (ttmm) REVERT: L 115 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8990 (tp30) REVERT: L 147 ASN cc_start: 0.9191 (m-40) cc_final: 0.8626 (t0) REVERT: L 150 ASP cc_start: 0.8788 (m-30) cc_final: 0.8241 (t0) REVERT: L 177 PHE cc_start: 0.9190 (m-80) cc_final: 0.8863 (m-80) REVERT: L 178 MET cc_start: 0.9285 (mmm) cc_final: 0.8960 (mmm) REVERT: L 181 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.8936 (ttp80) REVERT: M 7 ARG cc_start: 0.8409 (mtt180) cc_final: 0.8126 (mmm-85) REVERT: M 8 ASP cc_start: 0.9151 (t0) cc_final: 0.8948 (t0) REVERT: M 10 ARG cc_start: 0.8909 (ttp80) cc_final: 0.8615 (ttp80) REVERT: M 22 ASP cc_start: 0.9007 (t0) cc_final: 0.8664 (t0) REVERT: M 27 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8505 (tp30) REVERT: M 28 ASP cc_start: 0.9328 (m-30) cc_final: 0.8635 (p0) REVERT: N 277 CYS cc_start: 0.9616 (OUTLIER) cc_final: 0.9177 (p) REVERT: N 299 TRP cc_start: 0.9100 (OUTLIER) cc_final: 0.8362 (t-100) REVERT: N 361 LEU cc_start: 0.9505 (tp) cc_final: 0.9177 (tp) REVERT: N 373 GLN cc_start: 0.9642 (OUTLIER) cc_final: 0.9237 (tm-30) REVERT: N 622 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: N 632 MET cc_start: 0.8495 (mpp) cc_final: 0.8167 (mpp) REVERT: N 653 ARG cc_start: 0.6706 (mmm160) cc_final: 0.6429 (mmm160) REVERT: N 670 PHE cc_start: 0.2938 (OUTLIER) cc_final: 0.2037 (m-80) REVERT: N 696 MET cc_start: 0.8579 (tpp) cc_final: 0.8363 (tmm) REVERT: N 705 LEU cc_start: 0.5776 (OUTLIER) cc_final: 0.5538 (mt) REVERT: O 287 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8990 (mp0) REVERT: O 419 ASP cc_start: 0.9260 (m-30) cc_final: 0.8904 (p0) REVERT: O 440 GLN cc_start: 0.9369 (tm-30) cc_final: 0.8925 (tm-30) REVERT: O 636 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8942 (pt) REVERT: O 654 ASP cc_start: 0.9621 (OUTLIER) cc_final: 0.9417 (p0) REVERT: O 735 MET cc_start: 0.9551 (OUTLIER) cc_final: 0.9170 (mtt) REVERT: P 148 ASN cc_start: 0.8860 (m110) cc_final: 0.8582 (p0) REVERT: P 246 GLU cc_start: 0.9543 (tp30) cc_final: 0.9329 (tm-30) REVERT: P 295 TYR cc_start: 0.9523 (m-80) cc_final: 0.9313 (m-80) REVERT: P 298 GLU cc_start: 0.9519 (tt0) cc_final: 0.9273 (mp0) REVERT: P 325 GLU cc_start: 0.9640 (tp30) cc_final: 0.9298 (tm-30) REVERT: S 361 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8507 (mp0) REVERT: S 362 PHE cc_start: 0.7669 (m-80) cc_final: 0.7366 (m-80) REVERT: S 375 LEU cc_start: 0.7928 (mp) cc_final: 0.7479 (tt) REVERT: S 386 LYS cc_start: 0.8067 (tppt) cc_final: 0.7703 (mmmm) REVERT: S 411 CYS cc_start: 0.8988 (t) cc_final: 0.8541 (p) REVERT: S 412 ASN cc_start: 0.7339 (m-40) cc_final: 0.6597 (t0) REVERT: S 413 TYR cc_start: 0.6461 (t80) cc_final: 0.6179 (t80) REVERT: W 2 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8784 (tp) REVERT: W 4 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8836 (ptm160) REVERT: W 11 LEU cc_start: 0.8703 (mp) cc_final: 0.8447 (mt) REVERT: W 17 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8778 (tm-30) REVERT: W 21 ASN cc_start: 0.8601 (m-40) cc_final: 0.7873 (m-40) REVERT: X 44 MET cc_start: 0.9566 (mmm) cc_final: 0.9192 (mpp) REVERT: X 92 GLU cc_start: 0.9348 (mt-10) cc_final: 0.9115 (tp30) REVERT: X 137 GLU cc_start: 0.9682 (mt-10) cc_final: 0.9326 (tm-30) REVERT: X 299 MET cc_start: 0.9404 (mmm) cc_final: 0.9175 (mmt) REVERT: X 427 MET cc_start: 0.8960 (tmm) cc_final: 0.8702 (tpp) REVERT: X 459 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8647 (mp0) REVERT: X 529 MET cc_start: 0.5174 (OUTLIER) cc_final: 0.4934 (tpp) REVERT: Y 52 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8973 (m-40) REVERT: Y 71 PHE cc_start: 0.8741 (m-80) cc_final: 0.8236 (m-80) REVERT: Y 173 MET cc_start: 0.9608 (ttp) cc_final: 0.9378 (tmm) REVERT: Y 429 MET cc_start: 0.9632 (OUTLIER) cc_final: 0.9417 (ptp) REVERT: Y 451 CYS cc_start: 0.9339 (m) cc_final: 0.9065 (p) REVERT: Y 541 ASN cc_start: 0.9194 (m-40) cc_final: 0.8886 (t0) outliers start: 452 outliers final: 223 residues processed: 1076 average time/residue: 0.6206 time to fit residues: 1159.3030 Evaluate side-chains 910 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 631 time to evaluate : 7.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 871 ARG Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1075 GLN Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1413 LEU Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1646 GLN Chi-restraints excluded: chain A residue 1650 GLU Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1665 GLN Chi-restraints excluded: chain A residue 1666 ILE Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1684 THR Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1854 THR Chi-restraints excluded: chain A residue 1861 GLN Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 434 ARG Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 549 ASP Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 685 SER Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 536 MET Chi-restraints excluded: chain H residue 562 MET Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 579 LEU Chi-restraints excluded: chain H residue 699 ASP Chi-restraints excluded: chain H residue 704 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 273 CYS Chi-restraints excluded: chain I residue 281 MET Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 423 VAL Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 632 ARG Chi-restraints excluded: chain I residue 652 VAL Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 250 CYS Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 343 SER Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 400 GLU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain J residue 500 ASP Chi-restraints excluded: chain K residue 8 LYS Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 246 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 359 THR Chi-restraints excluded: chain K residue 395 LEU Chi-restraints excluded: chain K residue 407 GLU Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 497 ASN Chi-restraints excluded: chain K residue 506 LEU Chi-restraints excluded: chain K residue 510 ARG Chi-restraints excluded: chain K residue 518 MET Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 277 CYS Chi-restraints excluded: chain N residue 299 TRP Chi-restraints excluded: chain N residue 373 GLN Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 513 ASP Chi-restraints excluded: chain N residue 560 MET Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 625 LYS Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 218 GLN Chi-restraints excluded: chain O residue 219 GLN Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 299 SER Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain O residue 369 VAL Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 541 ILE Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 634 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 654 ASP Chi-restraints excluded: chain O residue 713 VAL Chi-restraints excluded: chain O residue 735 MET Chi-restraints excluded: chain O residue 752 ILE Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 51 SER Chi-restraints excluded: chain P residue 97 LYS Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 321 HIS Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 382 SER Chi-restraints excluded: chain P residue 435 MET Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 57 TRP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 393 LEU Chi-restraints excluded: chain R residue 488 LEU Chi-restraints excluded: chain S residue 326 LYS Chi-restraints excluded: chain S residue 389 CYS Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain S residue 401 CYS Chi-restraints excluded: chain W residue 2 LEU Chi-restraints excluded: chain W residue 4 ARG Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 229 THR Chi-restraints excluded: chain X residue 305 ILE Chi-restraints excluded: chain X residue 329 CYS Chi-restraints excluded: chain X residue 355 TYR Chi-restraints excluded: chain X residue 450 VAL Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain X residue 465 LEU Chi-restraints excluded: chain X residue 506 GLN Chi-restraints excluded: chain X residue 529 MET Chi-restraints excluded: chain Y residue 52 ASN Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 198 GLN Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain Y residue 303 TYR Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 423 ILE Chi-restraints excluded: chain Y residue 429 MET Chi-restraints excluded: chain Y residue 450 VAL Chi-restraints excluded: chain Y residue 452 LEU Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 472 GLU Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 551 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 753 optimal weight: 1.9990 chunk 573 optimal weight: 20.0000 chunk 395 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 363 optimal weight: 4.9990 chunk 511 optimal weight: 2.9990 chunk 765 optimal weight: 20.0000 chunk 810 optimal weight: 0.9980 chunk 399 optimal weight: 7.9990 chunk 725 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 125 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 ASN ** A1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1604 GLN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN C 202 HIS F 90 GLN F 595 GLN H 599 ASN H 657 HIS ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 318 HIS J 342 HIS ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 HIS N 266 HIS ** N 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN O 753 ASN ** R 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 289 ASN X 348 HIS X 390 GLN ** X 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 550 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 67835 Z= 0.257 Angle : 0.729 18.882 91891 Z= 0.370 Chirality : 0.042 0.265 10362 Planarity : 0.005 0.093 11673 Dihedral : 7.827 80.721 9434 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.24 % Favored : 94.22 % Rotamer: Outliers : 5.31 % Allowed : 20.88 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.38 % Twisted Proline : 0.65 % Twisted General : 0.05 % 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: 0.70 (0.09), residues: 8323 helix: 1.51 (0.07), residues: 5447 sheet: -0.39 (0.21), residues: 559 loop : -1.86 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 16 HIS 0.017 0.001 HIS M 66 PHE 0.023 0.001 PHE X 350 TYR 0.037 0.002 TYR O 161 ARG 0.009 0.000 ARG S 398 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 370 poor density : 702 time to evaluate : 6.093 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: A 11 MET cc_start: 0.6822 (mmt) cc_final: 0.6435 (mpp) REVERT: A 90 ASP cc_start: 0.9491 (OUTLIER) cc_final: 0.9289 (p0) REVERT: A 125 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.9258 (mt0) REVERT: A 159 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8887 (tt) REVERT: A 161 MET cc_start: 0.9296 (mpp) cc_final: 0.8903 (mmt) REVERT: A 170 ILE cc_start: 0.9224 (mt) cc_final: 0.8940 (mm) REVERT: A 257 MET cc_start: 0.9300 (tpp) cc_final: 0.9069 (tpp) REVERT: A 435 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8476 (p0) REVERT: A 449 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8680 (mp10) REVERT: A 483 GLU cc_start: 0.9687 (tt0) cc_final: 0.9457 (pt0) REVERT: A 488 MET cc_start: 0.8925 (ppp) cc_final: 0.8518 (ppp) REVERT: A 617 LEU cc_start: 0.9184 (mm) cc_final: 0.8805 (tp) REVERT: A 637 MET cc_start: 0.9533 (ppp) cc_final: 0.9328 (ppp) REVERT: A 788 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8833 (tm-30) REVERT: A 871 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8341 (ptp-110) REVERT: A 934 MET cc_start: 0.9683 (ttm) cc_final: 0.9276 (tpp) REVERT: A 945 GLU cc_start: 0.9530 (OUTLIER) cc_final: 0.9251 (mt-10) REVERT: A 1075 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8574 (mm110) REVERT: A 1203 MET cc_start: 0.9215 (tpp) cc_final: 0.8629 (mmt) REVERT: A 1320 ASN cc_start: 0.8544 (t0) cc_final: 0.8131 (t0) REVERT: A 1397 ASP cc_start: 0.9246 (m-30) cc_final: 0.8852 (t0) REVERT: A 1623 ASP cc_start: 0.9303 (t0) cc_final: 0.9049 (t0) REVERT: A 1646 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8535 (tp40) REVERT: A 1665 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: A 1766 GLN cc_start: 0.9383 (mp10) cc_final: 0.9172 (mp10) REVERT: A 1808 MET cc_start: 0.7818 (ttm) cc_final: 0.6975 (ttm) REVERT: A 1861 GLN cc_start: 0.9625 (OUTLIER) cc_final: 0.9339 (pp30) REVERT: B 1 MET cc_start: 0.6822 (mmm) cc_final: 0.5636 (ttt) REVERT: B 43 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.7008 (t0) REVERT: C 84 MET cc_start: 0.9389 (tpp) cc_final: 0.9151 (tpp) REVERT: C 161 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8750 (mp) REVERT: C 168 ASP cc_start: 0.9186 (t70) cc_final: 0.8874 (m-30) REVERT: C 218 MET cc_start: 0.9435 (ttp) cc_final: 0.8933 (ptm) REVERT: C 234 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9212 (tp) REVERT: C 238 TYR cc_start: 0.9229 (m-10) cc_final: 0.8895 (m-80) REVERT: C 244 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8559 (mm) REVERT: C 257 VAL cc_start: 0.9351 (OUTLIER) cc_final: 0.9097 (m) REVERT: C 468 MET cc_start: 0.9107 (mmm) cc_final: 0.8821 (ptp) REVERT: D 31 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8875 (tm-30) REVERT: D 36 GLN cc_start: 0.9565 (OUTLIER) cc_final: 0.9345 (tm-30) REVERT: D 42 GLN cc_start: 0.9596 (mt0) cc_final: 0.9349 (mp10) REVERT: E 56 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8864 (mm-30) REVERT: E 80 GLU cc_start: 0.9572 (tp30) cc_final: 0.9287 (pt0) REVERT: F 128 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8828 (p) REVERT: F 534 GLU cc_start: 0.9207 (tp30) cc_final: 0.8618 (tt0) REVERT: F 568 GLU cc_start: 0.9412 (mt-10) cc_final: 0.9160 (mp0) REVERT: F 735 LYS cc_start: 0.9326 (mttt) cc_final: 0.9015 (mttp) REVERT: G 5 LYS cc_start: 0.9623 (pmtt) cc_final: 0.9410 (mtmm) REVERT: G 12 LYS cc_start: 0.8304 (mmmm) cc_final: 0.8099 (mtmm) REVERT: H 89 GLU cc_start: 0.9710 (tt0) cc_final: 0.9437 (tm-30) REVERT: H 496 TYR cc_start: 0.9030 (t80) cc_final: 0.8769 (t80) REVERT: H 643 MET cc_start: 0.9286 (mtp) cc_final: 0.9052 (mmm) REVERT: H 699 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8610 (t0) REVERT: H 733 VAL cc_start: 0.9398 (OUTLIER) cc_final: 0.9123 (p) REVERT: I 185 ILE cc_start: 0.9747 (OUTLIER) cc_final: 0.9501 (tp) REVERT: I 281 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8348 (pmm) REVERT: I 440 MET cc_start: 0.8688 (mpp) cc_final: 0.8383 (mpp) REVERT: I 632 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8050 (ttm110) REVERT: I 717 MET cc_start: 0.8193 (tpt) cc_final: 0.7822 (tpt) REVERT: J 202 ARG cc_start: 0.9606 (OUTLIER) cc_final: 0.9311 (mtm110) REVERT: J 400 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.9090 (pm20) REVERT: J 448 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.8972 (mm) REVERT: J 477 GLN cc_start: 0.9393 (OUTLIER) cc_final: 0.9036 (mm110) REVERT: K 8 LYS cc_start: 0.9616 (OUTLIER) cc_final: 0.9299 (pttm) REVERT: K 283 GLU cc_start: 0.9710 (mm-30) cc_final: 0.9381 (mp0) REVERT: K 354 MET cc_start: 0.9520 (tpp) cc_final: 0.8950 (mpp) REVERT: K 395 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9494 (pp) REVERT: K 454 VAL cc_start: 0.9383 (OUTLIER) cc_final: 0.9180 (p) REVERT: L 17 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9142 (mt-10) REVERT: L 48 ASP cc_start: 0.9555 (t0) cc_final: 0.9150 (m-30) REVERT: L 63 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9106 (mt) REVERT: L 71 LYS cc_start: 0.9040 (tttm) cc_final: 0.8680 (ttmm) REVERT: L 128 HIS cc_start: 0.7757 (m90) cc_final: 0.7540 (m90) REVERT: L 150 ASP cc_start: 0.8873 (m-30) cc_final: 0.8306 (t0) REVERT: L 177 PHE cc_start: 0.9173 (m-80) cc_final: 0.8828 (m-80) REVERT: L 178 MET cc_start: 0.9212 (mmm) cc_final: 0.8918 (mmm) REVERT: L 181 ARG cc_start: 0.9383 (OUTLIER) cc_final: 0.8960 (ttp80) REVERT: M 27 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8480 (tp30) REVERT: M 28 ASP cc_start: 0.9295 (m-30) cc_final: 0.8597 (p0) REVERT: M 51 LYS cc_start: 0.8517 (ptpp) cc_final: 0.8203 (ptpp) REVERT: M 66 HIS cc_start: 0.9000 (t-90) cc_final: 0.8793 (t-90) REVERT: N 277 CYS cc_start: 0.9563 (OUTLIER) cc_final: 0.9223 (p) REVERT: N 361 LEU cc_start: 0.9485 (tp) cc_final: 0.9187 (tp) REVERT: N 622 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: N 670 PHE cc_start: 0.3038 (OUTLIER) cc_final: 0.1953 (m-80) REVERT: N 705 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5829 (mt) REVERT: O 287 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8973 (mp0) REVERT: O 440 GLN cc_start: 0.9291 (tm-30) cc_final: 0.8963 (tm-30) REVERT: O 517 ASP cc_start: 0.9669 (m-30) cc_final: 0.9299 (p0) REVERT: O 636 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8922 (pt) REVERT: O 735 MET cc_start: 0.9565 (OUTLIER) cc_final: 0.9158 (mtt) REVERT: P 148 ASN cc_start: 0.8884 (m110) cc_final: 0.8488 (p0) REVERT: P 246 GLU cc_start: 0.9542 (tp30) cc_final: 0.9321 (tm-30) REVERT: P 298 GLU cc_start: 0.9533 (tt0) cc_final: 0.9292 (mp0) REVERT: P 325 GLU cc_start: 0.9638 (tp30) cc_final: 0.9284 (tm-30) REVERT: P 524 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6659 (mmtm) REVERT: R 47 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8507 (mmm160) REVERT: S 361 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8502 (mp0) REVERT: S 362 PHE cc_start: 0.7627 (m-80) cc_final: 0.7262 (m-80) REVERT: S 375 LEU cc_start: 0.7929 (mp) cc_final: 0.7337 (tt) REVERT: S 386 LYS cc_start: 0.7965 (tppt) cc_final: 0.7562 (mmmm) REVERT: S 411 CYS cc_start: 0.8884 (t) cc_final: 0.8454 (p) REVERT: S 412 ASN cc_start: 0.6882 (m-40) cc_final: 0.6077 (t0) REVERT: W 11 LEU cc_start: 0.8602 (mp) cc_final: 0.8273 (mt) REVERT: W 17 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8673 (tm-30) REVERT: W 21 ASN cc_start: 0.8583 (m-40) cc_final: 0.7878 (m-40) REVERT: X 44 MET cc_start: 0.9585 (mmm) cc_final: 0.9336 (mmm) REVERT: X 92 GLU cc_start: 0.9359 (mt-10) cc_final: 0.9137 (tp30) REVERT: X 137 GLU cc_start: 0.9695 (mt-10) cc_final: 0.9325 (tm-30) REVERT: X 299 MET cc_start: 0.9446 (mmm) cc_final: 0.9224 (mmt) REVERT: X 367 GLN cc_start: 0.9593 (tm-30) cc_final: 0.9217 (pt0) REVERT: X 385 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.7934 (m110) REVERT: X 427 MET cc_start: 0.8954 (tmm) cc_final: 0.8641 (tpp) REVERT: X 459 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8660 (mp0) REVERT: Y 52 ASN cc_start: 0.9243 (OUTLIER) cc_final: 0.9023 (m-40) REVERT: Y 71 PHE cc_start: 0.8750 (m-80) cc_final: 0.8252 (m-80) REVERT: Y 173 MET cc_start: 0.9604 (ttp) cc_final: 0.9367 (tmm) REVERT: Y 304 LEU cc_start: 0.8670 (mt) cc_final: 0.8409 (tp) REVERT: Y 429 MET cc_start: 0.9627 (OUTLIER) cc_final: 0.9422 (ptp) REVERT: Y 451 CYS cc_start: 0.9372 (m) cc_final: 0.9094 (p) REVERT: Y 541 ASN cc_start: 0.9185 (m-40) cc_final: 0.8904 (t0) outliers start: 370 outliers final: 218 residues processed: 998 average time/residue: 0.6204 time to fit residues: 1080.7363 Evaluate side-chains 879 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 615 time to evaluate : 6.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 871 ARG Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1075 GLN Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1413 LEU Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1639 LYS Chi-restraints excluded: chain A residue 1646 GLN Chi-restraints excluded: chain A residue 1650 GLU Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1665 GLN Chi-restraints excluded: chain A residue 1666 ILE Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1684 THR Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1854 THR Chi-restraints excluded: chain A residue 1861 GLN Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 36 GLN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 549 ASP Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 685 SER Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 562 MET Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 579 LEU Chi-restraints excluded: chain H residue 699 ASP Chi-restraints excluded: chain H residue 733 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 273 CYS Chi-restraints excluded: chain I residue 281 MET Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 423 VAL Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 632 ARG Chi-restraints excluded: chain I residue 652 VAL Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 343 SER Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 400 GLU Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain K residue 8 LYS Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 246 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 359 THR Chi-restraints excluded: chain K residue 395 LEU Chi-restraints excluded: chain K residue 407 GLU Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 492 MET Chi-restraints excluded: chain K residue 497 ASN Chi-restraints excluded: chain K residue 506 LEU Chi-restraints excluded: chain K residue 518 MET Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 277 CYS Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 513 ASP Chi-restraints excluded: chain N residue 560 MET Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 625 LYS Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 676 TRP Chi-restraints excluded: chain N residue 696 MET Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 218 GLN Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 396 ASN Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 495 GLU Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 603 MET Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 634 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 680 GLN Chi-restraints excluded: chain O residue 735 MET Chi-restraints excluded: chain O residue 744 LEU Chi-restraints excluded: chain O residue 752 ILE Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 97 LYS Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 321 HIS Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 382 SER Chi-restraints excluded: chain P residue 435 MET Chi-restraints excluded: chain P residue 524 LYS Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 47 ARG Chi-restraints excluded: chain R residue 67 ASN Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 393 LEU Chi-restraints excluded: chain R residue 488 LEU Chi-restraints excluded: chain S residue 389 CYS Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 229 THR Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 329 CYS Chi-restraints excluded: chain X residue 355 TYR Chi-restraints excluded: chain X residue 385 ASN Chi-restraints excluded: chain X residue 450 VAL Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain X residue 465 LEU Chi-restraints excluded: chain X residue 506 GLN Chi-restraints excluded: chain Y residue 52 ASN Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 198 GLN Chi-restraints excluded: chain Y residue 229 THR Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 303 TYR Chi-restraints excluded: chain Y residue 359 LEU Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 423 ILE Chi-restraints excluded: chain Y residue 429 MET Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 526 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 674 optimal weight: 2.9990 chunk 459 optimal weight: 0.0270 chunk 11 optimal weight: 5.9990 chunk 603 optimal weight: 1.9990 chunk 334 optimal weight: 3.9990 chunk 691 optimal weight: 2.9990 chunk 559 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 413 optimal weight: 0.9980 chunk 727 optimal weight: 0.4980 chunk 204 optimal weight: 0.1980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 125 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 GLN ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN C 202 HIS ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 ASN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 696 GLN J 174 HIS ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 571 ASN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 276 HIS O 443 GLN P 202 HIS R 158 GLN ** X 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 531 GLN Y 367 GLN Y 531 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 67835 Z= 0.199 Angle : 0.710 18.860 91891 Z= 0.356 Chirality : 0.040 0.285 10362 Planarity : 0.004 0.092 11673 Dihedral : 7.232 79.966 9383 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.09 % Favored : 94.41 % Rotamer: Outliers : 5.00 % Allowed : 21.04 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.09), residues: 8323 helix: 1.55 (0.07), residues: 5455 sheet: -0.33 (0.21), residues: 545 loop : -1.76 (0.13), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 637 HIS 0.010 0.001 HIS X 395 PHE 0.021 0.001 PHE Y 294 TYR 0.035 0.001 TYR O 161 ARG 0.009 0.000 ARG N 526 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 703 time to evaluate : 6.769 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: A 11 MET cc_start: 0.6669 (mmt) cc_final: 0.6170 (mpp) REVERT: A 125 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.8934 (mt0) REVERT: A 161 MET cc_start: 0.9284 (mpp) cc_final: 0.8992 (mmt) REVERT: A 170 ILE cc_start: 0.9247 (mt) cc_final: 0.8998 (mm) REVERT: A 257 MET cc_start: 0.9322 (tpp) cc_final: 0.8887 (tpp) REVERT: A 449 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8697 (mp10) REVERT: A 483 GLU cc_start: 0.9674 (tt0) cc_final: 0.9470 (pt0) REVERT: A 488 MET cc_start: 0.8968 (ppp) cc_final: 0.8437 (ppp) REVERT: A 617 LEU cc_start: 0.9189 (mm) cc_final: 0.8854 (tp) REVERT: A 637 MET cc_start: 0.9522 (ppp) cc_final: 0.9314 (ppp) REVERT: A 788 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.8864 (tm-30) REVERT: A 871 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8288 (ptp-110) REVERT: A 934 MET cc_start: 0.9669 (ttm) cc_final: 0.9240 (tpp) REVERT: A 945 GLU cc_start: 0.9546 (OUTLIER) cc_final: 0.9261 (mt-10) REVERT: A 1024 MET cc_start: 0.9122 (ttm) cc_final: 0.8826 (ttm) REVERT: A 1073 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9283 (mm) REVERT: A 1075 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8622 (mm110) REVERT: A 1242 GLU cc_start: 0.8028 (mp0) cc_final: 0.7501 (tm-30) REVERT: A 1296 LEU cc_start: 0.9478 (tp) cc_final: 0.9101 (tt) REVERT: A 1320 ASN cc_start: 0.8579 (t0) cc_final: 0.8238 (t0) REVERT: A 1397 ASP cc_start: 0.9226 (m-30) cc_final: 0.8828 (t0) REVERT: A 1480 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8623 (tp30) REVERT: A 1623 ASP cc_start: 0.9307 (t0) cc_final: 0.9040 (t0) REVERT: A 1665 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: A 1816 GLN cc_start: 0.9023 (mt0) cc_final: 0.8557 (mm-40) REVERT: A 1861 GLN cc_start: 0.9593 (OUTLIER) cc_final: 0.9293 (pp30) REVERT: B 1 MET cc_start: 0.6276 (mmm) cc_final: 0.5044 (ttt) REVERT: B 16 TRP cc_start: 0.6538 (OUTLIER) cc_final: 0.5622 (t-100) REVERT: B 43 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.7122 (t0) REVERT: C 84 MET cc_start: 0.9382 (tpp) cc_final: 0.9149 (tpp) REVERT: C 161 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8733 (mp) REVERT: C 168 ASP cc_start: 0.9200 (t70) cc_final: 0.8873 (m-30) REVERT: C 218 MET cc_start: 0.9426 (ttp) cc_final: 0.8951 (ptm) REVERT: C 238 TYR cc_start: 0.9231 (m-10) cc_final: 0.8982 (m-80) REVERT: C 244 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8515 (mm) REVERT: C 257 VAL cc_start: 0.9375 (OUTLIER) cc_final: 0.9140 (m) REVERT: C 468 MET cc_start: 0.9073 (mmm) cc_final: 0.8805 (ptp) REVERT: D 31 GLN cc_start: 0.9119 (tt0) cc_final: 0.8836 (tm-30) REVERT: D 42 GLN cc_start: 0.9579 (mt0) cc_final: 0.9078 (tm-30) REVERT: E 57 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8932 (t) REVERT: E 68 LYS cc_start: 0.9473 (tttp) cc_final: 0.9189 (mtmm) REVERT: E 80 GLU cc_start: 0.9564 (tp30) cc_final: 0.9275 (pt0) REVERT: F 81 ASP cc_start: 0.9165 (m-30) cc_final: 0.8919 (p0) REVERT: F 534 GLU cc_start: 0.9232 (tp30) cc_final: 0.8639 (tt0) REVERT: F 568 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9072 (mp0) REVERT: F 735 LYS cc_start: 0.9312 (mttt) cc_final: 0.8995 (mttp) REVERT: G 5 LYS cc_start: 0.9645 (pmtt) cc_final: 0.9433 (mtmm) REVERT: G 12 LYS cc_start: 0.8085 (mmmm) cc_final: 0.7884 (mtmm) REVERT: H 89 GLU cc_start: 0.9677 (tt0) cc_final: 0.9433 (tm-30) REVERT: H 496 TYR cc_start: 0.8973 (t80) cc_final: 0.8620 (t80) REVERT: H 616 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8899 (mp0) REVERT: H 643 MET cc_start: 0.9288 (mtp) cc_final: 0.9036 (mmm) REVERT: H 699 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8565 (t0) REVERT: H 733 VAL cc_start: 0.9376 (OUTLIER) cc_final: 0.9152 (p) REVERT: I 185 ILE cc_start: 0.9737 (OUTLIER) cc_final: 0.9497 (tp) REVERT: I 365 GLU cc_start: 0.9664 (OUTLIER) cc_final: 0.9452 (mt-10) REVERT: I 440 MET cc_start: 0.8770 (mpp) cc_final: 0.8338 (mpp) REVERT: I 632 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8091 (ttm110) REVERT: I 717 MET cc_start: 0.7977 (tpt) cc_final: 0.7768 (tpt) REVERT: J 170 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9066 (pt) REVERT: J 400 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.9092 (pm20) REVERT: J 448 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8906 (mm) REVERT: J 477 GLN cc_start: 0.9421 (OUTLIER) cc_final: 0.9053 (mm110) REVERT: K 190 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8140 (tp) REVERT: K 283 GLU cc_start: 0.9704 (mm-30) cc_final: 0.9381 (mp0) REVERT: K 354 MET cc_start: 0.9497 (tpp) cc_final: 0.8945 (mpp) REVERT: L 12 ASP cc_start: 0.9291 (t70) cc_final: 0.8949 (t0) REVERT: L 17 GLU cc_start: 0.9336 (mm-30) cc_final: 0.9131 (mt-10) REVERT: L 28 GLN cc_start: 0.9189 (mt0) cc_final: 0.8987 (mp10) REVERT: L 63 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9150 (mt) REVERT: L 71 LYS cc_start: 0.9024 (tttm) cc_final: 0.8678 (ttmm) REVERT: L 84 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8813 (mmmt) REVERT: L 128 HIS cc_start: 0.7601 (m90) cc_final: 0.7366 (m90) REVERT: L 147 ASN cc_start: 0.9247 (m-40) cc_final: 0.8646 (t0) REVERT: L 150 ASP cc_start: 0.8861 (m-30) cc_final: 0.8321 (t0) REVERT: L 178 MET cc_start: 0.9172 (mmm) cc_final: 0.8838 (mmm) REVERT: L 181 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.8917 (ttp80) REVERT: M 27 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8426 (tp30) REVERT: M 28 ASP cc_start: 0.9312 (m-30) cc_final: 0.8589 (p0) REVERT: M 51 LYS cc_start: 0.8333 (ptpp) cc_final: 0.8006 (ptpp) REVERT: M 66 HIS cc_start: 0.9168 (t-90) cc_final: 0.8922 (t-90) REVERT: N 277 CYS cc_start: 0.9543 (OUTLIER) cc_final: 0.9227 (p) REVERT: N 361 LEU cc_start: 0.9525 (tp) cc_final: 0.9202 (tp) REVERT: N 369 ASP cc_start: 0.9424 (t0) cc_final: 0.9221 (t0) REVERT: N 373 GLN cc_start: 0.9582 (OUTLIER) cc_final: 0.9110 (tm-30) REVERT: N 622 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.6950 (m-80) REVERT: N 670 PHE cc_start: 0.2808 (OUTLIER) cc_final: 0.1901 (m-80) REVERT: O 287 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8979 (mp0) REVERT: O 419 ASP cc_start: 0.9259 (m-30) cc_final: 0.8999 (p0) REVERT: O 440 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8919 (tm-30) REVERT: O 517 ASP cc_start: 0.9660 (m-30) cc_final: 0.9286 (p0) REVERT: O 636 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8992 (pt) REVERT: O 735 MET cc_start: 0.9572 (OUTLIER) cc_final: 0.9152 (mtt) REVERT: P 148 ASN cc_start: 0.8920 (m110) cc_final: 0.8438 (p0) REVERT: P 246 GLU cc_start: 0.9526 (tp30) cc_final: 0.9306 (tm-30) REVERT: P 298 GLU cc_start: 0.9544 (tt0) cc_final: 0.9332 (mp0) REVERT: P 325 GLU cc_start: 0.9636 (tp30) cc_final: 0.9274 (tm-30) REVERT: P 441 GLU cc_start: 0.9784 (tt0) cc_final: 0.9577 (mm-30) REVERT: P 524 LYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6552 (mmpt) REVERT: R 128 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8715 (m-80) REVERT: S 361 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8431 (mp0) REVERT: S 386 LYS cc_start: 0.8065 (tppt) cc_final: 0.7601 (mmmt) REVERT: S 411 CYS cc_start: 0.8637 (t) cc_final: 0.8235 (p) REVERT: S 412 ASN cc_start: 0.7010 (m-40) cc_final: 0.6277 (t0) REVERT: W 11 LEU cc_start: 0.8409 (mp) cc_final: 0.7988 (mt) REVERT: W 17 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8635 (tm-30) REVERT: W 21 ASN cc_start: 0.8624 (m-40) cc_final: 0.7930 (m-40) REVERT: X 44 MET cc_start: 0.9592 (mmm) cc_final: 0.9332 (mmm) REVERT: X 92 GLU cc_start: 0.9323 (mt-10) cc_final: 0.9114 (tp30) REVERT: X 137 GLU cc_start: 0.9709 (mt-10) cc_final: 0.9340 (tm-30) REVERT: X 299 MET cc_start: 0.9452 (mmm) cc_final: 0.9223 (mmt) REVERT: X 395 HIS cc_start: 0.8387 (m170) cc_final: 0.7888 (m170) REVERT: X 427 MET cc_start: 0.8953 (tmm) cc_final: 0.8651 (tpp) REVERT: X 459 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8673 (mp0) REVERT: Y 71 PHE cc_start: 0.8759 (m-80) cc_final: 0.8279 (m-80) REVERT: Y 173 MET cc_start: 0.9594 (ttp) cc_final: 0.9363 (tmm) REVERT: Y 304 LEU cc_start: 0.8609 (mt) cc_final: 0.8312 (tp) REVERT: Y 451 CYS cc_start: 0.9373 (m) cc_final: 0.9080 (p) REVERT: Y 526 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7984 (tp40) REVERT: Y 541 ASN cc_start: 0.9170 (m-40) cc_final: 0.8881 (t0) outliers start: 348 outliers final: 200 residues processed: 982 average time/residue: 0.6077 time to fit residues: 1042.6611 Evaluate side-chains 856 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 620 time to evaluate : 6.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 871 ARG Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1075 GLN Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1522 SER Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1639 LYS Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1665 GLN Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1752 SER Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1854 THR Chi-restraints excluded: chain A residue 1861 GLN Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 549 ASP Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 596 VAL Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 549 ASP Chi-restraints excluded: chain H residue 562 MET Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 699 ASP Chi-restraints excluded: chain H residue 733 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 423 VAL Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 632 ARG Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 400 GLU Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain J residue 527 ILE Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 246 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 395 LEU Chi-restraints excluded: chain K residue 407 GLU Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 497 ASN Chi-restraints excluded: chain K residue 518 MET Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 277 CYS Chi-restraints excluded: chain N residue 373 GLN Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 513 ASP Chi-restraints excluded: chain N residue 560 MET Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 696 MET Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 396 ASN Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 495 GLU Chi-restraints excluded: chain O residue 541 ILE Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 680 GLN Chi-restraints excluded: chain O residue 735 MET Chi-restraints excluded: chain O residue 744 LEU Chi-restraints excluded: chain O residue 752 ILE Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 97 LYS Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 227 THR Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 321 HIS Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 382 SER Chi-restraints excluded: chain P residue 435 MET Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 524 LYS Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 393 LEU Chi-restraints excluded: chain R residue 488 LEU Chi-restraints excluded: chain S residue 389 CYS Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 305 ILE Chi-restraints excluded: chain X residue 355 TYR Chi-restraints excluded: chain X residue 385 ASN Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 450 VAL Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain X residue 465 LEU Chi-restraints excluded: chain X residue 506 GLN Chi-restraints excluded: chain X residue 515 LEU Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 198 GLN Chi-restraints excluded: chain Y residue 229 THR Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 303 TYR Chi-restraints excluded: chain Y residue 359 LEU Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 373 VAL Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 526 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 272 optimal weight: 2.9990 chunk 729 optimal weight: 30.0000 chunk 160 optimal weight: 9.9990 chunk 475 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 810 optimal weight: 9.9990 chunk 673 optimal weight: 9.9990 chunk 375 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 268 optimal weight: 7.9990 chunk 425 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 125 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1816 GLN A1872 HIS ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN C 236 HIS F 595 GLN H 599 ASN H 667 GLN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 314 HIS J 350 HIS ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 449 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 GLN ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 530 GLN O 211 GLN ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 342 HIS O 443 GLN O 645 HIS O 753 ASN ** R 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 404 ASN X 251 ASN X 298 GLN ** X 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 177 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 67835 Z= 0.397 Angle : 0.764 18.856 91891 Z= 0.392 Chirality : 0.043 0.277 10362 Planarity : 0.005 0.090 11673 Dihedral : 6.991 87.052 9343 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.64 % Favored : 93.90 % Rotamer: Outliers : 5.20 % Allowed : 21.86 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % Twisted General : 0.06 % 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: 0.75 (0.09), residues: 8323 helix: 1.53 (0.07), residues: 5467 sheet: -0.56 (0.21), residues: 566 loop : -1.77 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 641 HIS 0.010 0.001 HIS K 54 PHE 0.051 0.002 PHE X 294 TYR 0.038 0.002 TYR O 161 ARG 0.008 0.001 ARG A1540 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 595 time to evaluate : 6.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6961 (mmt) cc_final: 0.6491 (mpp) REVERT: A 42 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9096 (mt) REVERT: A 161 MET cc_start: 0.9341 (mpp) cc_final: 0.8893 (mmt) REVERT: A 257 MET cc_start: 0.9294 (tpp) cc_final: 0.8830 (tpp) REVERT: A 449 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8661 (mp10) REVERT: A 483 GLU cc_start: 0.9697 (tt0) cc_final: 0.9495 (pt0) REVERT: A 488 MET cc_start: 0.8975 (ppp) cc_final: 0.8460 (ppp) REVERT: A 617 LEU cc_start: 0.9266 (mm) cc_final: 0.8959 (tp) REVERT: A 788 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.8850 (tm-30) REVERT: A 871 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8331 (ptp-110) REVERT: A 934 MET cc_start: 0.9666 (ttm) cc_final: 0.9272 (tpp) REVERT: A 945 GLU cc_start: 0.9603 (OUTLIER) cc_final: 0.9350 (mt-10) REVERT: A 1203 MET cc_start: 0.9159 (tpp) cc_final: 0.8608 (mmt) REVERT: A 1242 GLU cc_start: 0.8082 (mp0) cc_final: 0.7605 (tm-30) REVERT: A 1279 ARG cc_start: 0.9413 (ttt180) cc_final: 0.9213 (ttt180) REVERT: A 1296 LEU cc_start: 0.9490 (tp) cc_final: 0.9169 (tt) REVERT: A 1320 ASN cc_start: 0.8658 (t0) cc_final: 0.8322 (t0) REVERT: A 1386 TRP cc_start: 0.9103 (OUTLIER) cc_final: 0.8586 (p90) REVERT: A 1397 ASP cc_start: 0.9234 (m-30) cc_final: 0.8829 (t0) REVERT: A 1480 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8581 (tp30) REVERT: A 1623 ASP cc_start: 0.9290 (t0) cc_final: 0.9027 (t70) REVERT: A 1665 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: A 1861 GLN cc_start: 0.9585 (OUTLIER) cc_final: 0.9293 (pp30) REVERT: B 16 TRP cc_start: 0.6658 (OUTLIER) cc_final: 0.5811 (t-100) REVERT: B 43 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.7088 (t0) REVERT: C 84 MET cc_start: 0.9374 (tpp) cc_final: 0.9148 (tpp) REVERT: C 161 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8739 (mp) REVERT: C 168 ASP cc_start: 0.9281 (t70) cc_final: 0.8942 (m-30) REVERT: C 218 MET cc_start: 0.9424 (ttp) cc_final: 0.8891 (ptm) REVERT: C 244 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8485 (mm) REVERT: C 257 VAL cc_start: 0.9375 (OUTLIER) cc_final: 0.9142 (m) REVERT: C 435 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8790 (mpp) REVERT: C 468 MET cc_start: 0.9195 (mmm) cc_final: 0.8987 (ptp) REVERT: C 480 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8932 (mp) REVERT: D 31 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8857 (tm-30) REVERT: D 42 GLN cc_start: 0.9548 (mt0) cc_final: 0.8824 (tm-30) REVERT: D 46 GLU cc_start: 0.9328 (mp0) cc_final: 0.8852 (mp0) REVERT: E 68 LYS cc_start: 0.9481 (tttp) cc_final: 0.9197 (mtmm) REVERT: F 534 GLU cc_start: 0.9220 (tp30) cc_final: 0.8600 (tt0) REVERT: F 568 GLU cc_start: 0.9405 (mt-10) cc_final: 0.9203 (mp0) REVERT: G 5 LYS cc_start: 0.9646 (OUTLIER) cc_final: 0.9436 (mtmm) REVERT: H 89 GLU cc_start: 0.9700 (tt0) cc_final: 0.9437 (tm-30) REVERT: H 496 TYR cc_start: 0.9204 (t80) cc_final: 0.8876 (t80) REVERT: H 616 GLU cc_start: 0.9330 (mt-10) cc_final: 0.8995 (pm20) REVERT: H 643 MET cc_start: 0.9298 (mtp) cc_final: 0.9074 (mmm) REVERT: H 699 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8658 (t0) REVERT: I 440 MET cc_start: 0.8786 (mpp) cc_final: 0.8422 (mpp) REVERT: I 632 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7925 (ttm110) REVERT: I 717 MET cc_start: 0.7734 (tpt) cc_final: 0.7462 (tpt) REVERT: J 170 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8917 (pt) REVERT: J 400 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8908 (pm20) REVERT: J 448 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8972 (mm) REVERT: J 477 GLN cc_start: 0.9381 (OUTLIER) cc_final: 0.8972 (mm110) REVERT: K 8 LYS cc_start: 0.9617 (OUTLIER) cc_final: 0.9280 (pttm) REVERT: K 190 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8199 (tp) REVERT: K 283 GLU cc_start: 0.9717 (mm-30) cc_final: 0.9391 (mp0) REVERT: K 347 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8655 (tm-30) REVERT: K 349 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9136 (mm-30) REVERT: K 454 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9226 (p) REVERT: L 12 ASP cc_start: 0.9322 (t70) cc_final: 0.8967 (t0) REVERT: L 17 GLU cc_start: 0.9373 (mm-30) cc_final: 0.9172 (mt-10) REVERT: L 48 ASP cc_start: 0.9506 (t0) cc_final: 0.9014 (m-30) REVERT: L 63 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9151 (mt) REVERT: L 178 MET cc_start: 0.9271 (mmm) cc_final: 0.8944 (mmm) REVERT: L 181 ARG cc_start: 0.9426 (OUTLIER) cc_final: 0.9028 (ttp80) REVERT: M 6 GLN cc_start: 0.8536 (pm20) cc_final: 0.8173 (pm20) REVERT: M 27 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8444 (tp30) REVERT: M 28 ASP cc_start: 0.9290 (m-30) cc_final: 0.8655 (p0) REVERT: M 66 HIS cc_start: 0.9217 (t-90) cc_final: 0.9017 (t-90) REVERT: N 277 CYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9172 (p) REVERT: N 361 LEU cc_start: 0.9446 (tp) cc_final: 0.9043 (tp) REVERT: N 373 GLN cc_start: 0.9565 (OUTLIER) cc_final: 0.9115 (tm-30) REVERT: N 622 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: N 670 PHE cc_start: 0.3189 (OUTLIER) cc_final: 0.2810 (m-80) REVERT: N 676 TRP cc_start: 0.6863 (m-10) cc_final: 0.6556 (m-10) REVERT: N 696 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8213 (mtt) REVERT: O 287 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8860 (mp0) REVERT: O 419 ASP cc_start: 0.9329 (m-30) cc_final: 0.8964 (p0) REVERT: O 440 GLN cc_start: 0.9291 (tm-30) cc_final: 0.9005 (tm-30) REVERT: O 495 GLU cc_start: 0.9443 (OUTLIER) cc_final: 0.9170 (pp20) REVERT: O 506 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8986 (pp) REVERT: O 517 ASP cc_start: 0.9675 (m-30) cc_final: 0.9327 (p0) REVERT: O 529 ASP cc_start: 0.9569 (t0) cc_final: 0.9247 (m-30) REVERT: O 636 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9149 (pt) REVERT: O 664 MET cc_start: 0.9504 (mmm) cc_final: 0.9066 (mmm) REVERT: O 735 MET cc_start: 0.9598 (OUTLIER) cc_final: 0.9177 (mtt) REVERT: P 148 ASN cc_start: 0.8937 (m110) cc_final: 0.8529 (p0) REVERT: P 246 GLU cc_start: 0.9547 (tp30) cc_final: 0.9333 (tm-30) REVERT: P 298 GLU cc_start: 0.9589 (tt0) cc_final: 0.9335 (mp0) REVERT: P 524 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6732 (mmmt) REVERT: S 361 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8530 (mp0) REVERT: S 362 PHE cc_start: 0.7556 (m-80) cc_final: 0.7299 (m-80) REVERT: S 386 LYS cc_start: 0.8015 (tppt) cc_final: 0.7554 (tptp) REVERT: S 411 CYS cc_start: 0.8359 (t) cc_final: 0.7999 (p) REVERT: S 412 ASN cc_start: 0.6874 (m-40) cc_final: 0.5990 (t0) REVERT: W 17 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8646 (tm-30) REVERT: W 21 ASN cc_start: 0.8582 (m-40) cc_final: 0.7823 (m-40) REVERT: X 79 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9447 (tp) REVERT: X 92 GLU cc_start: 0.9397 (mt-10) cc_final: 0.8969 (pm20) REVERT: X 136 ILE cc_start: 0.9528 (OUTLIER) cc_final: 0.9230 (tp) REVERT: X 137 GLU cc_start: 0.9703 (mt-10) cc_final: 0.9334 (tm-30) REVERT: X 427 MET cc_start: 0.8985 (tmm) cc_final: 0.8689 (tpp) REVERT: X 459 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8792 (mp0) REVERT: Y 71 PHE cc_start: 0.8696 (m-80) cc_final: 0.8235 (m-80) REVERT: Y 90 ASP cc_start: 0.9313 (t0) cc_final: 0.8941 (m-30) REVERT: Y 304 LEU cc_start: 0.8783 (mt) cc_final: 0.8547 (tp) REVERT: Y 451 CYS cc_start: 0.9383 (m) cc_final: 0.9103 (p) REVERT: Y 541 ASN cc_start: 0.9217 (m-40) cc_final: 0.8958 (t0) REVERT: Y 549 MET cc_start: 0.8954 (mmt) cc_final: 0.8639 (mmt) outliers start: 362 outliers final: 238 residues processed: 890 average time/residue: 0.6070 time to fit residues: 947.7741 Evaluate side-chains 848 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 570 time to evaluate : 6.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 871 ARG Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1324 GLN Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1413 LEU Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1522 SER Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1639 LYS Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1665 GLN Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1684 THR Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1854 THR Chi-restraints excluded: chain A residue 1861 GLN Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 549 ASP Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 685 SER Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 548 LYS Chi-restraints excluded: chain H residue 562 MET Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 579 LEU Chi-restraints excluded: chain H residue 699 ASP Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 423 VAL Chi-restraints excluded: chain I residue 477 GLN Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 560 THR Chi-restraints excluded: chain I residue 632 ARG Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 250 CYS Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 314 HIS Chi-restraints excluded: chain J residue 343 SER Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 400 GLU Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain J residue 527 ILE Chi-restraints excluded: chain K residue 8 LYS Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 246 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 359 THR Chi-restraints excluded: chain K residue 407 GLU Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 497 ASN Chi-restraints excluded: chain K residue 506 LEU Chi-restraints excluded: chain K residue 518 MET Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 277 CYS Chi-restraints excluded: chain N residue 368 THR Chi-restraints excluded: chain N residue 373 GLN Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 696 MET Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 465 SER Chi-restraints excluded: chain O residue 495 GLU Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 541 ILE Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 595 SER Chi-restraints excluded: chain O residue 598 THR Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 680 GLN Chi-restraints excluded: chain O residue 735 MET Chi-restraints excluded: chain O residue 744 LEU Chi-restraints excluded: chain O residue 752 ILE Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 51 SER Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 97 LYS Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 218 MET Chi-restraints excluded: chain P residue 227 THR Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 321 HIS Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 382 SER Chi-restraints excluded: chain P residue 435 MET Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 524 LYS Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 57 TRP Chi-restraints excluded: chain R residue 67 ASN Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 393 LEU Chi-restraints excluded: chain R residue 488 LEU Chi-restraints excluded: chain S residue 389 CYS Chi-restraints excluded: chain S residue 391 LEU Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 279 ASP Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 305 ILE Chi-restraints excluded: chain X residue 329 CYS Chi-restraints excluded: chain X residue 355 TYR Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 450 VAL Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain X residue 465 LEU Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 198 GLN Chi-restraints excluded: chain Y residue 229 THR Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 303 TYR Chi-restraints excluded: chain Y residue 359 LEU Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 423 ILE Chi-restraints excluded: chain Y residue 450 VAL Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 526 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 781 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 461 optimal weight: 3.9990 chunk 592 optimal weight: 0.7980 chunk 458 optimal weight: 7.9990 chunk 682 optimal weight: 9.9990 chunk 452 optimal weight: 0.9990 chunk 807 optimal weight: 5.9990 chunk 505 optimal weight: 1.9990 chunk 492 optimal weight: 7.9990 chunk 372 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 125 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1646 GLN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 ASN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 530 GLN ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 387 GLN O 443 GLN R 314 GLN ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 289 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 67835 Z= 0.258 Angle : 0.715 18.856 91891 Z= 0.361 Chirality : 0.041 0.301 10362 Planarity : 0.004 0.088 11673 Dihedral : 6.850 88.448 9335 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.31 % Favored : 94.24 % Rotamer: Outliers : 4.70 % Allowed : 22.40 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % 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: 0.85 (0.09), residues: 8323 helix: 1.62 (0.07), residues: 5459 sheet: -0.54 (0.21), residues: 563 loop : -1.74 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 641 HIS 0.033 0.001 HIS J 314 PHE 0.043 0.001 PHE X 294 TYR 0.037 0.001 TYR O 161 ARG 0.015 0.000 ARG I 739 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 628 time to evaluate : 6.291 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: A 11 MET cc_start: 0.6888 (mmt) cc_final: 0.6361 (mpp) REVERT: A 42 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9297 (mt) REVERT: A 125 GLN cc_start: 0.9407 (OUTLIER) cc_final: 0.9198 (mt0) REVERT: A 161 MET cc_start: 0.9397 (mpp) cc_final: 0.8939 (mmt) REVERT: A 170 ILE cc_start: 0.9218 (mt) cc_final: 0.8941 (mm) REVERT: A 257 MET cc_start: 0.9252 (tpp) cc_final: 0.8815 (tpp) REVERT: A 449 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8584 (mp10) REVERT: A 488 MET cc_start: 0.9007 (ppp) cc_final: 0.8445 (ppp) REVERT: A 617 LEU cc_start: 0.9243 (mm) cc_final: 0.8906 (tp) REVERT: A 788 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.8928 (tm-30) REVERT: A 871 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8258 (ptp-110) REVERT: A 934 MET cc_start: 0.9672 (ttm) cc_final: 0.9289 (tpp) REVERT: A 945 GLU cc_start: 0.9623 (OUTLIER) cc_final: 0.9362 (mt-10) REVERT: A 1203 MET cc_start: 0.9125 (tpp) cc_final: 0.8690 (mmt) REVERT: A 1242 GLU cc_start: 0.8089 (mp0) cc_final: 0.7535 (tm-30) REVERT: A 1320 ASN cc_start: 0.8646 (t0) cc_final: 0.8251 (t0) REVERT: A 1397 ASP cc_start: 0.9240 (m-30) cc_final: 0.8834 (t0) REVERT: A 1480 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8598 (tp30) REVERT: A 1574 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9111 (pp) REVERT: A 1623 ASP cc_start: 0.9280 (t0) cc_final: 0.9028 (t70) REVERT: A 1646 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8453 (tp40) REVERT: A 1665 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8437 (pm20) REVERT: A 1785 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8341 (mt-10) REVERT: A 1816 GLN cc_start: 0.9010 (mt0) cc_final: 0.8665 (mm110) REVERT: B 1 MET cc_start: 0.6546 (mmt) cc_final: 0.5441 (mtp) REVERT: B 14 TRP cc_start: 0.6758 (OUTLIER) cc_final: 0.5270 (p-90) REVERT: B 16 TRP cc_start: 0.7038 (OUTLIER) cc_final: 0.5733 (t-100) REVERT: B 79 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6178 (tm-30) REVERT: C 84 MET cc_start: 0.9364 (tpp) cc_final: 0.9126 (tpp) REVERT: C 98 GLU cc_start: 0.9150 (pt0) cc_final: 0.8874 (pt0) REVERT: C 161 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8747 (mp) REVERT: C 168 ASP cc_start: 0.9221 (t70) cc_final: 0.8888 (m-30) REVERT: C 218 MET cc_start: 0.9418 (ttp) cc_final: 0.8942 (ptm) REVERT: C 244 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8460 (mm) REVERT: C 257 VAL cc_start: 0.9381 (OUTLIER) cc_final: 0.9142 (m) REVERT: C 435 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8696 (mpp) REVERT: C 480 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8968 (mp) REVERT: D 31 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8817 (tm-30) REVERT: D 42 GLN cc_start: 0.9573 (mt0) cc_final: 0.8828 (tm-30) REVERT: D 46 GLU cc_start: 0.9335 (mp0) cc_final: 0.8851 (mp0) REVERT: E 68 LYS cc_start: 0.9475 (tttp) cc_final: 0.9193 (mtmm) REVERT: E 93 GLU cc_start: 0.9300 (pm20) cc_final: 0.9054 (pm20) REVERT: F 534 GLU cc_start: 0.9271 (tp30) cc_final: 0.8695 (tt0) REVERT: F 568 GLU cc_start: 0.9405 (mt-10) cc_final: 0.9176 (mp0) REVERT: G 5 LYS cc_start: 0.9636 (OUTLIER) cc_final: 0.9414 (mtmm) REVERT: G 17 GLU cc_start: 0.9571 (tp30) cc_final: 0.9336 (tm-30) REVERT: H 89 GLU cc_start: 0.9675 (tt0) cc_final: 0.9425 (tm-30) REVERT: H 496 TYR cc_start: 0.9089 (t80) cc_final: 0.8712 (t80) REVERT: H 616 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8978 (mp0) REVERT: H 643 MET cc_start: 0.9311 (mtp) cc_final: 0.9065 (mmm) REVERT: H 699 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8622 (t0) REVERT: H 733 VAL cc_start: 0.9365 (OUTLIER) cc_final: 0.9127 (p) REVERT: I 440 MET cc_start: 0.8779 (mpp) cc_final: 0.8396 (mpp) REVERT: J 170 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8954 (pt) REVERT: J 258 MET cc_start: 0.9061 (mmm) cc_final: 0.8832 (mmm) REVERT: J 400 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.9026 (pm20) REVERT: J 448 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8924 (mm) REVERT: J 477 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.8891 (mm110) REVERT: K 8 LYS cc_start: 0.9591 (OUTLIER) cc_final: 0.9320 (pttm) REVERT: K 164 PHE cc_start: 0.9422 (t80) cc_final: 0.8976 (t80) REVERT: K 190 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8227 (tp) REVERT: K 283 GLU cc_start: 0.9717 (mm-30) cc_final: 0.9399 (mp0) REVERT: K 347 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8541 (tm-30) REVERT: K 349 GLU cc_start: 0.9300 (mm-30) cc_final: 0.9053 (mm-30) REVERT: L 63 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9167 (mt) REVERT: L 71 LYS cc_start: 0.8979 (tttm) cc_final: 0.8639 (ttmm) REVERT: L 150 ASP cc_start: 0.8818 (m-30) cc_final: 0.8591 (m-30) REVERT: L 178 MET cc_start: 0.9245 (mmm) cc_final: 0.8914 (mmm) REVERT: L 181 ARG cc_start: 0.9396 (OUTLIER) cc_final: 0.9002 (ttp80) REVERT: M 6 GLN cc_start: 0.8534 (pm20) cc_final: 0.8193 (pm20) REVERT: M 23 LYS cc_start: 0.9380 (mmmt) cc_final: 0.9122 (mmmt) REVERT: M 27 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8388 (tp30) REVERT: M 28 ASP cc_start: 0.9305 (m-30) cc_final: 0.8673 (p0) REVERT: M 66 HIS cc_start: 0.9220 (t-90) cc_final: 0.9015 (t-90) REVERT: N 277 CYS cc_start: 0.9555 (OUTLIER) cc_final: 0.9223 (p) REVERT: N 361 LEU cc_start: 0.9443 (tp) cc_final: 0.9161 (tp) REVERT: N 373 GLN cc_start: 0.9527 (OUTLIER) cc_final: 0.9065 (tm-30) REVERT: N 622 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.6970 (m-80) REVERT: N 670 PHE cc_start: 0.3475 (OUTLIER) cc_final: 0.2482 (m-80) REVERT: N 676 TRP cc_start: 0.6792 (m-10) cc_final: 0.6426 (m-10) REVERT: N 687 MET cc_start: 0.1085 (mtt) cc_final: 0.0868 (mtt) REVERT: N 696 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8116 (tmm) REVERT: O 287 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8917 (mp0) REVERT: O 440 GLN cc_start: 0.9294 (tm-30) cc_final: 0.8973 (tm-30) REVERT: O 495 GLU cc_start: 0.9467 (OUTLIER) cc_final: 0.9174 (pp20) REVERT: O 506 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9030 (pp) REVERT: O 517 ASP cc_start: 0.9690 (m-30) cc_final: 0.9326 (p0) REVERT: O 529 ASP cc_start: 0.9574 (t0) cc_final: 0.9288 (m-30) REVERT: O 636 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9172 (pt) REVERT: O 664 MET cc_start: 0.9497 (mmm) cc_final: 0.9065 (mmm) REVERT: O 735 MET cc_start: 0.9594 (OUTLIER) cc_final: 0.9128 (mtt) REVERT: P 148 ASN cc_start: 0.8914 (m110) cc_final: 0.8417 (p0) REVERT: P 246 GLU cc_start: 0.9537 (tp30) cc_final: 0.9318 (tm-30) REVERT: P 298 GLU cc_start: 0.9562 (tt0) cc_final: 0.9307 (mp0) REVERT: P 524 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6742 (mmmt) REVERT: S 361 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8528 (mp0) REVERT: S 362 PHE cc_start: 0.7480 (m-80) cc_final: 0.7254 (m-80) REVERT: S 386 LYS cc_start: 0.8015 (tppt) cc_final: 0.7576 (tptp) REVERT: S 411 CYS cc_start: 0.8337 (t) cc_final: 0.7992 (p) REVERT: S 412 ASN cc_start: 0.6817 (m-40) cc_final: 0.5964 (t0) REVERT: W 17 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8651 (tm-30) REVERT: W 21 ASN cc_start: 0.8604 (m-40) cc_final: 0.7890 (m-40) REVERT: X 44 MET cc_start: 0.9660 (mmm) cc_final: 0.9439 (mmm) REVERT: X 79 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9458 (tp) REVERT: X 92 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8950 (pm20) REVERT: X 136 ILE cc_start: 0.9515 (OUTLIER) cc_final: 0.9208 (tp) REVERT: X 137 GLU cc_start: 0.9708 (mt-10) cc_final: 0.9344 (tm-30) REVERT: X 367 GLN cc_start: 0.9573 (tm-30) cc_final: 0.9197 (pt0) REVERT: X 427 MET cc_start: 0.8989 (tmm) cc_final: 0.8652 (tpp) REVERT: X 459 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8797 (mp0) REVERT: Y 71 PHE cc_start: 0.8707 (m-80) cc_final: 0.8276 (m-80) REVERT: Y 304 LEU cc_start: 0.8820 (mt) cc_final: 0.8549 (tp) REVERT: Y 378 LEU cc_start: 0.9277 (tt) cc_final: 0.9064 (pp) REVERT: Y 451 CYS cc_start: 0.9384 (m) cc_final: 0.9060 (p) REVERT: Y 541 ASN cc_start: 0.9219 (m-40) cc_final: 0.8958 (t0) REVERT: Y 549 MET cc_start: 0.8968 (mmt) cc_final: 0.8629 (mmt) outliers start: 327 outliers final: 229 residues processed: 893 average time/residue: 0.6054 time to fit residues: 947.2928 Evaluate side-chains 856 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 586 time to evaluate : 6.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 871 ARG Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1639 LYS Chi-restraints excluded: chain A residue 1646 GLN Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1665 GLN Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1752 SER Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1785 GLU Chi-restraints excluded: chain A residue 1786 THR Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1854 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 549 ASP Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 596 VAL Chi-restraints excluded: chain F residue 685 SER Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 548 LYS Chi-restraints excluded: chain H residue 562 MET Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 579 LEU Chi-restraints excluded: chain H residue 653 LEU Chi-restraints excluded: chain H residue 699 ASP Chi-restraints excluded: chain H residue 733 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 423 VAL Chi-restraints excluded: chain I residue 477 GLN Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 560 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 343 SER Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 400 GLU Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain J residue 527 ILE Chi-restraints excluded: chain K residue 8 LYS Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 246 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 407 GLU Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 497 ASN Chi-restraints excluded: chain K residue 518 MET Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 277 CYS Chi-restraints excluded: chain N residue 373 GLN Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 560 MET Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 696 MET Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 396 ASN Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 443 GLN Chi-restraints excluded: chain O residue 465 SER Chi-restraints excluded: chain O residue 495 GLU Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 541 ILE Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 595 SER Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 634 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 680 GLN Chi-restraints excluded: chain O residue 735 MET Chi-restraints excluded: chain O residue 744 LEU Chi-restraints excluded: chain O residue 752 ILE Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 97 LYS Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 218 MET Chi-restraints excluded: chain P residue 227 THR Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 321 HIS Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 382 SER Chi-restraints excluded: chain P residue 435 MET Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 524 LYS Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 67 ASN Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 340 TRP Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 393 LEU Chi-restraints excluded: chain R residue 488 LEU Chi-restraints excluded: chain S residue 389 CYS Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 329 CYS Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 450 VAL Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain X residue 465 LEU Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 229 THR Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 270 ASN Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 359 LEU Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 372 SER Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 526 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 499 optimal weight: 0.0870 chunk 322 optimal weight: 6.9990 chunk 482 optimal weight: 7.9990 chunk 243 optimal weight: 0.5980 chunk 158 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 513 optimal weight: 10.0000 chunk 550 optimal weight: 10.0000 chunk 399 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 634 optimal weight: 8.9990 overall best weight: 3.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 124 GLN A 125 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1646 GLN A1665 GLN F 595 GLN H 599 ASN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN O 753 ASN P 202 HIS R 158 GLN T 6 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 67835 Z= 0.293 Angle : 0.725 18.826 91891 Z= 0.367 Chirality : 0.041 0.316 10362 Planarity : 0.004 0.087 11673 Dihedral : 6.705 89.880 9324 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.60 % Favored : 93.97 % Rotamer: Outliers : 4.55 % Allowed : 22.81 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % 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: 0.84 (0.09), residues: 8323 helix: 1.63 (0.07), residues: 5453 sheet: -0.52 (0.21), residues: 548 loop : -1.78 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 641 HIS 0.014 0.001 HIS X 395 PHE 0.044 0.001 PHE X 294 TYR 0.037 0.001 TYR O 161 ARG 0.010 0.000 ARG S 393 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 605 time to evaluate : 6.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7017 (mmt) cc_final: 0.6399 (mpp) REVERT: A 42 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9136 (mt) REVERT: A 161 MET cc_start: 0.9391 (mpp) cc_final: 0.8948 (mmt) REVERT: A 170 ILE cc_start: 0.9192 (mt) cc_final: 0.8911 (mm) REVERT: A 257 MET cc_start: 0.9259 (tpp) cc_final: 0.8813 (tpp) REVERT: A 449 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8528 (mp10) REVERT: A 488 MET cc_start: 0.9011 (ppp) cc_final: 0.8444 (ppp) REVERT: A 617 LEU cc_start: 0.9274 (mm) cc_final: 0.8963 (tp) REVERT: A 667 MET cc_start: 0.8775 (mmm) cc_final: 0.8414 (tpt) REVERT: A 788 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.8903 (tm-30) REVERT: A 871 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8263 (ptp-110) REVERT: A 934 MET cc_start: 0.9672 (ttm) cc_final: 0.9291 (tpp) REVERT: A 945 GLU cc_start: 0.9630 (OUTLIER) cc_final: 0.9367 (mt-10) REVERT: A 1203 MET cc_start: 0.9139 (tpp) cc_final: 0.8651 (mmt) REVERT: A 1242 GLU cc_start: 0.8169 (mp0) cc_final: 0.7674 (tm-30) REVERT: A 1320 ASN cc_start: 0.8649 (t0) cc_final: 0.8268 (t0) REVERT: A 1397 ASP cc_start: 0.9238 (m-30) cc_final: 0.8831 (t0) REVERT: A 1480 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8664 (tp30) REVERT: A 1574 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9094 (pp) REVERT: A 1623 ASP cc_start: 0.9273 (t0) cc_final: 0.9009 (t70) REVERT: A 1646 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8423 (tp40) REVERT: A 1665 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: A 1785 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8350 (mt-10) REVERT: B 1 MET cc_start: 0.6661 (mmt) cc_final: 0.5773 (mtp) REVERT: B 14 TRP cc_start: 0.6532 (OUTLIER) cc_final: 0.4740 (p-90) REVERT: B 16 TRP cc_start: 0.6999 (OUTLIER) cc_final: 0.5679 (t-100) REVERT: C 84 MET cc_start: 0.9360 (tpp) cc_final: 0.9126 (tpp) REVERT: C 98 GLU cc_start: 0.9177 (pt0) cc_final: 0.8900 (pt0) REVERT: C 168 ASP cc_start: 0.9265 (t70) cc_final: 0.8932 (m-30) REVERT: C 218 MET cc_start: 0.9433 (ttp) cc_final: 0.8950 (ptm) REVERT: C 244 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8558 (mm) REVERT: C 257 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9139 (m) REVERT: C 435 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8706 (mpp) REVERT: C 480 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8976 (mp) REVERT: D 31 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8863 (tm-30) REVERT: D 42 GLN cc_start: 0.9574 (mt0) cc_final: 0.8815 (tm-30) REVERT: D 46 GLU cc_start: 0.9323 (mp0) cc_final: 0.8831 (mp0) REVERT: E 68 LYS cc_start: 0.9471 (tttp) cc_final: 0.9191 (mtmm) REVERT: E 80 GLU cc_start: 0.9539 (mm-30) cc_final: 0.9186 (pt0) REVERT: E 93 GLU cc_start: 0.9310 (pm20) cc_final: 0.9052 (pm20) REVERT: F 534 GLU cc_start: 0.9223 (tp30) cc_final: 0.8638 (tt0) REVERT: G 5 LYS cc_start: 0.9633 (OUTLIER) cc_final: 0.9419 (mtmm) REVERT: H 89 GLU cc_start: 0.9677 (tt0) cc_final: 0.9424 (tm-30) REVERT: H 98 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.8045 (t0) REVERT: H 496 TYR cc_start: 0.9096 (t80) cc_final: 0.8695 (t80) REVERT: H 616 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8880 (pm20) REVERT: H 643 MET cc_start: 0.9313 (mtp) cc_final: 0.9081 (mmm) REVERT: H 699 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8664 (t0) REVERT: H 733 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9111 (p) REVERT: I 185 ILE cc_start: 0.9714 (OUTLIER) cc_final: 0.9466 (tp) REVERT: I 440 MET cc_start: 0.8785 (mpp) cc_final: 0.8419 (mpp) REVERT: J 400 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.9025 (pm20) REVERT: J 448 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8942 (mm) REVERT: J 477 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8784 (mm110) REVERT: K 8 LYS cc_start: 0.9593 (OUTLIER) cc_final: 0.9318 (pttm) REVERT: K 164 PHE cc_start: 0.9410 (t80) cc_final: 0.9204 (t80) REVERT: K 190 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8232 (tp) REVERT: K 283 GLU cc_start: 0.9711 (mm-30) cc_final: 0.9372 (mp0) REVERT: K 347 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8528 (tm-30) REVERT: K 349 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8999 (mm-30) REVERT: K 454 VAL cc_start: 0.9418 (OUTLIER) cc_final: 0.9208 (p) REVERT: L 63 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9175 (mt) REVERT: L 71 LYS cc_start: 0.8972 (tttm) cc_final: 0.8634 (ttmm) REVERT: L 178 MET cc_start: 0.9249 (mmm) cc_final: 0.8934 (mmm) REVERT: L 181 ARG cc_start: 0.9398 (OUTLIER) cc_final: 0.8963 (ttp80) REVERT: M 6 GLN cc_start: 0.8547 (pm20) cc_final: 0.8220 (pm20) REVERT: M 27 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8373 (tp30) REVERT: M 28 ASP cc_start: 0.9303 (m-30) cc_final: 0.8672 (p0) REVERT: N 277 CYS cc_start: 0.9578 (OUTLIER) cc_final: 0.9267 (p) REVERT: N 361 LEU cc_start: 0.9435 (tp) cc_final: 0.9139 (tp) REVERT: N 373 GLN cc_start: 0.9506 (OUTLIER) cc_final: 0.9021 (tm-30) REVERT: N 387 LEU cc_start: 0.8834 (mt) cc_final: 0.8481 (mt) REVERT: N 622 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.6945 (m-80) REVERT: N 670 PHE cc_start: 0.3479 (OUTLIER) cc_final: 0.2643 (m-80) REVERT: N 676 TRP cc_start: 0.6772 (m-10) cc_final: 0.6408 (m-10) REVERT: N 696 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8068 (tmm) REVERT: O 287 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8920 (mp0) REVERT: O 329 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8786 (ttp-110) REVERT: O 419 ASP cc_start: 0.9388 (m-30) cc_final: 0.8972 (p0) REVERT: O 440 GLN cc_start: 0.9311 (tm-30) cc_final: 0.9107 (pp30) REVERT: O 495 GLU cc_start: 0.9492 (OUTLIER) cc_final: 0.9207 (pp20) REVERT: O 506 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9035 (pp) REVERT: O 517 ASP cc_start: 0.9684 (m-30) cc_final: 0.9327 (p0) REVERT: O 529 ASP cc_start: 0.9559 (t0) cc_final: 0.9300 (m-30) REVERT: O 636 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9177 (pt) REVERT: O 664 MET cc_start: 0.9492 (mmm) cc_final: 0.9067 (mmm) REVERT: P 148 ASN cc_start: 0.8904 (m110) cc_final: 0.8410 (p0) REVERT: P 246 GLU cc_start: 0.9603 (tp30) cc_final: 0.9377 (tm-30) REVERT: P 298 GLU cc_start: 0.9527 (tt0) cc_final: 0.9269 (mp0) REVERT: P 524 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6640 (mmmt) REVERT: R 266 MET cc_start: 0.2556 (tpp) cc_final: 0.2230 (tpt) REVERT: S 361 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8505 (mp0) REVERT: S 362 PHE cc_start: 0.7352 (m-80) cc_final: 0.7094 (m-80) REVERT: S 386 LYS cc_start: 0.7902 (tppt) cc_final: 0.7520 (tptp) REVERT: S 411 CYS cc_start: 0.8299 (t) cc_final: 0.7961 (p) REVERT: S 412 ASN cc_start: 0.6807 (m-40) cc_final: 0.5937 (t0) REVERT: W 17 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8647 (tm-30) REVERT: W 21 ASN cc_start: 0.8606 (m-40) cc_final: 0.7894 (m-40) REVERT: X 44 MET cc_start: 0.9658 (mmm) cc_final: 0.9413 (mmm) REVERT: X 79 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9458 (tp) REVERT: X 92 GLU cc_start: 0.9411 (mt-10) cc_final: 0.8969 (pm20) REVERT: X 136 ILE cc_start: 0.9514 (OUTLIER) cc_final: 0.9210 (tp) REVERT: X 137 GLU cc_start: 0.9708 (mt-10) cc_final: 0.9341 (tm-30) REVERT: X 427 MET cc_start: 0.8975 (tmm) cc_final: 0.8690 (tpp) REVERT: Y 71 PHE cc_start: 0.8721 (m-80) cc_final: 0.8287 (m-80) REVERT: Y 294 PHE cc_start: 0.8351 (t80) cc_final: 0.8081 (t80) REVERT: Y 304 LEU cc_start: 0.8833 (mt) cc_final: 0.8552 (tp) REVERT: Y 451 CYS cc_start: 0.9381 (m) cc_final: 0.8969 (p) REVERT: Y 541 ASN cc_start: 0.9225 (m-40) cc_final: 0.8973 (t0) REVERT: Y 549 MET cc_start: 0.8977 (mmt) cc_final: 0.8653 (mmt) outliers start: 317 outliers final: 240 residues processed: 864 average time/residue: 0.5980 time to fit residues: 907.4535 Evaluate side-chains 857 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 576 time to evaluate : 7.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 871 ARG Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1639 LYS Chi-restraints excluded: chain A residue 1646 GLN Chi-restraints excluded: chain A residue 1650 GLU Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1665 GLN Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1684 THR Chi-restraints excluded: chain A residue 1752 SER Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1785 GLU Chi-restraints excluded: chain A residue 1786 THR Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 549 ASP Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 685 SER Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 548 LYS Chi-restraints excluded: chain H residue 549 ASP Chi-restraints excluded: chain H residue 562 MET Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 579 LEU Chi-restraints excluded: chain H residue 653 LEU Chi-restraints excluded: chain H residue 699 ASP Chi-restraints excluded: chain H residue 733 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 423 VAL Chi-restraints excluded: chain I residue 477 GLN Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 560 THR Chi-restraints excluded: chain I residue 722 VAL Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 179 GLN Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 250 CYS Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 343 SER Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 400 GLU Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain J residue 527 ILE Chi-restraints excluded: chain K residue 8 LYS Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 246 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 407 GLU Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 497 ASN Chi-restraints excluded: chain K residue 518 MET Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 7 ARG Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 277 CYS Chi-restraints excluded: chain N residue 373 GLN Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 560 MET Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 696 MET Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain O residue 329 ARG Chi-restraints excluded: chain O residue 369 VAL Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 396 ASN Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 465 SER Chi-restraints excluded: chain O residue 495 GLU Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 595 SER Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 634 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 680 GLN Chi-restraints excluded: chain O residue 744 LEU Chi-restraints excluded: chain O residue 752 ILE Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 51 SER Chi-restraints excluded: chain P residue 97 LYS Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 218 MET Chi-restraints excluded: chain P residue 227 THR Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 321 HIS Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 382 SER Chi-restraints excluded: chain P residue 435 MET Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 524 LYS Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 67 ASN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 340 TRP Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 393 LEU Chi-restraints excluded: chain R residue 488 LEU Chi-restraints excluded: chain S residue 389 CYS Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 303 TYR Chi-restraints excluded: chain X residue 329 CYS Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 450 VAL Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain X residue 465 LEU Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 229 THR Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 270 ASN Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 359 LEU Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 372 SER Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 515 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 734 optimal weight: 7.9990 chunk 773 optimal weight: 8.9990 chunk 705 optimal weight: 7.9990 chunk 752 optimal weight: 6.9990 chunk 453 optimal weight: 8.9990 chunk 327 optimal weight: 9.9990 chunk 591 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 680 optimal weight: 8.9990 chunk 711 optimal weight: 30.0000 chunk 750 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 595 GLN H 599 ASN H 759 ASN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 235 GLN ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 HIS ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN R 56 ASN X 66 ASN X 458 GLN X 471 GLN Y 374 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 67835 Z= 0.374 Angle : 0.762 18.817 91891 Z= 0.388 Chirality : 0.043 0.355 10362 Planarity : 0.005 0.086 11673 Dihedral : 6.675 87.144 9314 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.08 % Favored : 93.48 % Rotamer: Outliers : 4.50 % Allowed : 23.11 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.09), residues: 8323 helix: 1.54 (0.07), residues: 5461 sheet: -0.62 (0.21), residues: 576 loop : -1.83 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 641 HIS 0.014 0.001 HIS M 66 PHE 0.045 0.002 PHE X 294 TYR 0.038 0.002 TYR O 161 ARG 0.009 0.001 ARG S 393 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 582 time to evaluate : 6.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7121 (mmt) cc_final: 0.6521 (mpp) REVERT: A 42 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9096 (mt) REVERT: A 257 MET cc_start: 0.9236 (tpp) cc_final: 0.8844 (tpp) REVERT: A 449 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8569 (mp10) REVERT: A 488 MET cc_start: 0.9080 (ppp) cc_final: 0.8497 (ppp) REVERT: A 617 LEU cc_start: 0.9367 (mm) cc_final: 0.9062 (tp) REVERT: A 667 MET cc_start: 0.8824 (mmm) cc_final: 0.8463 (tpt) REVERT: A 788 GLU cc_start: 0.9325 (OUTLIER) cc_final: 0.8911 (tm-30) REVERT: A 871 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8289 (ttp-110) REVERT: A 934 MET cc_start: 0.9672 (ttm) cc_final: 0.9298 (tpp) REVERT: A 945 GLU cc_start: 0.9635 (OUTLIER) cc_final: 0.9368 (mt-10) REVERT: A 1171 GLU cc_start: 0.9409 (pt0) cc_final: 0.8943 (pm20) REVERT: A 1203 MET cc_start: 0.9111 (tpp) cc_final: 0.8682 (mmt) REVERT: A 1320 ASN cc_start: 0.8693 (t0) cc_final: 0.8324 (t0) REVERT: A 1397 ASP cc_start: 0.9237 (m-30) cc_final: 0.8829 (t0) REVERT: A 1480 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8665 (tp30) REVERT: A 1574 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9126 (pp) REVERT: A 1623 ASP cc_start: 0.9241 (t0) cc_final: 0.8993 (t70) REVERT: A 1665 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8476 (pm20) REVERT: A 1785 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8401 (mt-10) REVERT: B 1 MET cc_start: 0.6305 (mmt) cc_final: 0.5718 (mtp) REVERT: B 14 TRP cc_start: 0.6470 (OUTLIER) cc_final: 0.4221 (p-90) REVERT: B 16 TRP cc_start: 0.6780 (OUTLIER) cc_final: 0.5627 (t-100) REVERT: B 81 LYS cc_start: 0.8382 (pttm) cc_final: 0.8176 (mmmt) REVERT: C 84 MET cc_start: 0.9366 (tpp) cc_final: 0.9130 (tpp) REVERT: C 98 GLU cc_start: 0.9219 (pt0) cc_final: 0.9015 (pt0) REVERT: C 133 GLU cc_start: 0.9135 (pt0) cc_final: 0.8793 (pp20) REVERT: C 168 ASP cc_start: 0.9284 (t70) cc_final: 0.8946 (m-30) REVERT: C 218 MET cc_start: 0.9433 (ttp) cc_final: 0.8943 (ptm) REVERT: C 244 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8541 (mm) REVERT: C 257 VAL cc_start: 0.9364 (OUTLIER) cc_final: 0.9129 (m) REVERT: C 435 MET cc_start: 0.9173 (mmt) cc_final: 0.8861 (mpp) REVERT: C 480 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8917 (mp) REVERT: D 31 GLN cc_start: 0.9079 (tt0) cc_final: 0.8862 (tm-30) REVERT: D 42 GLN cc_start: 0.9575 (mt0) cc_final: 0.9043 (tm-30) REVERT: E 68 LYS cc_start: 0.9462 (tttp) cc_final: 0.9180 (mtmm) REVERT: E 80 GLU cc_start: 0.9527 (mm-30) cc_final: 0.9177 (pt0) REVERT: E 93 GLU cc_start: 0.9280 (pm20) cc_final: 0.9065 (pm20) REVERT: F 469 MET cc_start: 0.9471 (OUTLIER) cc_final: 0.9242 (mpp) REVERT: F 534 GLU cc_start: 0.9265 (tp30) cc_final: 0.8635 (tm-30) REVERT: G 5 LYS cc_start: 0.9607 (OUTLIER) cc_final: 0.9394 (mtmm) REVERT: H 89 GLU cc_start: 0.9703 (tt0) cc_final: 0.9445 (tm-30) REVERT: H 616 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8972 (mp0) REVERT: H 643 MET cc_start: 0.9319 (mtp) cc_final: 0.9088 (mmm) REVERT: H 699 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8613 (t0) REVERT: H 733 VAL cc_start: 0.9382 (OUTLIER) cc_final: 0.9128 (p) REVERT: I 185 ILE cc_start: 0.9703 (OUTLIER) cc_final: 0.9453 (tp) REVERT: I 440 MET cc_start: 0.8814 (mpp) cc_final: 0.8468 (mpp) REVERT: J 239 GLU cc_start: 0.9447 (tt0) cc_final: 0.9239 (pt0) REVERT: J 258 MET cc_start: 0.9102 (mmm) cc_final: 0.8895 (mmm) REVERT: J 400 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.9012 (pm20) REVERT: J 448 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8988 (mm) REVERT: J 477 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.8823 (mm110) REVERT: K 8 LYS cc_start: 0.9597 (OUTLIER) cc_final: 0.9315 (pttm) REVERT: K 72 CYS cc_start: 0.9240 (m) cc_final: 0.8755 (t) REVERT: K 164 PHE cc_start: 0.9410 (t80) cc_final: 0.9158 (t80) REVERT: K 190 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8265 (tp) REVERT: K 283 GLU cc_start: 0.9711 (mm-30) cc_final: 0.9369 (mp0) REVERT: K 347 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8733 (tm-30) REVERT: L 63 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9071 (mt) REVERT: L 71 LYS cc_start: 0.8935 (tttm) cc_final: 0.8603 (ttmm) REVERT: L 178 MET cc_start: 0.9248 (mmm) cc_final: 0.9009 (mmm) REVERT: L 181 ARG cc_start: 0.9424 (OUTLIER) cc_final: 0.9143 (tmm-80) REVERT: M 27 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8360 (tp30) REVERT: M 28 ASP cc_start: 0.9292 (m-30) cc_final: 0.8698 (p0) REVERT: N 277 CYS cc_start: 0.9588 (m) cc_final: 0.9244 (p) REVERT: N 369 ASP cc_start: 0.9476 (t0) cc_final: 0.9062 (m-30) REVERT: N 373 GLN cc_start: 0.9503 (OUTLIER) cc_final: 0.9147 (tp40) REVERT: N 622 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.6909 (m-80) REVERT: N 670 PHE cc_start: 0.3575 (OUTLIER) cc_final: 0.2530 (m-80) REVERT: N 696 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8072 (tmm) REVERT: O 287 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8932 (mp0) REVERT: O 419 ASP cc_start: 0.9344 (m-30) cc_final: 0.8952 (p0) REVERT: O 440 GLN cc_start: 0.9344 (tm-30) cc_final: 0.8990 (tm-30) REVERT: O 495 GLU cc_start: 0.9501 (OUTLIER) cc_final: 0.9284 (pp20) REVERT: O 506 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9028 (pp) REVERT: O 517 ASP cc_start: 0.9702 (m-30) cc_final: 0.9330 (p0) REVERT: O 529 ASP cc_start: 0.9610 (t0) cc_final: 0.9335 (m-30) REVERT: O 636 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9144 (pt) REVERT: O 664 MET cc_start: 0.9496 (mmm) cc_final: 0.9062 (mmm) REVERT: O 735 MET cc_start: 0.9482 (tmm) cc_final: 0.9052 (mtt) REVERT: P 84 MET cc_start: 0.9324 (tpp) cc_final: 0.8970 (tpp) REVERT: P 148 ASN cc_start: 0.8881 (m110) cc_final: 0.8489 (p0) REVERT: P 246 GLU cc_start: 0.9608 (tp30) cc_final: 0.9381 (tm-30) REVERT: P 298 GLU cc_start: 0.9528 (tt0) cc_final: 0.9274 (mp0) REVERT: R 454 ASP cc_start: 0.4703 (p0) cc_final: 0.4443 (m-30) REVERT: S 361 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8534 (mp0) REVERT: S 386 LYS cc_start: 0.7852 (tppt) cc_final: 0.7514 (tptp) REVERT: S 411 CYS cc_start: 0.8276 (t) cc_final: 0.7966 (p) REVERT: S 412 ASN cc_start: 0.6635 (m-40) cc_final: 0.5855 (t0) REVERT: W 17 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8689 (tm-30) REVERT: W 21 ASN cc_start: 0.8627 (m-40) cc_final: 0.7940 (m-40) REVERT: X 79 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9457 (tp) REVERT: X 92 GLU cc_start: 0.9455 (mt-10) cc_final: 0.9009 (pm20) REVERT: X 137 GLU cc_start: 0.9704 (mt-10) cc_final: 0.9306 (tm-30) REVERT: X 367 GLN cc_start: 0.9481 (tm-30) cc_final: 0.9139 (pt0) REVERT: X 427 MET cc_start: 0.9013 (tmm) cc_final: 0.8718 (tpp) REVERT: Y 71 PHE cc_start: 0.8604 (m-80) cc_final: 0.8193 (m-80) REVERT: Y 294 PHE cc_start: 0.8321 (t80) cc_final: 0.8012 (t80) REVERT: Y 304 LEU cc_start: 0.9015 (mt) cc_final: 0.8786 (tp) REVERT: Y 451 CYS cc_start: 0.9323 (m) cc_final: 0.8947 (p) REVERT: Y 549 MET cc_start: 0.8985 (mmt) cc_final: 0.8641 (mmt) outliers start: 313 outliers final: 249 residues processed: 843 average time/residue: 0.6339 time to fit residues: 941.1044 Evaluate side-chains 845 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 563 time to evaluate : 6.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 871 ARG Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1639 LYS Chi-restraints excluded: chain A residue 1650 GLU Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1665 GLN Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1684 THR Chi-restraints excluded: chain A residue 1752 SER Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1785 GLU Chi-restraints excluded: chain A residue 1786 THR Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 549 ASP Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 685 SER Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 548 LYS Chi-restraints excluded: chain H residue 549 ASP Chi-restraints excluded: chain H residue 562 MET Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 579 LEU Chi-restraints excluded: chain H residue 653 LEU Chi-restraints excluded: chain H residue 699 ASP Chi-restraints excluded: chain H residue 733 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 423 VAL Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 477 GLN Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 560 THR Chi-restraints excluded: chain I residue 631 VAL Chi-restraints excluded: chain I residue 717 MET Chi-restraints excluded: chain I residue 722 VAL Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 179 GLN Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 250 CYS Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 343 SER Chi-restraints excluded: chain J residue 378 TYR Chi-restraints excluded: chain J residue 400 GLU Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain J residue 527 ILE Chi-restraints excluded: chain K residue 8 LYS Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 246 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 359 THR Chi-restraints excluded: chain K residue 407 GLU Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 497 ASN Chi-restraints excluded: chain K residue 506 LEU Chi-restraints excluded: chain K residue 518 MET Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 7 ARG Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 368 THR Chi-restraints excluded: chain N residue 373 GLN Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 396 ILE Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 696 MET Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain O residue 329 ARG Chi-restraints excluded: chain O residue 369 VAL Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 396 ASN Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 443 GLN Chi-restraints excluded: chain O residue 465 SER Chi-restraints excluded: chain O residue 495 GLU Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 595 SER Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 634 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 680 GLN Chi-restraints excluded: chain O residue 744 LEU Chi-restraints excluded: chain O residue 752 ILE Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 51 SER Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 97 LYS Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 227 THR Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 321 HIS Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 382 SER Chi-restraints excluded: chain P residue 435 MET Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 524 LYS Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 67 ASN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 340 TRP Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 393 LEU Chi-restraints excluded: chain R residue 488 LEU Chi-restraints excluded: chain S residue 389 CYS Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 329 CYS Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 450 VAL Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain X residue 465 LEU Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 229 THR Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 270 ASN Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 359 LEU Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 372 SER Chi-restraints excluded: chain Y residue 373 VAL Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 513 ARG Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 526 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 494 optimal weight: 0.9980 chunk 795 optimal weight: 0.9980 chunk 485 optimal weight: 0.2980 chunk 377 optimal weight: 0.0000 chunk 553 optimal weight: 2.9990 chunk 834 optimal weight: 2.9990 chunk 768 optimal weight: 5.9990 chunk 664 optimal weight: 0.0470 chunk 69 optimal weight: 0.9980 chunk 513 optimal weight: 10.0000 chunk 407 optimal weight: 0.6980 overall best weight: 0.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 125 GLN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 GLN A1161 ASN ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 GLN ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 ASN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 235 GLN J 314 HIS ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 GLN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN O 753 ASN ** X 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 458 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 67835 Z= 0.195 Angle : 0.734 18.847 91891 Z= 0.363 Chirality : 0.041 0.307 10362 Planarity : 0.004 0.086 11673 Dihedral : 6.459 89.195 9312 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.14 % Favored : 94.45 % Rotamer: Outliers : 3.46 % Allowed : 24.17 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.09), residues: 8323 helix: 1.65 (0.07), residues: 5454 sheet: -0.43 (0.21), residues: 555 loop : -1.80 (0.13), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP O 507 HIS 0.008 0.001 HIS Y 348 PHE 0.040 0.001 PHE X 294 TYR 0.035 0.001 TYR O 161 ARG 0.009 0.001 ARG S 393 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 651 time to evaluate : 6.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6947 (mmt) cc_final: 0.6186 (mpp) REVERT: A 125 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8942 (mt0) REVERT: A 170 ILE cc_start: 0.9154 (mt) cc_final: 0.8871 (mm) REVERT: A 257 MET cc_start: 0.9194 (tpp) cc_final: 0.8821 (tpp) REVERT: A 449 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8558 (mp10) REVERT: A 488 MET cc_start: 0.9109 (ppp) cc_final: 0.8550 (ppp) REVERT: A 617 LEU cc_start: 0.9298 (mm) cc_final: 0.8957 (tp) REVERT: A 871 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8215 (ttp-110) REVERT: A 934 MET cc_start: 0.9674 (ttm) cc_final: 0.9321 (tpp) REVERT: A 945 GLU cc_start: 0.9614 (OUTLIER) cc_final: 0.9352 (mt-10) REVERT: A 1107 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8579 (mt) REVERT: A 1203 MET cc_start: 0.9123 (tpp) cc_final: 0.8724 (mmt) REVERT: A 1242 GLU cc_start: 0.8296 (mp0) cc_final: 0.7954 (tm-30) REVERT: A 1320 ASN cc_start: 0.8642 (t0) cc_final: 0.8248 (t0) REVERT: A 1373 MET cc_start: 0.9484 (mtm) cc_final: 0.9015 (ptp) REVERT: A 1397 ASP cc_start: 0.9236 (m-30) cc_final: 0.8830 (t0) REVERT: A 1480 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8715 (tp30) REVERT: A 1574 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9050 (pp) REVERT: A 1623 ASP cc_start: 0.9271 (t0) cc_final: 0.9007 (t70) REVERT: A 1665 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8600 (pm20) REVERT: A 1816 GLN cc_start: 0.8995 (mt0) cc_final: 0.8536 (mm-40) REVERT: B 1 MET cc_start: 0.6218 (mmt) cc_final: 0.5683 (mtp) REVERT: B 6 LYS cc_start: 0.5421 (OUTLIER) cc_final: 0.5170 (mtmm) REVERT: B 14 TRP cc_start: 0.6271 (OUTLIER) cc_final: 0.4508 (p-90) REVERT: B 16 TRP cc_start: 0.6712 (OUTLIER) cc_final: 0.5732 (t-100) REVERT: B 43 ASP cc_start: 0.7963 (t0) cc_final: 0.7747 (t0) REVERT: B 79 GLU cc_start: 0.7363 (tm-30) cc_final: 0.7140 (tm-30) REVERT: C 84 MET cc_start: 0.9371 (tpp) cc_final: 0.9130 (tpp) REVERT: C 98 GLU cc_start: 0.9016 (pt0) cc_final: 0.8734 (pt0) REVERT: C 168 ASP cc_start: 0.9244 (t70) cc_final: 0.8913 (m-30) REVERT: C 218 MET cc_start: 0.9464 (ttp) cc_final: 0.9133 (ptm) REVERT: C 257 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9138 (m) REVERT: C 435 MET cc_start: 0.9179 (mmt) cc_final: 0.8760 (mpp) REVERT: C 480 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8934 (mp) REVERT: D 31 GLN cc_start: 0.9084 (tt0) cc_final: 0.8788 (tm-30) REVERT: D 42 GLN cc_start: 0.9588 (mt0) cc_final: 0.8840 (tm-30) REVERT: D 46 GLU cc_start: 0.9242 (mp0) cc_final: 0.8823 (mp0) REVERT: E 68 LYS cc_start: 0.9445 (tttp) cc_final: 0.9154 (mtmm) REVERT: E 80 GLU cc_start: 0.9487 (mm-30) cc_final: 0.9151 (pt0) REVERT: F 469 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.9083 (mpp) REVERT: F 534 GLU cc_start: 0.9246 (tp30) cc_final: 0.8753 (tm-30) REVERT: G 5 LYS cc_start: 0.9628 (OUTLIER) cc_final: 0.9401 (mtmm) REVERT: H 89 GLU cc_start: 0.9682 (tt0) cc_final: 0.9384 (tm-30) REVERT: H 519 GLU cc_start: 0.9417 (tm-30) cc_final: 0.9159 (pp20) REVERT: H 616 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8816 (mp0) REVERT: H 643 MET cc_start: 0.9312 (mtp) cc_final: 0.9058 (mmm) REVERT: H 699 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8585 (t0) REVERT: I 185 ILE cc_start: 0.9716 (OUTLIER) cc_final: 0.9471 (tp) REVERT: I 440 MET cc_start: 0.8680 (mpp) cc_final: 0.8186 (mpp) REVERT: I 727 PHE cc_start: 0.9270 (t80) cc_final: 0.8752 (t80) REVERT: J 239 GLU cc_start: 0.9431 (tt0) cc_final: 0.9191 (pt0) REVERT: J 364 MET cc_start: 0.8956 (mtm) cc_final: 0.8745 (mtp) REVERT: J 400 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.9081 (pm20) REVERT: J 448 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8891 (mm) REVERT: J 477 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.8798 (mm110) REVERT: K 8 LYS cc_start: 0.9606 (OUTLIER) cc_final: 0.9327 (pttm) REVERT: K 190 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8164 (tp) REVERT: K 283 GLU cc_start: 0.9700 (mm-30) cc_final: 0.9382 (mp0) REVERT: K 347 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8755 (tm-30) REVERT: K 349 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9032 (mm-30) REVERT: L 63 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9133 (mt) REVERT: L 71 LYS cc_start: 0.8876 (tttm) cc_final: 0.8462 (ttmm) REVERT: L 150 ASP cc_start: 0.8868 (m-30) cc_final: 0.8411 (t0) REVERT: L 178 MET cc_start: 0.9141 (mmm) cc_final: 0.8908 (mmm) REVERT: L 181 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.9141 (tmm-80) REVERT: M 23 LYS cc_start: 0.9339 (mmmt) cc_final: 0.9118 (mmmt) REVERT: M 27 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8371 (tp30) REVERT: M 28 ASP cc_start: 0.9161 (m-30) cc_final: 0.8587 (p0) REVERT: N 277 CYS cc_start: 0.9570 (m) cc_final: 0.9269 (p) REVERT: N 369 ASP cc_start: 0.9464 (t0) cc_final: 0.9155 (m-30) REVERT: N 373 GLN cc_start: 0.9490 (OUTLIER) cc_final: 0.9059 (tp-100) REVERT: N 387 LEU cc_start: 0.8904 (mt) cc_final: 0.8588 (mt) REVERT: N 622 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.6919 (m-80) REVERT: N 670 PHE cc_start: 0.3111 (OUTLIER) cc_final: 0.2530 (m-80) REVERT: N 676 TRP cc_start: 0.6278 (m-10) cc_final: 0.5933 (m-10) REVERT: N 696 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8013 (tmm) REVERT: O 273 SER cc_start: 0.9554 (m) cc_final: 0.9213 (p) REVERT: O 287 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8956 (mp0) REVERT: O 329 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8791 (ttp-110) REVERT: O 419 ASP cc_start: 0.9358 (m-30) cc_final: 0.8946 (p0) REVERT: O 440 GLN cc_start: 0.9244 (tm-30) cc_final: 0.9030 (tm-30) REVERT: O 495 GLU cc_start: 0.9551 (OUTLIER) cc_final: 0.9333 (pp20) REVERT: O 517 ASP cc_start: 0.9683 (m-30) cc_final: 0.9315 (p0) REVERT: O 529 ASP cc_start: 0.9553 (t0) cc_final: 0.9287 (m-30) REVERT: O 539 ASN cc_start: 0.9178 (t0) cc_final: 0.8960 (t0) REVERT: O 636 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8995 (pt) REVERT: O 664 MET cc_start: 0.9501 (mmm) cc_final: 0.9083 (mmm) REVERT: O 735 MET cc_start: 0.9494 (tmm) cc_final: 0.9000 (mtt) REVERT: P 148 ASN cc_start: 0.8915 (m110) cc_final: 0.8478 (p0) REVERT: P 246 GLU cc_start: 0.9586 (tp30) cc_final: 0.9354 (tm-30) REVERT: P 524 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6473 (mmpt) REVERT: R 128 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8736 (m-80) REVERT: R 266 MET cc_start: 0.2398 (tpp) cc_final: 0.2005 (tpt) REVERT: S 361 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8521 (mp0) REVERT: S 411 CYS cc_start: 0.8275 (t) cc_final: 0.7995 (p) REVERT: S 412 ASN cc_start: 0.6750 (m-40) cc_final: 0.5861 (t0) REVERT: W 17 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8700 (tm-30) REVERT: W 21 ASN cc_start: 0.8519 (m-40) cc_final: 0.7673 (m-40) REVERT: X 44 MET cc_start: 0.9652 (mmm) cc_final: 0.9249 (mpp) REVERT: X 49 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8992 (pt) REVERT: X 92 GLU cc_start: 0.9391 (mt-10) cc_final: 0.8944 (pm20) REVERT: X 137 GLU cc_start: 0.9711 (mt-10) cc_final: 0.9255 (tm-30) REVERT: X 367 GLN cc_start: 0.9486 (tm-30) cc_final: 0.9124 (pt0) REVERT: X 427 MET cc_start: 0.9023 (tmm) cc_final: 0.8725 (tpp) REVERT: Y 71 PHE cc_start: 0.8655 (m-80) cc_final: 0.8244 (m-80) REVERT: Y 294 PHE cc_start: 0.8415 (t80) cc_final: 0.8161 (t80) REVERT: Y 304 LEU cc_start: 0.8931 (mt) cc_final: 0.8713 (tp) REVERT: Y 451 CYS cc_start: 0.9313 (m) cc_final: 0.8895 (p) REVERT: Y 513 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8952 (tmm-80) REVERT: Y 526 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8457 (tp40) REVERT: Y 549 MET cc_start: 0.8978 (mmt) cc_final: 0.8614 (mmt) outliers start: 241 outliers final: 170 residues processed: 850 average time/residue: 0.6041 time to fit residues: 899.3424 Evaluate side-chains 802 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 597 time to evaluate : 6.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 269 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 871 ARG Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1386 TRP Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1565 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1639 LYS Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1665 GLN Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1786 THR Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 TRP Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 549 ASP Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 548 LYS Chi-restraints excluded: chain H residue 549 ASP Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 653 LEU Chi-restraints excluded: chain H residue 699 ASP Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 423 VAL Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 631 VAL Chi-restraints excluded: chain I residue 722 VAL Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 179 GLN Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 314 HIS Chi-restraints excluded: chain J residue 378 TYR Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 400 GLU Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 477 GLN Chi-restraints excluded: chain J residue 527 ILE Chi-restraints excluded: chain K residue 8 LYS Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 246 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 497 ASN Chi-restraints excluded: chain K residue 518 MET Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 373 GLN Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 396 ILE Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 622 TYR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain N residue 696 MET Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 329 ARG Chi-restraints excluded: chain O residue 394 THR Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 495 GLU Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 595 SER Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 680 GLN Chi-restraints excluded: chain O residue 744 LEU Chi-restraints excluded: chain O residue 752 ILE Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 97 LYS Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 227 THR Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 435 MET Chi-restraints excluded: chain P residue 524 LYS Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 340 TRP Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 393 LEU Chi-restraints excluded: chain R residue 488 LEU Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 154 ASP Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 305 ILE Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 450 VAL Chi-restraints excluded: chain X residue 457 THR Chi-restraints excluded: chain X residue 465 LEU Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 359 LEU Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 373 VAL Chi-restraints excluded: chain Y residue 465 LEU Chi-restraints excluded: chain Y residue 513 ARG Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 526 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 528 optimal weight: 6.9990 chunk 708 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 612 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 665 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 683 optimal weight: 0.8980 chunk 84 optimal weight: 0.0980 chunk 122 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 125 GLN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 595 GLN H 599 ASN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 HIS J 314 HIS ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 177 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.069021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.052155 restraints weight = 326005.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.053733 restraints weight = 168576.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054774 restraints weight = 108334.575| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 67835 Z= 0.192 Angle : 0.725 18.809 91891 Z= 0.358 Chirality : 0.041 0.307 10362 Planarity : 0.004 0.085 11673 Dihedral : 6.278 89.216 9300 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.41 % Favored : 94.20 % Rotamer: Outliers : 3.12 % Allowed : 24.46 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.09), residues: 8323 helix: 1.65 (0.07), residues: 5470 sheet: -0.33 (0.21), residues: 572 loop : -1.80 (0.13), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 73 HIS 0.013 0.001 HIS J 314 PHE 0.043 0.001 PHE X 294 TYR 0.046 0.001 TYR A1610 ARG 0.013 0.000 ARG C 514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17257.39 seconds wall clock time: 303 minutes 55.13 seconds (18235.13 seconds total)