Starting phenix.real_space_refine on Sat Jan 25 23:45:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eh0_48042/01_2025/9eh0_48042.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eh0_48042/01_2025/9eh0_48042.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/cci-nas-00/data/ceres_data/9eh0_48042/01_2025/9eh0_48042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eh0_48042/01_2025/9eh0_48042.map" model { file = "/net/cci-nas-00/data/ceres_data/9eh0_48042/01_2025/9eh0_48042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eh0_48042/01_2025/9eh0_48042.cif" } 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= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4827 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 9 6.06 5 P 387 5.49 5 Mg 1 5.21 5 S 316 5.16 5 C 44625 2.51 5 N 13323 2.21 5 O 14777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 73438 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 11255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1426, 11255 Classifications: {'peptide': 1426} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1353} Chain breaks: 7 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 8980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8980 Classifications: {'peptide': 1122} Link IDs: {'PTRANS': 52, 'TRANS': 1069} Chain breaks: 4 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1333 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1197 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 397 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "M" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 4883 Classifications: {'peptide': 1002} Incomplete info: {'backbone_only': 747, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 44, 'TRANS': 957} Chain breaks: 12 Unresolved non-hydrogen bonds: 3453 Unresolved non-hydrogen angles: 4931 Unresolved non-hydrogen dihedrals: 2238 Unresolved non-hydrogen chiralities: 969 Planarities with less than four sites: {'GLN:plan1': 41, 'HIS:plan': 21, 'TYR:plan': 31, 'ASN:plan1': 31, 'TRP:plan': 8, 'ASP:plan': 50, 'PHE:plan': 36, 'GLU:plan': 82, 'ARG:plan': 58} Unresolved non-hydrogen planarities: 1808 Chain: "N" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 3695 Classifications: {'DNA': 181} Link IDs: {'rna3p': 180} Chain breaks: 1 Chain: "O" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1046 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 233 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "Q" Number of atoms: 7226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7226 Classifications: {'peptide': 890} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 19, 'TRANS': 868} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1836 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 235} Chain breaks: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 101 Chain: "S" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 657 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 148} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain breaks: 1 Unresolved non-hydrogen bonds: 628 Unresolved non-hydrogen angles: 894 Unresolved non-hydrogen dihedrals: 391 Unresolved non-hydrogen chiralities: 187 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 297 Chain: "T" Number of atoms: 3955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3955 Classifications: {'DNA': 192} Link IDs: {'rna3p': 191} Chain: "U" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 856 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 4, 'PHE:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "V" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1703 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'CIS': 2, 'PTRANS': 14, 'TRANS': 227} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 9, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 240 Chain: "W" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2333 Classifications: {'peptide': 300} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 291} Chain: "X" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 353 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 4025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4025 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 490} Chain breaks: 5 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "a" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 823 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "b" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "c" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "d" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "e" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 776 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Chain: "f" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "h" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "l" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 2893 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 11, 'TRANS': 400} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 466 Unresolved non-hydrogen angles: 585 Unresolved non-hydrogen dihedrals: 386 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 224 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" 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} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 147.168 110.301 195.297 1.00217.27 S ATOM 494 SG CYS A 74 150.502 108.353 195.580 1.00212.64 S ATOM 541 SG CYS A 81 147.470 107.417 197.793 1.00210.54 S ATOM 19805 SG CYS B1119 164.502 113.524 201.295 1.00216.09 S ATOM 19827 SG CYS B1122 162.526 116.267 203.215 1.00215.16 S ATOM 19942 SG CYS B1137 161.330 115.009 199.845 1.00222.51 S ATOM 19963 SG CYS B1140 164.510 117.157 200.225 1.00220.98 S ATOM 20929 SG CYS C 88 112.966 54.527 212.848 1.00193.02 S ATOM 20942 SG CYS C 90 111.311 54.860 210.789 1.00194.77 S ATOM 20999 SG CYS C 97 110.205 55.380 214.819 1.00177.17 S ATOM 28249 SG CYS I 17 121.751 167.339 264.694 1.00181.36 S ATOM 28273 SG CYS I 20 122.360 166.715 261.637 1.00183.91 S ATOM 28434 SG CYS I 39 125.266 166.815 262.045 1.00182.91 S ATOM 28811 SG CYS I 86 109.438 131.555 288.830 1.00161.98 S ATOM 28835 SG CYS I 89 105.709 131.006 288.973 1.00161.96 S ATOM 29039 SG CYS I 114 107.453 129.888 285.848 1.00159.53 S ATOM 29074 SG CYS I 119 107.311 133.568 286.582 1.00163.30 S ATOM 29184 SG CYS J 7 107.667 71.575 242.918 1.00123.52 S ATOM 29472 SG CYS J 44 108.634 70.454 246.268 1.00132.41 S ATOM 29478 SG CYS J 45 105.677 69.461 245.050 1.00130.40 S ATOM 59887 SG CYS Y 19 124.878 168.960 184.651 1.00125.92 S Residues with excluded nonbonded symmetry interactions: 94 residue: pdb=" N ASN M1145 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN M1145 " occ=0.00 residue: pdb=" N THR M1146 " occ=0.00 ... (2 atoms not shown) pdb=" O THR M1146 " occ=0.00 residue: pdb=" N GLU M1147 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1147 " occ=0.00 residue: pdb=" N GLU M1148 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1148 " occ=0.00 residue: pdb=" N ILE M1149 " occ=0.00 ... (2 atoms not shown) pdb=" O ILE M1149 " occ=0.00 residue: pdb=" N PHE M1150 " occ=0.00 ... (2 atoms not shown) pdb=" O PHE M1150 " occ=0.00 residue: pdb=" N ASN M1151 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN M1151 " occ=0.00 residue: pdb=" N MET M1152 " occ=0.00 ... (2 atoms not shown) pdb=" O MET M1152 " occ=0.00 residue: pdb=" N LEU M1153 " occ=0.00 ... (2 atoms not shown) pdb=" O LEU M1153 " occ=0.00 residue: pdb=" N THR M1154 " occ=0.00 ... (2 atoms not shown) pdb=" O THR M1154 " occ=0.00 residue: pdb=" N LYS M1155 " occ=0.00 ... (2 atoms not shown) pdb=" O LYS M1155 " occ=0.00 residue: pdb=" N GLU M1156 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1156 " occ=0.00 ... (remaining 82 not shown) Time building chain proxies: 30.13, per 1000 atoms: 0.41 Number of scatterers: 73438 At special positions: 0 Unit cell: (231, 188.1, 347.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 9 29.99 S 316 16.00 P 387 15.00 Mg 1 11.99 O 14777 8.00 N 13323 7.00 C 44625 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 - 3.00 Amino acid : True - 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: 14.34 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " Number of angles added : 15 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14818 Finding SS restraints... Secondary structure from input PDB file: 333 helices and 90 sheets defined 45.2% alpha, 11.5% beta 190 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 21.60 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.724A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.576A pdb=" N VAL A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.999A pdb=" N VAL A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.526A pdb=" N VAL A 260 " --> pdb=" O PRO A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 301 through 319 removed outlier: 4.302A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.652A pdb=" N ALA A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.606A pdb=" N LEU A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 439' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 493 removed outlier: 4.070A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 524 Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.852A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 removed outlier: 3.673A pdb=" N MET A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.917A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.770A pdb=" N ASN A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 697 through 723 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 773 removed outlier: 3.507A pdb=" N SER A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 826 through 830 removed outlier: 3.855A pdb=" N GLY A 830 " --> pdb=" O TYR A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.422A pdb=" N GLY A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.536A pdb=" N ARG A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.628A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 4.087A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.544A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1039 through 1049 Processing helix chain 'A' and resid 1050 through 1055 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix removed outlier: 3.880A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1151 through 1162 removed outlier: 4.116A pdb=" N ASP A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 Processing helix chain 'A' and resid 1190 through 1195 removed outlier: 3.650A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1225 Processing helix chain 'A' and resid 1227 through 1239 removed outlier: 3.667A pdb=" N PHE A1239 " --> pdb=" O ILE A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1295 removed outlier: 3.679A pdb=" N LEU A1285 " --> pdb=" O ASP A1281 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A1295 " --> pdb=" O ASN A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1348 removed outlier: 3.659A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.894A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.897A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 3.939A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 Processing helix chain 'A' and resid 1478 through 1482 Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.884A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.332A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.614A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.677A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.603A pdb=" N ALA B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 425 removed outlier: 3.664A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 458 through 462 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.737A pdb=" N TRP B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.616A pdb=" N ASN B 585 " --> pdb=" O GLU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 660 removed outlier: 3.728A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 removed outlier: 4.023A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 4.110A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 768 removed outlier: 3.543A pdb=" N LEU B 767 " --> pdb=" O SER B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 772 Processing helix chain 'B' and resid 798 through 804 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.222A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.826A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1016 removed outlier: 3.553A pdb=" N ILE B1011 " --> pdb=" O ASN B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 60 through 70 removed outlier: 4.082A pdb=" N ILE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.502A pdb=" N SER C 98 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 270 Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.763A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.792A pdb=" N SER D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 69 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.671A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.806A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.791A pdb=" N ILE D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.621A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.955A pdb=" N PHE E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 95 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.631A pdb=" N LYS E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 32 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.849A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.685A pdb=" N GLU J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 removed outlier: 4.180A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.695A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG J 47 " --> pdb=" O TYR J 43 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS J 52 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 4.047A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.755A pdb=" N GLU K 8 " --> pdb=" O PRO K 5 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 5 through 10' Processing helix chain 'K' and resid 40 through 53 removed outlier: 4.336A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'M' and resid 285 through 291 removed outlier: 3.511A pdb=" N ILE M 289 " --> pdb=" O GLN M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 302 Processing helix chain 'M' and resid 309 through 323 removed outlier: 3.977A pdb=" N GLU M 314 " --> pdb=" O ASP M 310 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU M 315 " --> pdb=" O ASP M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 370 Processing helix chain 'M' and resid 372 through 380 Processing helix chain 'M' and resid 392 through 429 Processing helix chain 'M' and resid 445 through 453 removed outlier: 3.971A pdb=" N GLU M 449 " --> pdb=" O THR M 445 " (cutoff:3.500A) Processing helix chain 'M' and resid 457 through 472 Processing helix chain 'M' and resid 542 through 553 Processing helix chain 'M' and resid 565 through 570 Processing helix chain 'M' and resid 586 through 598 removed outlier: 3.540A pdb=" N MET M 591 " --> pdb=" O GLY M 587 " (cutoff:3.500A) Processing helix chain 'M' and resid 599 through 607 Processing helix chain 'M' and resid 623 through 629 removed outlier: 3.590A pdb=" N ASP M 629 " --> pdb=" O ARG M 625 " (cutoff:3.500A) Processing helix chain 'M' and resid 632 through 637 removed outlier: 4.329A pdb=" N PHE M 637 " --> pdb=" O TYR M 633 " (cutoff:3.500A) Processing helix chain 'M' and resid 644 through 650 removed outlier: 3.805A pdb=" N LEU M 648 " --> pdb=" O PRO M 644 " (cutoff:3.500A) Processing helix chain 'M' and resid 651 through 664 removed outlier: 3.594A pdb=" N LYS M 655 " --> pdb=" O ASP M 651 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU M 664 " --> pdb=" O GLU M 660 " (cutoff:3.500A) Processing helix chain 'M' and resid 685 through 692 removed outlier: 4.197A pdb=" N ILE M 689 " --> pdb=" O TYR M 685 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS M 690 " --> pdb=" O PHE M 686 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN M 691 " --> pdb=" O GLU M 687 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE M 692 " --> pdb=" O GLU M 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 685 through 692' Processing helix chain 'M' and resid 700 through 721 Processing helix chain 'M' and resid 721 through 754 removed outlier: 3.548A pdb=" N ARG M 754 " --> pdb=" O TYR M 750 " (cutoff:3.500A) Processing helix chain 'M' and resid 759 through 763 removed outlier: 3.665A pdb=" N GLN M 763 " --> pdb=" O PRO M 760 " (cutoff:3.500A) Processing helix chain 'M' and resid 830 through 843 removed outlier: 3.636A pdb=" N LYS M 843 " --> pdb=" O PHE M 839 " (cutoff:3.500A) Processing helix chain 'M' and resid 854 through 872 Processing helix chain 'M' and resid 888 through 895 removed outlier: 3.912A pdb=" N LEU M 892 " --> pdb=" O GLU M 888 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN M 895 " --> pdb=" O ILE M 891 " (cutoff:3.500A) Processing helix chain 'M' and resid 896 through 903 Processing helix chain 'M' and resid 907 through 922 Processing helix chain 'M' and resid 922 through 929 Processing helix chain 'M' and resid 936 through 940 removed outlier: 4.162A pdb=" N LEU M 940 " --> pdb=" O ASP M 936 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 936 through 940' Processing helix chain 'M' and resid 943 through 949 removed outlier: 4.173A pdb=" N GLU M 947 " --> pdb=" O HIS M 943 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N HIS M 948 " --> pdb=" O PRO M 944 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL M 949 " --> pdb=" O LEU M 945 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 943 through 949' Processing helix chain 'M' and resid 950 through 970 removed outlier: 3.978A pdb=" N LEU M 954 " --> pdb=" O VAL M 950 " (cutoff:3.500A) Processing helix chain 'M' and resid 974 through 979 removed outlier: 4.042A pdb=" N ALA M 978 " --> pdb=" O ASN M 974 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS M 979 " --> pdb=" O ARG M 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 974 through 979' Processing helix chain 'M' and resid 993 through 1008 Processing helix chain 'M' and resid 1015 through 1020 Processing helix chain 'M' and resid 1024 through 1031 Processing helix chain 'M' and resid 1059 through 1075 removed outlier: 4.502A pdb=" N GLU M1064 " --> pdb=" O PRO M1060 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TRP M1065 " --> pdb=" O GLU M1061 " (cutoff:3.500A) Processing helix chain 'M' and resid 1086 through 1095 removed outlier: 3.891A pdb=" N ILE M1092 " --> pdb=" O ALA M1088 " (cutoff:3.500A) Processing helix chain 'M' and resid 1103 through 1114 Processing helix chain 'M' and resid 1121 through 1132 removed outlier: 4.150A pdb=" N ASP M1125 " --> pdb=" O ILE M1121 " (cutoff:3.500A) Processing helix chain 'M' and resid 1145 through 1154 Processing helix chain 'M' and resid 1241 through 1246 removed outlier: 3.761A pdb=" N LEU M1245 " --> pdb=" O PRO M1241 " (cutoff:3.500A) Processing helix chain 'M' and resid 1282 through 1287 removed outlier: 3.856A pdb=" N LEU M1286 " --> pdb=" O ARG M1282 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET M1287 " --> pdb=" O THR M1283 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1282 through 1287' Processing helix chain 'M' and resid 1342 through 1347 removed outlier: 3.539A pdb=" N MET M1347 " --> pdb=" O GLU M1344 " (cutoff:3.500A) Processing helix chain 'M' and resid 1402 through 1406 Processing helix chain 'M' and resid 1410 through 1416 Processing helix chain 'M' and resid 1416 through 1428 removed outlier: 3.615A pdb=" N LEU M1426 " --> pdb=" O PHE M1422 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU M1427 " --> pdb=" O ALA M1423 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN M1428 " --> pdb=" O ARG M1424 " (cutoff:3.500A) Processing helix chain 'M' and resid 1434 through 1439 removed outlier: 3.787A pdb=" N ASP M1439 " --> pdb=" O CYS M1435 " (cutoff:3.500A) Processing helix chain 'M' and resid 1441 through 1452 removed outlier: 4.321A pdb=" N GLU M1445 " --> pdb=" O LYS M1441 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU M1446 " --> pdb=" O LYS M1442 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU M1447 " --> pdb=" O LEU M1443 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE M1448 " --> pdb=" O GLU M1444 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS M1452 " --> pdb=" O ILE M1448 " (cutoff:3.500A) Processing helix chain 'M' and resid 1503 through 1512 removed outlier: 4.033A pdb=" N LEU M1507 " --> pdb=" O THR M1503 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE M1508 " --> pdb=" O VAL M1504 " (cutoff:3.500A) Processing helix chain 'O' and resid 555 through 580 Processing helix chain 'O' and resid 585 through 599 Proline residue: O 592 - end of helix removed outlier: 3.742A pdb=" N HIS O 597 " --> pdb=" O ALA O 593 " (cutoff:3.500A) Processing helix chain 'O' and resid 600 through 602 No H-bonds generated for 'chain 'O' and resid 600 through 602' Processing helix chain 'O' and resid 603 through 611 removed outlier: 3.605A pdb=" N GLY O 611 " --> pdb=" O PHE O 607 " (cutoff:3.500A) Processing helix chain 'O' and resid 611 through 621 Processing helix chain 'O' and resid 630 through 642 removed outlier: 3.747A pdb=" N GLU O 636 " --> pdb=" O LYS O 632 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS O 639 " --> pdb=" O GLU O 635 " (cutoff:3.500A) Processing helix chain 'O' and resid 648 through 656 removed outlier: 3.576A pdb=" N LEU O 652 " --> pdb=" O SER O 648 " (cutoff:3.500A) Processing helix chain 'O' and resid 656 through 667 Processing helix chain 'O' and resid 671 through 685 removed outlier: 3.707A pdb=" N LYS O 675 " --> pdb=" O SER O 671 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET O 677 " --> pdb=" O SER O 673 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 37 removed outlier: 4.097A pdb=" N ILE Q 31 " --> pdb=" O GLY Q 27 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER Q 32 " --> pdb=" O ASP Q 28 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU Q 37 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 53 removed outlier: 4.175A pdb=" N TRP Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE Q 45 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 64 removed outlier: 4.016A pdb=" N LEU Q 64 " --> pdb=" O PHE Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 69 removed outlier: 3.793A pdb=" N ARG Q 68 " --> pdb=" O GLU Q 65 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE Q 69 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 65 through 69' Processing helix chain 'Q' and resid 78 through 98 removed outlier: 3.595A pdb=" N GLN Q 82 " --> pdb=" O HIS Q 78 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR Q 88 " --> pdb=" O THR Q 84 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU Q 89 " --> pdb=" O CYS Q 85 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR Q 93 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL Q 94 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG Q 98 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 122 removed outlier: 3.698A pdb=" N LEU Q 109 " --> pdb=" O ASN Q 105 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN Q 112 " --> pdb=" O ASP Q 108 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU Q 116 " --> pdb=" O GLN Q 112 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR Q 118 " --> pdb=" O THR Q 114 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET Q 119 " --> pdb=" O LEU Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 142 removed outlier: 3.647A pdb=" N PHE Q 137 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS Q 138 " --> pdb=" O ARG Q 134 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU Q 139 " --> pdb=" O ALA Q 135 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU Q 140 " --> pdb=" O CYS Q 136 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 removed outlier: 3.620A pdb=" N PHE Q 154 " --> pdb=" O ALA Q 150 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL Q 155 " --> pdb=" O GLN Q 151 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU Q 156 " --> pdb=" O PHE Q 152 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN Q 157 " --> pdb=" O HIS Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 176 removed outlier: 3.669A pdb=" N GLY Q 168 " --> pdb=" O PRO Q 164 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LYS Q 169 " --> pdb=" O ALA Q 165 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA Q 170 " --> pdb=" O LEU Q 166 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS Q 171 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE Q 172 " --> pdb=" O GLY Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 187 Processing helix chain 'Q' and resid 187 through 192 removed outlier: 3.858A pdb=" N ARG Q 191 " --> pdb=" O LYS Q 187 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR Q 192 " --> pdb=" O LYS Q 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 187 through 192' Processing helix chain 'Q' and resid 200 through 208 removed outlier: 3.898A pdb=" N MET Q 204 " --> pdb=" O VAL Q 200 " (cutoff:3.500A) Processing helix chain 'Q' and resid 213 through 228 removed outlier: 4.232A pdb=" N LEU Q 219 " --> pdb=" O GLU Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 243 removed outlier: 4.195A pdb=" N LEU Q 238 " --> pdb=" O ALA Q 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 249 through 255 removed outlier: 3.783A pdb=" N ASN Q 253 " --> pdb=" O ASP Q 249 " (cutoff:3.500A) Processing helix chain 'Q' and resid 258 through 265 Processing helix chain 'Q' and resid 268 through 282 removed outlier: 3.793A pdb=" N PHE Q 281 " --> pdb=" O ASN Q 277 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS Q 282 " --> pdb=" O HIS Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 284 through 298 removed outlier: 3.817A pdb=" N VAL Q 288 " --> pdb=" O ASP Q 284 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS Q 290 " --> pdb=" O SER Q 286 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU Q 293 " --> pdb=" O GLN Q 289 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS Q 294 " --> pdb=" O HIS Q 290 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN Q 298 " --> pdb=" O HIS Q 294 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 319 removed outlier: 3.919A pdb=" N GLN Q 305 " --> pdb=" O VAL Q 301 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU Q 307 " --> pdb=" O ALA Q 303 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL Q 318 " --> pdb=" O ARG Q 314 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN Q 319 " --> pdb=" O SER Q 315 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 336 removed outlier: 3.848A pdb=" N ALA Q 325 " --> pdb=" O ASP Q 321 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN Q 327 " --> pdb=" O ASP Q 323 " (cutoff:3.500A) Processing helix chain 'Q' and resid 341 through 351 Processing helix chain 'Q' and resid 352 through 355 Processing helix chain 'Q' and resid 356 through 371 removed outlier: 3.724A pdb=" N ALA Q 360 " --> pdb=" O ASP Q 356 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS Q 366 " --> pdb=" O GLN Q 362 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL Q 367 " --> pdb=" O CYS Q 363 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU Q 368 " --> pdb=" O PHE Q 364 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS Q 369 " --> pdb=" O GLU Q 365 " (cutoff:3.500A) Processing helix chain 'Q' and resid 373 through 383 removed outlier: 4.344A pdb=" N MET Q 378 " --> pdb=" O ASN Q 374 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS Q 379 " --> pdb=" O TYR Q 375 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE Q 380 " --> pdb=" O GLU Q 376 " (cutoff:3.500A) Processing helix chain 'Q' and resid 390 through 407 removed outlier: 5.053A pdb=" N ILE Q 396 " --> pdb=" O GLU Q 392 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA Q 397 " --> pdb=" O LYS Q 393 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU Q 406 " --> pdb=" O LYS Q 402 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN Q 407 " --> pdb=" O LYS Q 403 " (cutoff:3.500A) Processing helix chain 'Q' and resid 413 through 423 Processing helix chain 'Q' and resid 426 through 440 removed outlier: 3.781A pdb=" N ALA Q 430 " --> pdb=" O ASP Q 426 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG Q 439 " --> pdb=" O GLY Q 435 " (cutoff:3.500A) Processing helix chain 'Q' and resid 450 through 463 removed outlier: 3.837A pdb=" N LEU Q 454 " --> pdb=" O PRO Q 450 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG Q 463 " --> pdb=" O ALA Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 466 through 484 Processing helix chain 'Q' and resid 491 through 510 Processing helix chain 'Q' and resid 512 through 527 removed outlier: 3.788A pdb=" N GLU Q 526 " --> pdb=" O ASN Q 522 " (cutoff:3.500A) Processing helix chain 'Q' and resid 531 through 545 removed outlier: 3.674A pdb=" N GLY Q 538 " --> pdb=" O TYR Q 534 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS Q 544 " --> pdb=" O MET Q 540 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY Q 545 " --> pdb=" O ALA Q 541 " (cutoff:3.500A) Processing helix chain 'Q' and resid 548 through 561 removed outlier: 3.965A pdb=" N ASP Q 552 " --> pdb=" O TYR Q 548 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS Q 555 " --> pdb=" O SER Q 551 " (cutoff:3.500A) Processing helix chain 'Q' and resid 564 through 575 removed outlier: 3.779A pdb=" N HIS Q 575 " --> pdb=" O ILE Q 571 " (cutoff:3.500A) Processing helix chain 'Q' and resid 584 through 591 removed outlier: 4.278A pdb=" N PHE Q 588 " --> pdb=" O GLY Q 584 " (cutoff:3.500A) Processing helix chain 'Q' and resid 600 through 614 removed outlier: 3.516A pdb=" N MET Q 604 " --> pdb=" O ASP Q 600 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR Q 614 " --> pdb=" O VAL Q 610 " (cutoff:3.500A) Processing helix chain 'Q' and resid 619 through 623 Processing helix chain 'Q' and resid 624 through 643 Processing helix chain 'Q' and resid 646 through 661 removed outlier: 3.912A pdb=" N ALA Q 650 " --> pdb=" O ASN Q 646 " (cutoff:3.500A) Processing helix chain 'Q' and resid 665 through 677 removed outlier: 3.694A pdb=" N VAL Q 669 " --> pdb=" O GLU Q 665 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN Q 672 " --> pdb=" O ASP Q 668 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL Q 673 " --> pdb=" O VAL Q 669 " (cutoff:3.500A) Processing helix chain 'Q' and resid 680 through 694 removed outlier: 3.820A pdb=" N TRP Q 684 " --> pdb=" O ILE Q 680 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU Q 685 " --> pdb=" O SER Q 681 " (cutoff:3.500A) Processing helix chain 'Q' and resid 697 through 709 removed outlier: 4.372A pdb=" N GLN Q 702 " --> pdb=" O ILE Q 698 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N MET Q 703 " --> pdb=" O SER Q 699 " (cutoff:3.500A) Processing helix chain 'Q' and resid 716 through 724 removed outlier: 3.691A pdb=" N VAL Q 720 " --> pdb=" O ASN Q 716 " (cutoff:3.500A) Processing helix chain 'Q' and resid 729 through 732 Processing helix chain 'Q' and resid 733 through 747 removed outlier: 3.865A pdb=" N VAL Q 746 " --> pdb=" O LYS Q 742 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA Q 747 " --> pdb=" O ALA Q 743 " (cutoff:3.500A) Processing helix chain 'Q' and resid 750 through 770 removed outlier: 3.710A pdb=" N MET Q 754 " --> pdb=" O ASP Q 750 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA Q 758 " --> pdb=" O MET Q 754 " (cutoff:3.500A) Processing helix chain 'Q' and resid 775 through 797 removed outlier: 3.680A pdb=" N VAL Q 779 " --> pdb=" O ASN Q 775 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL Q 783 " --> pdb=" O VAL Q 779 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS Q 784 " --> pdb=" O LEU Q 780 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER Q 797 " --> pdb=" O PHE Q 793 " (cutoff:3.500A) Processing helix chain 'Q' and resid 807 through 809 No H-bonds generated for 'chain 'Q' and resid 807 through 809' Processing helix chain 'Q' and resid 810 through 892 removed outlier: 4.299A pdb=" N ALA Q 829 " --> pdb=" O GLN Q 825 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG Q 830 " --> pdb=" O TYR Q 826 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU Q 848 " --> pdb=" O LYS Q 844 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU Q 883 " --> pdb=" O ALA Q 879 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS Q 886 " --> pdb=" O VAL Q 882 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN Q 887 " --> pdb=" O GLU Q 883 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR Q 892 " --> pdb=" O ILE Q 888 " (cutoff:3.500A) Processing helix chain 'R' and resid 355 through 360 removed outlier: 3.553A pdb=" N LEU R 359 " --> pdb=" O LEU R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 363 No H-bonds generated for 'chain 'R' and resid 361 through 363' Processing helix chain 'R' and resid 368 through 372 Processing helix chain 'R' and resid 377 through 382 Processing helix chain 'R' and resid 448 through 463 Processing helix chain 'R' and resid 468 through 484 removed outlier: 4.117A pdb=" N LEU R 477 " --> pdb=" O ASN R 473 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER R 478 " --> pdb=" O LYS R 474 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE R 479 " --> pdb=" O LYS R 475 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS R 480 " --> pdb=" O GLU R 476 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN R 484 " --> pdb=" O LYS R 480 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 503 removed outlier: 3.769A pdb=" N PHE R 502 " --> pdb=" O GLU R 498 " (cutoff:3.500A) Processing helix chain 'R' and resid 510 through 525 Processing helix chain 'R' and resid 527 through 553 Processing helix chain 'R' and resid 556 through 585 removed outlier: 3.850A pdb=" N SER R 561 " --> pdb=" O ILE R 557 " (cutoff:3.500A) Processing helix chain 'S' and resid 138 through 154 Processing helix chain 'S' and resid 156 through 162 removed outlier: 3.597A pdb=" N ALA S 160 " --> pdb=" O ASP S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 164 through 181 Processing helix chain 'S' and resid 184 through 200 Processing helix chain 'S' and resid 203 through 212 removed outlier: 4.272A pdb=" N ARG S 207 " --> pdb=" O ASN S 203 " (cutoff:3.500A) Processing helix chain 'S' and resid 216 through 223 Processing helix chain 'S' and resid 224 through 229 Processing helix chain 'S' and resid 230 through 249 removed outlier: 3.594A pdb=" N GLN S 249 " --> pdb=" O ILE S 245 " (cutoff:3.500A) Processing helix chain 'U' and resid 379 through 383 Processing helix chain 'U' and resid 411 through 415 Processing helix chain 'V' and resid 63 through 68 Processing helix chain 'V' and resid 101 through 107 removed outlier: 3.803A pdb=" N LEU V 107 " --> pdb=" O ALA V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 122 through 126 removed outlier: 3.533A pdb=" N LYS V 126 " --> pdb=" O GLN V 123 " (cutoff:3.500A) Processing helix chain 'V' and resid 172 through 186 removed outlier: 3.780A pdb=" N THR V 177 " --> pdb=" O ASP V 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE V 183 " --> pdb=" O ILE V 179 " (cutoff:3.500A) Processing helix chain 'V' and resid 294 through 299 Processing helix chain 'X' and resid 219 through 226 Processing helix chain 'X' and resid 233 through 239 Processing helix chain 'X' and resid 246 through 260 removed outlier: 3.792A pdb=" N ALA X 251 " --> pdb=" O LYS X 247 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE X 252 " --> pdb=" O ASN X 248 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS X 257 " --> pdb=" O LEU X 253 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 31 Processing helix chain 'Y' and resid 46 through 53 Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 76 Processing helix chain 'Y' and resid 97 through 105 removed outlier: 3.886A pdb=" N LEU Y 101 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS Y 102 " --> pdb=" O VAL Y 98 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER Y 103 " --> pdb=" O ARG Y 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 231 through 239 removed outlier: 4.073A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 246 through 250 removed outlier: 4.495A pdb=" N TRP Z 250 " --> pdb=" O LEU Z 247 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 261 removed outlier: 4.203A pdb=" N THR Z 261 " --> pdb=" O LYS Z 258 " (cutoff:3.500A) Processing helix chain 'Z' and resid 389 through 396 Processing helix chain 'Z' and resid 630 through 634 Processing helix chain 'a' and resid 44 through 57 removed outlier: 3.651A pdb=" N SER a 57 " --> pdb=" O ARG a 53 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 76 Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.718A pdb=" N LEU a 92 " --> pdb=" O ALA a 88 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU a 109 " --> pdb=" O GLU a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 24 through 29 removed outlier: 3.725A pdb=" N GLN b 27 " --> pdb=" O ASP b 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE b 29 " --> pdb=" O ILE b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 42 Processing helix chain 'b' and resid 49 through 76 Processing helix chain 'b' and resid 82 through 94 removed outlier: 3.613A pdb=" N VAL b 86 " --> pdb=" O THR b 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 36 removed outlier: 3.697A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 73 removed outlier: 3.639A pdb=" N LEU c 65 " --> pdb=" O GLU c 61 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 89 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'd' and resid 37 through 49 removed outlier: 3.541A pdb=" N GLN d 47 " --> pdb=" O LYS d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 55 through 84 removed outlier: 3.664A pdb=" N ASN d 84 " --> pdb=" O LEU d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 104 through 123 removed outlier: 3.715A pdb=" N LYS d 108 " --> pdb=" O GLY d 104 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER d 123 " --> pdb=" O THR d 119 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 75 Processing helix chain 'e' and resid 85 through 114 removed outlier: 3.688A pdb=" N VAL e 89 " --> pdb=" O GLN e 85 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) Processing helix chain 'e' and resid 120 through 132 removed outlier: 3.618A pdb=" N GLY e 132 " --> pdb=" O ARG e 128 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 49 through 77 removed outlier: 4.068A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 94 removed outlier: 3.587A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 37 removed outlier: 3.700A pdb=" N VAL g 30 " --> pdb=" O PRO g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 72 removed outlier: 4.665A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 Processing helix chain 'g' and resid 90 through 97 removed outlier: 3.565A pdb=" N ASN g 94 " --> pdb=" O ASP g 90 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS g 95 " --> pdb=" O GLU g 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 37 through 49 removed outlier: 3.749A pdb=" N GLN h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL h 48 " --> pdb=" O VAL h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 55 through 84 removed outlier: 3.513A pdb=" N HIS h 82 " --> pdb=" O SER h 78 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN h 84 " --> pdb=" O LEU h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 103 through 123 removed outlier: 3.718A pdb=" N HIS h 109 " --> pdb=" O GLU h 105 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR h 122 " --> pdb=" O VAL h 118 " (cutoff:3.500A) Processing helix chain 'l' and resid 1535 through 1539 removed outlier: 4.002A pdb=" N CYS l1539 " --> pdb=" O GLY l1536 " (cutoff:3.500A) Processing helix chain 'l' and resid 1587 through 1597 removed outlier: 3.880A pdb=" N ALA l1591 " --> pdb=" O LYS l1587 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS l1594 " --> pdb=" O LYS l1590 " (cutoff:3.500A) Processing helix chain 'l' and resid 1598 through 1600 No H-bonds generated for 'chain 'l' and resid 1598 through 1600' Processing helix chain 'l' and resid 1622 through 1626 removed outlier: 4.117A pdb=" N PHE l1626 " --> pdb=" O CYS l1623 " (cutoff:3.500A) Processing helix chain 'l' and resid 1696 through 1702 Processing helix chain 'l' and resid 1711 through 1724 Processing helix chain 'l' and resid 1731 through 1745 removed outlier: 3.625A pdb=" N VAL l1743 " --> pdb=" O SER l1739 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG l1744 " --> pdb=" O ARG l1740 " (cutoff:3.500A) Processing helix chain 'l' and resid 1747 through 1761 Processing helix chain 'l' and resid 1763 through 1773 Processing helix chain 'l' and resid 1774 through 1787 removed outlier: 3.542A pdb=" N TRP l1782 " --> pdb=" O LEU l1778 " (cutoff:3.500A) Processing helix chain 'l' and resid 1788 through 1789 No H-bonds generated for 'chain 'l' and resid 1788 through 1789' Processing helix chain 'l' and resid 1790 through 1792 No H-bonds generated for 'chain 'l' and resid 1790 through 1792' Processing helix chain 'l' and resid 1793 through 1807 Processing helix chain 'l' and resid 1811 through 1818 removed outlier: 3.789A pdb=" N LEU l1815 " --> pdb=" O THR l1811 " (cutoff:3.500A) Processing helix chain 'l' and resid 1819 through 1827 removed outlier: 4.009A pdb=" N ILE l1823 " --> pdb=" O LYS l1819 " (cutoff:3.500A) Processing helix chain 'l' and resid 2006 through 2018 Processing helix chain 'l' and resid 2029 through 2039 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 3.633A pdb=" N VAL A 21 " --> pdb=" O ASP A1449 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 193 Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.735A pdb=" N LYS A 357 " --> pdb=" O PHE B1086 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 380 removed outlier: 5.795A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 470 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET A 501 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.074A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.852A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 581 removed outlier: 5.711A pdb=" N ILE A 579 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR H 93 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 581 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL H 91 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER H 117 " --> pdb=" O LYS H 95 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA H 114 " --> pdb=" O LEU H 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 5.711A pdb=" N ILE A 579 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR H 93 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 581 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL H 91 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.613A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 872 through 874 removed outlier: 3.793A pdb=" N THR A 878 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB4, first strand: chain 'A' and resid 1140 through 1142 removed outlier: 3.891A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A1337 " --> pdb=" O TYR A1308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1211 through 1216 removed outlier: 3.569A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 3.644A pdb=" N ARG A1260 " --> pdb=" O ASN A1244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1471 through 1475 removed outlier: 3.532A pdb=" N ASP A1472 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.917A pdb=" N VAL B 132 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B 140 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS B 134 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 87 through 93 removed outlier: 4.572A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.508A pdb=" N ALA B 196 " --> pdb=" O ARG B 484 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU B 198 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.907A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC5, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC6, first strand: chain 'B' and resid 572 through 577 removed outlier: 4.533A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 611 " --> pdb=" O ASP B 606 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.517A pdb=" N ALA B 748 " --> pdb=" O TYR B 811 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AC9, first strand: chain 'B' and resid 776 through 782 removed outlier: 4.052A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 936 " --> pdb=" O GLN B1049 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 776 through 782 removed outlier: 4.052A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 826 through 829 removed outlier: 4.059A pdb=" N GLU B 826 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 837 through 839 Processing sheet with id=AD4, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD5, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.790A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.904A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.518A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 62 through 63 removed outlier: 3.890A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET E 72 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE E 73 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.561A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.527A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE G 46 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.527A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU G 67 " --> pdb=" O VAL G 58 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 107 through 109 removed outlier: 6.499A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 128 through 129 Processing sheet with id=AE5, first strand: chain 'H' and resid 38 through 44 removed outlier: 3.707A pdb=" N LEU H 41 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG H 27 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE H 15 " --> pdb=" O ARG H 27 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS H 13 " --> pdb=" O HIS H 29 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS H 146 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 24 through 29 Processing sheet with id=AE7, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'M' and resid 804 through 810 removed outlier: 5.423A pdb=" N VAL M 805 " --> pdb=" O ASN M 800 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ASN M 800 " --> pdb=" O VAL M 805 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL M 848 " --> pdb=" O GLU M 883 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 971 through 972 removed outlier: 5.958A pdb=" N VAL M 971 " --> pdb=" O LYS M1036 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'M' and resid 1237 through 1240 removed outlier: 6.597A pdb=" N ARG M1231 " --> pdb=" O VAL M1171 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL M1171 " --> pdb=" O ARG M1231 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS M1265 " --> pdb=" O ILE M1167 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG M1266 " --> pdb=" O THR M1280 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 1355 through 1359 removed outlier: 3.639A pdb=" N LEU M1367 " --> pdb=" O VAL M1383 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP M1371 " --> pdb=" O GLN M1379 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN M1379 " --> pdb=" O TRP M1371 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 1461 through 1464 removed outlier: 4.157A pdb=" N PHE M1461 " --> pdb=" O GLY M1475 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY M1475 " --> pdb=" O PHE M1461 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR M1488 " --> pdb=" O ARG M1495 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 5 through 7 removed outlier: 4.410A pdb=" N ILE Q 6 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU Q 19 " --> pdb=" O ILE Q 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'R' and resid 386 through 387 removed outlier: 3.998A pdb=" N VAL R 387 " --> pdb=" O ALA R 403 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA R 403 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N ARG R 421 " --> pdb=" O LYS R 413 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N LYS R 413 " --> pdb=" O ARG R 421 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ASN R 423 " --> pdb=" O THR R 411 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL R 409 " --> pdb=" O GLY R 425 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 386 through 387 removed outlier: 3.998A pdb=" N VAL R 387 " --> pdb=" O ALA R 403 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA R 403 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU R 426 " --> pdb=" O PHE R 437 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE R 437 " --> pdb=" O LEU R 426 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU R 428 " --> pdb=" O ARG R 435 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG R 435 " --> pdb=" O LEU R 428 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP R 433 " --> pdb=" O HIS R 430 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 256 through 258 Processing sheet with id=AF9, first strand: chain 'U' and resid 376 through 377 removed outlier: 3.537A pdb=" N PHE V 312 " --> pdb=" O VAL U 376 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 494 through 495 removed outlier: 3.829A pdb=" N HIS U 494 " --> pdb=" O TYR U 460 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR U 460 " --> pdb=" O HIS U 494 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET U 448 " --> pdb=" O VAL U 459 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS U 451 " --> pdb=" O ARG U 439 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG U 439 " --> pdb=" O HIS U 451 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE U 440 " --> pdb=" O VAL V 204 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL V 204 " --> pdb=" O ILE U 440 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS U 442 " --> pdb=" O VAL V 202 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 221 through 222 removed outlier: 3.554A pdb=" N ARG V 331 " --> pdb=" O LYS V 292 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER V 333 " --> pdb=" O LYS V 290 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS V 290 " --> pdb=" O SER V 333 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 250 through 251 removed outlier: 3.679A pdb=" N GLN V 250 " --> pdb=" O VAL V 261 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 6 through 11 removed outlier: 4.884A pdb=" N ILE W 7 " --> pdb=" O ASP W 302 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP W 302 " --> pdb=" O ILE W 7 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY W 279 " --> pdb=" O VAL W 292 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 19 through 24 removed outlier: 6.156A pdb=" N VAL W 44 " --> pdb=" O SER W 59 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER W 59 " --> pdb=" O VAL W 44 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL W 46 " --> pdb=" O GLN W 57 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 67 through 72 removed outlier: 7.188A pdb=" N SER W 82 " --> pdb=" O VAL W 68 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL W 70 " --> pdb=" O ALA W 80 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA W 80 " --> pdb=" O VAL W 70 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE W 72 " --> pdb=" O ILE W 78 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE W 78 " --> pdb=" O ILE W 72 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER W 83 " --> pdb=" O HIS W 87 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N HIS W 87 " --> pdb=" O SER W 83 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS W 100 " --> pdb=" O LEU W 90 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP W 92 " --> pdb=" O GLN W 98 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLN W 98 " --> pdb=" O ASP W 92 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 120 through 124 removed outlier: 3.699A pdb=" N VAL W 130 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY W 134 " --> pdb=" O LYS W 140 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS W 140 " --> pdb=" O GLY W 134 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 151 through 156 removed outlier: 6.316A pdb=" N GLY W 166 " --> pdb=" O LEU W 152 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE W 154 " --> pdb=" O ALA W 164 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA W 164 " --> pdb=" O ILE W 154 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 195 through 198 removed outlier: 3.671A pdb=" N SER W 195 " --> pdb=" O ALA W 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR W 197 " --> pdb=" O VAL W 206 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL W 206 " --> pdb=" O THR W 197 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR W 207 " --> pdb=" O LYS W 215 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS W 215 " --> pdb=" O THR W 207 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE W 214 " --> pdb=" O THR W 227 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N THR W 227 " --> pdb=" O ILE W 214 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE W 216 " --> pdb=" O ALA W 225 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'W' and resid 235 through 240 removed outlier: 3.728A pdb=" N HIS W 268 " --> pdb=" O VAL W 258 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 13 through 15 removed outlier: 3.523A pdb=" N LYS Y 23 " --> pdb=" O ARG Y 14 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Y' and resid 57 through 58 Processing sheet with id=AH4, first strand: chain 'Y' and resid 61 through 63 Processing sheet with id=AH5, first strand: chain 'Z' and resid 224 through 229 removed outlier: 4.065A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Z' and resid 290 through 292 Processing sheet with id=AH7, first strand: chain 'Z' and resid 302 through 303 Processing sheet with id=AH8, first strand: chain 'Z' and resid 353 through 354 Processing sheet with id=AH9, first strand: chain 'Z' and resid 367 through 368 Processing sheet with id=AI1, first strand: chain 'Z' and resid 438 through 439 Processing sheet with id=AI2, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.550A pdb=" N VAL Z 478 " --> pdb=" O GLY Z 490 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY Z 490 " --> pdb=" O VAL Z 478 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU Z 491 " --> pdb=" O PHE Z 503 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL Z 500 " --> pdb=" O VAL Z 513 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL Z 513 " --> pdb=" O VAL Z 500 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.151A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL Z 551 " --> pdb=" O GLN Z 559 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN Z 541 " --> pdb=" O THR Z 576 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR Z 576 " --> pdb=" O GLN Z 541 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Z' and resid 622 through 625 removed outlier: 6.918A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY Z 612 " --> pdb=" O VAL Z 600 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL Z 600 " --> pdb=" O GLY Z 612 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.607A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'a' and resid 83 through 84 removed outlier: 7.167A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AI8, first strand: chain 'b' and resid 96 through 98 removed outlier: 6.386A pdb=" N THR b 96 " --> pdb=" O THR g 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.095A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI9 Processing sheet with id=AJ1, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AJ2, first strand: chain 'c' and resid 101 through 102 removed outlier: 6.894A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.918A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AJ5, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.015A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 Processing sheet with id=AJ6, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AJ7, first strand: chain 'l' and resid 1556 through 1558 removed outlier: 4.259A pdb=" N GLU l1558 " --> pdb=" O GLY l1561 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'l' and resid 1575 through 1578 removed outlier: 6.885A pdb=" N PHE l1650 " --> pdb=" O VAL l1576 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU l1578 " --> pdb=" O VAL l1648 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL l1648 " --> pdb=" O GLU l1578 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'l' and resid 1582 through 1583 2887 hydrogen bonds defined for protein. 8250 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 481 hydrogen bonds 962 hydrogen bond angles 0 basepair planarities 190 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 50.35 Time building geometry restraints manager: 17.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16920 1.33 - 1.45: 17297 1.45 - 1.57: 40041 1.57 - 1.70: 773 1.70 - 1.82: 497 Bond restraints: 75528 Sorted by residual: bond pdb=" CA PRO Q 450 " pdb=" C PRO Q 450 " ideal model delta sigma weight residual 1.514 1.567 -0.053 5.50e-03 3.31e+04 9.27e+01 bond pdb=" OG1 TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" OG1 TPO Z 775 " pdb=" P TPO Z 775 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" P DG T 11 " pdb=" OP2 DG T 11 " ideal model delta sigma weight residual 1.480 1.397 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" O3P TPO Z 775 " pdb=" P TPO Z 775 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 75523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 102680 2.58 - 5.16: 623 5.16 - 7.74: 20 7.74 - 10.32: 14 10.32 - 12.90: 6 Bond angle restraints: 103343 Sorted by residual: angle pdb=" O PRO Q 450 " pdb=" C PRO Q 450 " pdb=" N PRO Q 451 " ideal model delta sigma weight residual 121.31 124.78 -3.47 4.60e-01 4.73e+00 5.69e+01 angle pdb=" C GLU Q 772 " pdb=" N LYS Q 773 " pdb=" CA LYS Q 773 " ideal model delta sigma weight residual 121.70 132.21 -10.51 1.80e+00 3.09e-01 3.41e+01 angle pdb=" C TYR V 61 " pdb=" N LYS V 62 " pdb=" CA LYS V 62 " ideal model delta sigma weight residual 121.70 131.31 -9.61 1.80e+00 3.09e-01 2.85e+01 angle pdb=" N LEU l2019 " pdb=" CA LEU l2019 " pdb=" C LEU l2019 " ideal model delta sigma weight residual 112.13 118.33 -6.20 1.37e+00 5.33e-01 2.05e+01 angle pdb=" O3' DC N 45 " pdb=" P DC N 46 " pdb=" OP1 DC N 46 " ideal model delta sigma weight residual 108.00 120.90 -12.90 3.00e+00 1.11e-01 1.85e+01 ... (remaining 103338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 42012 35.23 - 70.45: 1616 70.45 - 105.68: 24 105.68 - 140.91: 1 140.91 - 176.13: 5 Dihedral angle restraints: 43658 sinusoidal: 19844 harmonic: 23814 Sorted by residual: dihedral pdb=" CA GLU l2021 " pdb=" C GLU l2021 " pdb=" N VAL l2022 " pdb=" CA VAL l2022 " ideal model delta harmonic sigma weight residual 180.00 122.01 57.99 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" C4' A P 18 " pdb=" C3' A P 18 " pdb=" C2' A P 18 " pdb=" C1' A P 18 " ideal model delta sinusoidal sigma weight residual -35.00 34.31 -69.31 1 8.00e+00 1.56e-02 9.70e+01 dihedral pdb=" C5' A P 18 " pdb=" C4' A P 18 " pdb=" C3' A P 18 " pdb=" O3' A P 18 " ideal model delta sinusoidal sigma weight residual 147.00 81.18 65.82 1 8.00e+00 1.56e-02 8.86e+01 ... (remaining 43655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 10462 0.090 - 0.180: 558 0.180 - 0.270: 1 0.270 - 0.359: 3 0.359 - 0.449: 7 Chirality restraints: 11031 Sorted by residual: chirality pdb=" P DC N 46 " pdb=" OP1 DC N 46 " pdb=" OP2 DC N 46 " pdb=" O5' DC N 46 " both_signs ideal model delta sigma weight residual True 2.35 -2.79 -0.45 2.00e-01 2.50e+01 5.05e+00 chirality pdb=" P DC T -49 " pdb=" OP1 DC T -49 " pdb=" OP2 DC T -49 " pdb=" O5' DC T -49 " both_signs ideal model delta sigma weight residual True 2.35 -2.78 -0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" P DA N 47 " pdb=" OP1 DA N 47 " pdb=" OP2 DA N 47 " pdb=" O5' DA N 47 " both_signs ideal model delta sigma weight residual True 2.35 -2.75 -0.41 2.00e-01 2.50e+01 4.16e+00 ... (remaining 11028 not shown) Planarity restraints: 12367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 219 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C GLY B 219 " -0.036 2.00e-02 2.50e+03 pdb=" O GLY B 219 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU B 220 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 190 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C ARG A 190 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG A 190 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 191 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG T 9 " -0.029 2.00e-02 2.50e+03 1.19e-02 4.25e+00 pdb=" N9 DG T 9 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG T 9 " 0.009 2.00e-02 2.50e+03 pdb=" N7 DG T 9 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG T 9 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG T 9 " -0.008 2.00e-02 2.50e+03 pdb=" O6 DG T 9 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG T 9 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG T 9 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG T 9 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG T 9 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG T 9 " 0.004 2.00e-02 2.50e+03 ... (remaining 12364 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 509 2.50 - 3.10: 57249 3.10 - 3.70: 112032 3.70 - 4.30: 159400 4.30 - 4.90: 255097 Nonbonded interactions: 584287 Sorted by model distance: nonbonded pdb=" N CYS J 45 " pdb="ZN ZN J 101 " model vdw 1.904 2.310 nonbonded pdb=" O ASN D 76 " pdb=" OG1 THR D 79 " model vdw 1.933 3.040 nonbonded pdb=" O3' C P 26 " pdb="MG MG A2003 " model vdw 1.942 2.170 nonbonded pdb=" O MET A 535 " pdb=" OH TYR A 669 " model vdw 1.972 3.040 nonbonded pdb=" N ASN A1172 " pdb=" OE2 GLU A1215 " model vdw 1.987 3.120 ... (remaining 584282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and (resid 39 through 76 or resid 78 through 133)) selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 15 through 117) selection = chain 'g' } ncs_group { reference = (chain 'd' and resid 35 through 123) selection = chain 'h' } 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=0.99 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: 9.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.430 Construct map_model_manager: 0.100 Extract box with map and model: 2.590 Check model and map are aligned: 0.430 Set scattering table: 0.510 Process input model: 173.060 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 191.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 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 : 0.004 0.107 75528 Z= 0.242 Angle : 0.590 12.897 103343 Z= 0.332 Chirality : 0.042 0.449 11031 Planarity : 0.004 0.050 12367 Dihedral : 14.798 176.132 28840 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.48 % Favored : 94.45 % Rotamer: Outliers : 0.49 % Allowed : 3.67 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.01 (0.09), residues: 8646 helix: 1.29 (0.09), residues: 3498 sheet: -2.38 (0.16), residues: 859 loop : -2.05 (0.09), residues: 4289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 27 HIS 0.007 0.001 HIS f 75 PHE 0.021 0.001 PHE A1366 TYR 0.015 0.001 TYR l1671 ARG 0.009 0.000 ARG l1670 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 1271 time to evaluate : 5.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8632 (mtmt) REVERT: A 58 MET cc_start: 0.7454 (tpp) cc_final: 0.7043 (tpp) REVERT: A 85 PHE cc_start: 0.5291 (m-80) cc_final: 0.5059 (m-80) REVERT: A 278 HIS cc_start: 0.8700 (m170) cc_final: 0.8301 (m-70) REVERT: A 350 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8646 (m) REVERT: A 354 LEU cc_start: 0.8446 (mt) cc_final: 0.8236 (mm) REVERT: A 466 LYS cc_start: 0.9332 (ttpt) cc_final: 0.8831 (tttt) REVERT: A 467 MET cc_start: 0.8461 (mmt) cc_final: 0.8147 (mmm) REVERT: A 483 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7235 (mpp80) REVERT: A 500 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7958 (mm-30) REVERT: A 561 MET cc_start: 0.8537 (mtm) cc_final: 0.7912 (mtt) REVERT: A 571 ASP cc_start: 0.8576 (p0) cc_final: 0.8232 (p0) REVERT: A 735 GLN cc_start: 0.8918 (mt0) cc_final: 0.8451 (mt0) REVERT: A 782 SER cc_start: 0.9100 (t) cc_final: 0.8760 (p) REVERT: A 841 MET cc_start: 0.8536 (mtp) cc_final: 0.8205 (mtm) REVERT: A 869 GLU cc_start: 0.7393 (pt0) cc_final: 0.7145 (tt0) REVERT: A 891 TYR cc_start: 0.8530 (t80) cc_final: 0.8257 (t80) REVERT: A 905 ASN cc_start: 0.9106 (p0) cc_final: 0.8881 (p0) REVERT: A 928 ARG cc_start: 0.8952 (mtp85) cc_final: 0.8678 (mtp85) REVERT: A 1038 THR cc_start: 0.9113 (m) cc_final: 0.8726 (t) REVERT: A 1054 MET cc_start: 0.8390 (tpp) cc_final: 0.8084 (tpt) REVERT: A 1078 GLN cc_start: 0.9141 (mt0) cc_final: 0.8652 (mm-40) REVERT: A 1086 MET cc_start: 0.8482 (mmm) cc_final: 0.8037 (mmm) REVERT: A 1167 ARG cc_start: 0.8268 (ttp-110) cc_final: 0.7917 (ttm-80) REVERT: A 1412 MET cc_start: 0.8154 (ptm) cc_final: 0.7563 (ppp) REVERT: A 1428 MET cc_start: 0.8867 (ttt) cc_final: 0.8662 (mtp) REVERT: B 53 MET cc_start: 0.9007 (mmt) cc_final: 0.8558 (mmt) REVERT: B 121 SER cc_start: 0.8696 (p) cc_final: 0.8372 (m) REVERT: B 160 TYR cc_start: 0.8262 (m-80) cc_final: 0.7668 (m-80) REVERT: B 297 MET cc_start: 0.8995 (ttt) cc_final: 0.8603 (ttm) REVERT: B 597 ILE cc_start: 0.9611 (mt) cc_final: 0.9402 (mm) REVERT: B 675 LEU cc_start: 0.9343 (tp) cc_final: 0.9033 (tp) REVERT: B 697 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7983 (mt-10) REVERT: B 718 GLN cc_start: 0.8678 (tt0) cc_final: 0.8437 (mt0) REVERT: B 731 GLN cc_start: 0.8523 (mp-120) cc_final: 0.8244 (mp10) REVERT: B 751 LEU cc_start: 0.8782 (tp) cc_final: 0.8512 (tt) REVERT: B 789 ASN cc_start: 0.8369 (p0) cc_final: 0.8013 (p0) REVERT: B 958 CYS cc_start: 0.8419 (m) cc_final: 0.7841 (m) REVERT: B 966 ILE cc_start: 0.6224 (mt) cc_final: 0.5984 (mt) REVERT: B 1022 LEU cc_start: 0.9222 (pt) cc_final: 0.8936 (pt) REVERT: B 1051 LEU cc_start: 0.9207 (mt) cc_final: 0.9006 (mt) REVERT: B 1090 GLU cc_start: 0.8673 (mp0) cc_final: 0.7942 (mp0) REVERT: B 1125 MET cc_start: 0.8800 (mtm) cc_final: 0.8279 (mtm) REVERT: B 1151 MET cc_start: 0.7874 (ptp) cc_final: 0.7639 (ptp) REVERT: B 1161 GLU cc_start: 0.9357 (mt-10) cc_final: 0.9096 (mt-10) REVERT: B 1165 MET cc_start: 0.8329 (mtm) cc_final: 0.8121 (ptm) REVERT: B 1172 MET cc_start: 0.7994 (tpp) cc_final: 0.7622 (mpp) REVERT: C 154 ARG cc_start: 0.7401 (ttt180) cc_final: 0.6950 (ttm-80) REVERT: C 185 GLU cc_start: 0.8029 (tt0) cc_final: 0.7622 (tt0) REVERT: C 207 GLU cc_start: 0.8880 (tt0) cc_final: 0.8555 (tt0) REVERT: C 208 TYR cc_start: 0.8731 (m-80) cc_final: 0.8381 (m-80) REVERT: C 247 SER cc_start: 0.9006 (m) cc_final: 0.8801 (t) REVERT: C 268 GLN cc_start: 0.9005 (tp40) cc_final: 0.8751 (tm-30) REVERT: D 62 MET cc_start: 0.9301 (mtt) cc_final: 0.9084 (mmm) REVERT: D 80 ILE cc_start: 0.8948 (mt) cc_final: 0.8431 (mt) REVERT: D 138 ARG cc_start: 0.8476 (mtp180) cc_final: 0.8215 (mtp85) REVERT: E 143 GLU cc_start: 0.8807 (tp30) cc_final: 0.8569 (tp30) REVERT: E 178 PRO cc_start: 0.8781 (Cg_exo) cc_final: 0.8480 (Cg_endo) REVERT: E 203 TYR cc_start: 0.7465 (t80) cc_final: 0.6950 (t80) REVERT: F 83 LEU cc_start: 0.8953 (mp) cc_final: 0.8540 (mm) REVERT: F 87 THR cc_start: 0.8799 (p) cc_final: 0.8566 (t) REVERT: F 91 LEU cc_start: 0.9241 (mt) cc_final: 0.9021 (tp) REVERT: F 92 ILE cc_start: 0.9015 (mt) cc_final: 0.8772 (mt) REVERT: F 94 MET cc_start: 0.9280 (tpt) cc_final: 0.8948 (tpp) REVERT: G 156 ASP cc_start: 0.5824 (m-30) cc_final: 0.5388 (m-30) REVERT: H 12 VAL cc_start: 0.9523 (t) cc_final: 0.9146 (m) REVERT: H 100 GLU cc_start: 0.7565 (tp30) cc_final: 0.7293 (tt0) REVERT: H 111 ARG cc_start: 0.7354 (mtp85) cc_final: 0.6715 (mtp85) REVERT: I 71 ASP cc_start: 0.8969 (m-30) cc_final: 0.8499 (m-30) REVERT: I 125 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8054 (mt-10) REVERT: J 60 LEU cc_start: 0.9030 (mt) cc_final: 0.8708 (tp) REVERT: K 7 PHE cc_start: 0.8829 (p90) cc_final: 0.8286 (p90) REVERT: K 13 PHE cc_start: 0.7851 (t80) cc_final: 0.7388 (t80) REVERT: K 26 LYS cc_start: 0.8751 (mttt) cc_final: 0.8536 (mtpp) REVERT: K 57 LEU cc_start: 0.8992 (mt) cc_final: 0.8480 (mp) REVERT: K 62 LYS cc_start: 0.7826 (ptmt) cc_final: 0.7618 (pttt) REVERT: K 76 GLN cc_start: 0.8622 (tt0) cc_final: 0.8221 (tm-30) REVERT: L 43 ILE cc_start: 0.8763 (mt) cc_final: 0.8561 (pt) REVERT: L 44 MET cc_start: 0.8379 (ptp) cc_final: 0.7952 (mtm) REVERT: O 652 LEU cc_start: -0.2769 (OUTLIER) cc_final: -0.3049 (pt) REVERT: Q 604 MET cc_start: 0.6996 (mtt) cc_final: 0.6553 (mtt) REVERT: V 51 TYR cc_start: 0.4799 (t80) cc_final: 0.4545 (t80) REVERT: V 126 LYS cc_start: 0.8357 (mmmt) cc_final: 0.7708 (mmmm) REVERT: V 131 MET cc_start: 0.5138 (mtt) cc_final: 0.4474 (mtm) REVERT: V 134 THR cc_start: 0.3397 (t) cc_final: 0.2872 (t) REVERT: V 183 PHE cc_start: 0.1140 (m-80) cc_final: 0.0859 (m-80) REVERT: Z 307 MET cc_start: 0.3043 (tpt) cc_final: 0.2726 (ptp) REVERT: Z 635 MET cc_start: 0.5572 (ttt) cc_final: 0.4161 (tmm) REVERT: a 45 THR cc_start: 0.9061 (m) cc_final: 0.8748 (p) REVERT: a 50 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8697 (mt-10) REVERT: a 53 ARG cc_start: 0.8838 (tmt90) cc_final: 0.8239 (tpt90) REVERT: a 58 THR cc_start: 0.8835 (p) cc_final: 0.8282 (t) REVERT: a 73 GLU cc_start: 0.8929 (tt0) cc_final: 0.8541 (tm-30) REVERT: a 74 ILE cc_start: 0.8677 (pt) cc_final: 0.8245 (tp) REVERT: a 76 GLN cc_start: 0.8963 (mt0) cc_final: 0.8714 (mt0) REVERT: a 81 ASP cc_start: 0.8165 (t0) cc_final: 0.7902 (t0) REVERT: a 93 GLN cc_start: 0.8687 (tt0) cc_final: 0.8212 (tp40) REVERT: a 125 GLN cc_start: 0.9557 (mt0) cc_final: 0.9070 (mp10) REVERT: a 129 ARG cc_start: 0.9270 (tpt90) cc_final: 0.8688 (tpm170) REVERT: b 27 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8706 (mm-40) REVERT: b 30 THR cc_start: 0.8289 (p) cc_final: 0.7979 (t) REVERT: b 68 ASP cc_start: 0.9219 (m-30) cc_final: 0.8804 (p0) REVERT: b 74 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8730 (mm-30) REVERT: b 97 LEU cc_start: 0.8465 (tp) cc_final: 0.8225 (tp) REVERT: b 98 TYR cc_start: 0.8150 (m-10) cc_final: 0.7940 (m-80) REVERT: c 92 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7478 (mt-10) REVERT: c 95 LYS cc_start: 0.9527 (tttt) cc_final: 0.9095 (tmtt) REVERT: c 104 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7640 (tp-100) REVERT: d 57 LYS cc_start: 0.9205 (mmpt) cc_final: 0.8333 (tppp) REVERT: d 96 THR cc_start: 0.9076 (m) cc_final: 0.8685 (p) REVERT: d 108 LYS cc_start: 0.9408 (mmtt) cc_final: 0.9204 (ttpp) REVERT: e 51 ILE cc_start: 0.9140 (mt) cc_final: 0.8789 (mm) REVERT: e 97 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6767 (mm-30) REVERT: e 108 ASN cc_start: 0.8698 (t0) cc_final: 0.8447 (t0) REVERT: e 120 MET cc_start: 0.8413 (mtt) cc_final: 0.8048 (mtt) REVERT: e 129 ARG cc_start: 0.8968 (tpt90) cc_final: 0.8675 (tpt90) REVERT: f 26 ILE cc_start: 0.9212 (tp) cc_final: 0.8966 (tp) REVERT: f 32 PRO cc_start: 0.8835 (Cg_exo) cc_final: 0.8622 (Cg_endo) REVERT: f 49 LEU cc_start: 0.9298 (mt) cc_final: 0.8394 (mp) REVERT: f 79 LYS cc_start: 0.7591 (mmtm) cc_final: 0.7099 (tttt) REVERT: f 84 MET cc_start: 0.8547 (mmm) cc_final: 0.7972 (mmm) REVERT: f 96 THR cc_start: 0.7644 (m) cc_final: 0.7429 (p) REVERT: g 92 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8689 (mt-10) REVERT: g 95 LYS cc_start: 0.9090 (ttmt) cc_final: 0.8764 (tmtt) REVERT: g 111 ILE cc_start: 0.9044 (mt) cc_final: 0.8654 (pt) REVERT: g 114 VAL cc_start: 0.8527 (m) cc_final: 0.8313 (p) REVERT: h 57 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8466 (tptt) REVERT: h 68 ASP cc_start: 0.8350 (t0) cc_final: 0.8027 (t0) REVERT: h 105 GLU cc_start: 0.7916 (tp30) cc_final: 0.7531 (tp30) outliers start: 32 outliers final: 8 residues processed: 1301 average time/residue: 0.7017 time to fit residues: 1540.9385 Evaluate side-chains 760 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 750 time to evaluate : 5.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain O residue 652 LEU Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain Q residue 552 ASP Chi-restraints excluded: chain Q residue 667 ARG Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 272 ASP Chi-restraints excluded: chain l residue 1489 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 763 optimal weight: 9.9990 chunk 685 optimal weight: 30.0000 chunk 380 optimal weight: 0.8980 chunk 234 optimal weight: 0.3980 chunk 462 optimal weight: 0.4980 chunk 366 optimal weight: 0.7980 chunk 708 optimal weight: 30.0000 chunk 274 optimal weight: 5.9990 chunk 430 optimal weight: 9.9990 chunk 527 optimal weight: 30.0000 chunk 820 optimal weight: 7.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 288 ASN A 301 HIS A 341 GLN A 387 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 GLN A 757 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 GLN A1044 HIS A1332 GLN A1457 ASN A1462 GLN B 43 GLN B 98 HIS ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 420 GLN B 471 ASN B 649 ASN B 725 GLN B 980 HIS B1025 ASN B1071 ASN B1097 HIS ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN H 29 HIS H 131 ASN I 41 ASN Q 38 HIS ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 ASN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 228 ASN Q 244 ASN Q 268 ASN ** Q 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 502 ASN Q 527 HIS ** Q 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 617 GLN Q 628 HIS ** Q 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 762 GLN ** Q 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 187 GLN W 27 ASN W 268 HIS W 273 HIS Z 446 ASN a 113 HIS c 94 ASN d 49 HIS d 82 HIS d 109 HIS g 38 ASN h 49 HIS h 63 ASN h 84 ASN ** l1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l1549 HIS Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.126122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.087880 restraints weight = 305293.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.088207 restraints weight = 146425.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.089405 restraints weight = 93486.020| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 442 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 443 | |-----------------------------------------------------------------------------| r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 75528 Z= 0.269 Angle : 0.641 12.541 103343 Z= 0.337 Chirality : 0.044 0.308 11031 Planarity : 0.004 0.073 12367 Dihedral : 18.262 172.523 13740 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 2.06 % Allowed : 9.12 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.09), residues: 8646 helix: 1.36 (0.09), residues: 3520 sheet: -2.08 (0.16), residues: 897 loop : -1.81 (0.09), residues: 4229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP W 20 HIS 0.014 0.001 HIS Q 745 PHE 0.029 0.002 PHE B 408 TYR 0.031 0.002 TYR B 766 ARG 0.011 0.001 ARG O 659 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 793 time to evaluate : 5.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8619 (mtmt) REVERT: A 58 MET cc_start: 0.7497 (tpp) cc_final: 0.7023 (tpp) REVERT: A 104 MET cc_start: 0.8423 (tpp) cc_final: 0.7539 (mmm) REVERT: A 278 HIS cc_start: 0.8753 (m170) cc_final: 0.8067 (t-90) REVERT: A 354 LEU cc_start: 0.8440 (mt) cc_final: 0.8029 (mt) REVERT: A 483 ARG cc_start: 0.8068 (mtt90) cc_final: 0.7507 (mtt90) REVERT: A 500 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7674 (mm-30) REVERT: A 501 MET cc_start: 0.8437 (mtp) cc_final: 0.7747 (mtp) REVERT: A 524 MET cc_start: 0.8178 (mmt) cc_final: 0.7726 (mmt) REVERT: A 565 MET cc_start: 0.8930 (mmm) cc_final: 0.8670 (tpt) REVERT: A 571 ASP cc_start: 0.8659 (p0) cc_final: 0.8425 (p0) REVERT: A 639 ILE cc_start: 0.8890 (mt) cc_final: 0.8603 (mm) REVERT: A 683 GLU cc_start: 0.8431 (tp30) cc_final: 0.8112 (tp30) REVERT: A 782 SER cc_start: 0.9203 (t) cc_final: 0.8856 (p) REVERT: A 845 GLU cc_start: 0.8648 (tt0) cc_final: 0.8281 (tt0) REVERT: A 902 GLU cc_start: 0.7615 (tt0) cc_final: 0.7208 (tt0) REVERT: A 928 ARG cc_start: 0.9042 (mtp85) cc_final: 0.8754 (mtp85) REVERT: A 986 MET cc_start: 0.8705 (mmt) cc_final: 0.8122 (mpp) REVERT: A 1038 THR cc_start: 0.9072 (m) cc_final: 0.8836 (t) REVERT: A 1078 GLN cc_start: 0.9174 (mt0) cc_final: 0.8763 (mm-40) REVERT: A 1094 SER cc_start: 0.9055 (m) cc_final: 0.8653 (p) REVERT: A 1167 ARG cc_start: 0.8461 (ttp-110) cc_final: 0.8193 (ttm-80) REVERT: A 1412 MET cc_start: 0.8305 (ptm) cc_final: 0.7987 (ppp) REVERT: A 1428 MET cc_start: 0.8742 (ttt) cc_final: 0.8372 (mtm) REVERT: B 108 MET cc_start: 0.8505 (ptm) cc_final: 0.8254 (ptp) REVERT: B 508 MET cc_start: 0.8337 (mpp) cc_final: 0.7876 (mpp) REVERT: B 597 ILE cc_start: 0.9520 (mt) cc_final: 0.9276 (pt) REVERT: B 629 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7408 (mm-30) REVERT: B 675 LEU cc_start: 0.9432 (tp) cc_final: 0.9210 (tp) REVERT: B 731 GLN cc_start: 0.8676 (mp-120) cc_final: 0.8367 (mp10) REVERT: B 789 ASN cc_start: 0.7980 (p0) cc_final: 0.7489 (p0) REVERT: B 958 CYS cc_start: 0.8125 (m) cc_final: 0.7089 (m) REVERT: B 1015 LEU cc_start: 0.9553 (tp) cc_final: 0.9217 (tt) REVERT: B 1039 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8775 (p) REVERT: B 1054 MET cc_start: 0.8508 (mmm) cc_final: 0.7800 (mmm) REVERT: B 1090 GLU cc_start: 0.8879 (mp0) cc_final: 0.8069 (mp0) REVERT: B 1135 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: B 1151 MET cc_start: 0.8006 (ptp) cc_final: 0.7757 (ptp) REVERT: B 1157 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9043 (tp) REVERT: C 154 ARG cc_start: 0.7680 (ttt180) cc_final: 0.7293 (ttm-80) REVERT: C 247 SER cc_start: 0.9025 (m) cc_final: 0.8742 (t) REVERT: D 19 GLN cc_start: 0.9221 (mm-40) cc_final: 0.9004 (mm-40) REVERT: D 74 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7977 (p90) REVERT: D 132 ASP cc_start: 0.9156 (m-30) cc_final: 0.8939 (t0) REVERT: D 138 ARG cc_start: 0.8475 (mtp180) cc_final: 0.8069 (mtp180) REVERT: E 121 MET cc_start: 0.6216 (tpp) cc_final: 0.6015 (tpp) REVERT: E 143 GLU cc_start: 0.8640 (tp30) cc_final: 0.8373 (tp30) REVERT: E 178 PRO cc_start: 0.8796 (Cg_exo) cc_final: 0.8445 (Cg_endo) REVERT: E 203 TYR cc_start: 0.7745 (t80) cc_final: 0.7244 (t80) REVERT: F 87 THR cc_start: 0.8859 (p) cc_final: 0.8320 (t) REVERT: F 115 TYR cc_start: 0.8464 (p90) cc_final: 0.8074 (p90) REVERT: G 60 GLN cc_start: 0.8459 (mm110) cc_final: 0.8257 (mm110) REVERT: G 156 ASP cc_start: 0.6804 (m-30) cc_final: 0.6461 (m-30) REVERT: H 103 GLU cc_start: 0.7393 (mp0) cc_final: 0.7188 (mp0) REVERT: I 71 ASP cc_start: 0.8966 (m-30) cc_final: 0.8604 (m-30) REVERT: I 125 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7839 (mt-10) REVERT: J 29 TYR cc_start: 0.8480 (m-80) cc_final: 0.8209 (m-10) REVERT: J 41 LYS cc_start: 0.9287 (mmmt) cc_final: 0.8807 (mmtt) REVERT: K 7 PHE cc_start: 0.8586 (p90) cc_final: 0.8161 (p90) REVERT: K 13 PHE cc_start: 0.7605 (t80) cc_final: 0.7388 (t80) REVERT: K 26 LYS cc_start: 0.8684 (mttt) cc_final: 0.8475 (mtpp) REVERT: K 38 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7964 (mm-30) REVERT: K 85 GLU cc_start: 0.7920 (pt0) cc_final: 0.7705 (pt0) REVERT: K 111 ASP cc_start: 0.8332 (m-30) cc_final: 0.8097 (m-30) REVERT: O 594 VAL cc_start: 0.0361 (m) cc_final: -0.0065 (m) REVERT: O 652 LEU cc_start: -0.1390 (OUTLIER) cc_final: -0.2124 (pp) REVERT: O 659 ARG cc_start: 0.2551 (tpt90) cc_final: 0.2128 (tmt170) REVERT: Q 604 MET cc_start: 0.7384 (mtt) cc_final: 0.6893 (mtt) REVERT: Q 803 MET cc_start: 0.7759 (pmm) cc_final: 0.7457 (pmm) REVERT: Q 890 MET cc_start: 0.1225 (ptt) cc_final: 0.0753 (ptt) REVERT: U 448 MET cc_start: 0.3072 (ptt) cc_final: 0.2298 (tpt) REVERT: V 47 LYS cc_start: 0.8484 (mmmt) cc_final: 0.8028 (mmmt) REVERT: V 183 PHE cc_start: 0.1541 (m-80) cc_final: 0.1251 (m-80) REVERT: V 205 MET cc_start: -0.1653 (tpt) cc_final: -0.2889 (ttm) REVERT: W 237 ASN cc_start: 0.8553 (t0) cc_final: 0.8078 (t0) REVERT: X 228 GLU cc_start: 0.8942 (pp20) cc_final: 0.8611 (pp20) REVERT: Y 63 MET cc_start: -0.1852 (mmm) cc_final: -0.2165 (ptt) REVERT: Z 307 MET cc_start: 0.2246 (tpt) cc_final: 0.1931 (ptp) REVERT: Z 460 MET cc_start: 0.0317 (mmt) cc_final: -0.0924 (mtm) REVERT: Z 491 LEU cc_start: 0.8946 (mp) cc_final: 0.8742 (mt) REVERT: a 45 THR cc_start: 0.9279 (m) cc_final: 0.8920 (p) REVERT: a 50 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8835 (mp0) REVERT: a 53 ARG cc_start: 0.8931 (tmt90) cc_final: 0.8333 (tmt-80) REVERT: a 54 TYR cc_start: 0.9257 (m-80) cc_final: 0.8991 (m-80) REVERT: a 73 GLU cc_start: 0.8921 (tt0) cc_final: 0.7843 (tp30) REVERT: a 76 GLN cc_start: 0.9008 (mt0) cc_final: 0.8714 (mt0) REVERT: a 93 GLN cc_start: 0.8756 (tt0) cc_final: 0.8510 (tp40) REVERT: a 129 ARG cc_start: 0.9214 (tpt90) cc_final: 0.8679 (tpm170) REVERT: b 74 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8588 (mm-30) REVERT: b 98 TYR cc_start: 0.9199 (m-10) cc_final: 0.8946 (m-80) REVERT: c 36 LYS cc_start: 0.7064 (pttt) cc_final: 0.6781 (pttm) REVERT: c 104 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7807 (tp-100) REVERT: d 59 MET cc_start: 0.8937 (tpp) cc_final: 0.8386 (tpp) REVERT: d 71 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8019 (tp30) REVERT: d 93 GLU cc_start: 0.8577 (mp0) cc_final: 0.8177 (mp0) REVERT: d 108 LYS cc_start: 0.9379 (mmtt) cc_final: 0.9110 (ttpp) REVERT: e 45 THR cc_start: 0.8745 (m) cc_final: 0.8402 (p) REVERT: e 50 GLU cc_start: 0.8851 (tt0) cc_final: 0.7603 (tp30) REVERT: e 51 ILE cc_start: 0.9079 (mt) cc_final: 0.8768 (mm) REVERT: e 97 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7235 (mm-30) REVERT: e 106 ASP cc_start: 0.8918 (m-30) cc_final: 0.8622 (m-30) REVERT: e 129 ARG cc_start: 0.9052 (tpt90) cc_final: 0.8769 (tpt90) REVERT: f 30 THR cc_start: 0.8305 (p) cc_final: 0.7461 (t) REVERT: f 32 PRO cc_start: 0.9277 (Cg_exo) cc_final: 0.8780 (Cg_endo) REVERT: f 79 LYS cc_start: 0.7785 (mmtm) cc_final: 0.7399 (mmtp) REVERT: f 84 MET cc_start: 0.8329 (mmm) cc_final: 0.7662 (mmm) REVERT: f 96 THR cc_start: 0.8149 (m) cc_final: 0.7788 (p) REVERT: g 111 ILE cc_start: 0.9202 (mt) cc_final: 0.8875 (pt) REVERT: h 68 ASP cc_start: 0.8986 (t0) cc_final: 0.8585 (t0) REVERT: h 79 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8763 (mpp80) REVERT: l 1526 MET cc_start: 0.7810 (mmm) cc_final: 0.7544 (mmm) REVERT: l 1627 MET cc_start: 0.6321 (tpp) cc_final: 0.4760 (tpp) outliers start: 135 outliers final: 71 residues processed: 885 average time/residue: 0.6862 time to fit residues: 1044.1949 Evaluate side-chains 763 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 686 time to evaluate : 5.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 1039 SER Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain O residue 652 LEU Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 262 TYR Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain Q residue 418 LEU Chi-restraints excluded: chain Q residue 510 MET Chi-restraints excluded: chain Q residue 790 HIS Chi-restraints excluded: chain V residue 31 CYS Chi-restraints excluded: chain V residue 123 GLN Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 154 ILE Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain d residue 39 ILE Chi-restraints excluded: chain d residue 64 SER Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 104 PHE Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain g residue 78 ILE Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 221 optimal weight: 3.9990 chunk 452 optimal weight: 30.0000 chunk 782 optimal weight: 30.0000 chunk 629 optimal weight: 10.0000 chunk 601 optimal weight: 0.0770 chunk 354 optimal weight: 10.0000 chunk 493 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 522 optimal weight: 4.9990 chunk 296 optimal weight: 0.7980 chunk 641 optimal weight: 30.0000 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 227 ASN B1021 HIS B1025 ASN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS G 91 GLN L 23 HIS ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 289 GLN Q 305 GLN ** Q 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 689 HIS Q 775 ASN ** Q 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 473 ASN ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 567 ASN W 98 GLN Z 625 HIS b 75 HIS e 108 ASN h 49 HIS h 84 ASN ** l1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.123414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.083371 restraints weight = 300606.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.084468 restraints weight = 146065.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.085561 restraints weight = 93719.148| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 443 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 444 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 75528 Z= 0.287 Angle : 0.608 13.095 103343 Z= 0.321 Chirality : 0.042 0.293 11031 Planarity : 0.004 0.055 12367 Dihedral : 18.372 172.491 13722 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.12 % Favored : 94.83 % Rotamer: Outliers : 2.20 % Allowed : 10.87 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.09), residues: 8646 helix: 1.38 (0.09), residues: 3539 sheet: -1.82 (0.17), residues: 848 loop : -1.72 (0.09), residues: 4259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP l1460 HIS 0.007 0.001 HIS G 9 PHE 0.035 0.002 PHE H 35 TYR 0.033 0.002 TYR R 562 ARG 0.013 0.001 ARG B1170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 752 time to evaluate : 6.140 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: A 19 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8701 (mtmt) REVERT: A 58 MET cc_start: 0.7592 (tpp) cc_final: 0.7018 (tpp) REVERT: A 85 PHE cc_start: 0.6390 (OUTLIER) cc_final: 0.6070 (t80) REVERT: A 104 MET cc_start: 0.8433 (tpp) cc_final: 0.7416 (mmm) REVERT: A 278 HIS cc_start: 0.8748 (m170) cc_final: 0.8320 (m-70) REVERT: A 329 MET cc_start: 0.7947 (tpp) cc_final: 0.7482 (tpp) REVERT: A 354 LEU cc_start: 0.8511 (mt) cc_final: 0.8053 (mt) REVERT: A 450 MET cc_start: 0.7766 (ttm) cc_final: 0.7506 (ttm) REVERT: A 500 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7720 (mm-30) REVERT: A 501 MET cc_start: 0.8447 (mtp) cc_final: 0.7447 (mtp) REVERT: A 539 GLN cc_start: 0.7571 (tp-100) cc_final: 0.7102 (tp-100) REVERT: A 561 MET cc_start: 0.8509 (mtt) cc_final: 0.7923 (mtt) REVERT: A 565 MET cc_start: 0.9184 (mmm) cc_final: 0.8742 (mmm) REVERT: A 571 ASP cc_start: 0.8682 (p0) cc_final: 0.8480 (p0) REVERT: A 637 MET cc_start: 0.8466 (mtt) cc_final: 0.8266 (mtt) REVERT: A 683 GLU cc_start: 0.8389 (tp30) cc_final: 0.7981 (tp30) REVERT: A 762 GLU cc_start: 0.8801 (pm20) cc_final: 0.8585 (pm20) REVERT: A 792 ASN cc_start: 0.8930 (m-40) cc_final: 0.8496 (m-40) REVERT: A 900 SER cc_start: 0.9341 (m) cc_final: 0.8779 (p) REVERT: A 902 GLU cc_start: 0.7495 (tt0) cc_final: 0.7073 (tt0) REVERT: A 928 ARG cc_start: 0.9141 (mtp85) cc_final: 0.8866 (mtp85) REVERT: A 1038 THR cc_start: 0.9060 (m) cc_final: 0.8780 (t) REVERT: A 1078 GLN cc_start: 0.9126 (mt0) cc_final: 0.8845 (mm-40) REVERT: A 1094 SER cc_start: 0.9080 (m) cc_final: 0.8714 (p) REVERT: A 1167 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8361 (ttm-80) REVERT: A 1210 TRP cc_start: 0.6465 (OUTLIER) cc_final: 0.5484 (p90) REVERT: A 1412 MET cc_start: 0.8492 (ptm) cc_final: 0.8254 (ppp) REVERT: A 1428 MET cc_start: 0.8772 (ttt) cc_final: 0.8466 (mtm) REVERT: A 1440 MET cc_start: 0.9216 (mmt) cc_final: 0.8627 (mmm) REVERT: A 1459 MET cc_start: 0.8732 (mtp) cc_final: 0.8502 (mtm) REVERT: B 93 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9106 (tp) REVERT: B 108 MET cc_start: 0.8526 (ptm) cc_final: 0.8220 (ptp) REVERT: B 298 MET cc_start: 0.8870 (ttm) cc_final: 0.8622 (ttm) REVERT: B 407 MET cc_start: 0.7920 (mtt) cc_final: 0.7707 (mtt) REVERT: B 508 MET cc_start: 0.8346 (mpp) cc_final: 0.7440 (mpp) REVERT: B 520 VAL cc_start: 0.9384 (p) cc_final: 0.9169 (t) REVERT: B 522 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8802 (mm) REVERT: B 675 LEU cc_start: 0.9238 (tp) cc_final: 0.8976 (tp) REVERT: B 728 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8025 (ttm) REVERT: B 731 GLN cc_start: 0.8683 (mp-120) cc_final: 0.8315 (mp10) REVERT: B 767 LEU cc_start: 0.9535 (tp) cc_final: 0.9185 (tt) REVERT: B 890 ARG cc_start: 0.9000 (ttm170) cc_final: 0.8709 (ttp-170) REVERT: B 897 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7349 (mtt180) REVERT: B 908 MET cc_start: 0.9062 (ttp) cc_final: 0.8839 (ttp) REVERT: B 1015 LEU cc_start: 0.9625 (tp) cc_final: 0.9339 (tt) REVERT: B 1039 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8559 (p) REVERT: B 1054 MET cc_start: 0.8586 (mmm) cc_final: 0.7846 (mmm) REVERT: B 1089 MET cc_start: 0.7741 (mtm) cc_final: 0.7440 (mtp) REVERT: B 1090 GLU cc_start: 0.8856 (mp0) cc_final: 0.8070 (mp0) REVERT: B 1135 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.7723 (m-80) REVERT: B 1151 MET cc_start: 0.7982 (ptp) cc_final: 0.7734 (ptp) REVERT: B 1172 MET cc_start: 0.8239 (mmt) cc_final: 0.7911 (mmt) REVERT: C 185 GLU cc_start: 0.7958 (tt0) cc_final: 0.7093 (mt-10) REVERT: D 19 GLN cc_start: 0.9339 (mm-40) cc_final: 0.9110 (mm-40) REVERT: D 61 PHE cc_start: 0.8976 (m-10) cc_final: 0.8745 (m-80) REVERT: D 74 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.8112 (p90) REVERT: D 138 ARG cc_start: 0.8449 (mtp180) cc_final: 0.7964 (mtp180) REVERT: E 18 MET cc_start: 0.9378 (mmp) cc_final: 0.9025 (tpp) REVERT: E 121 MET cc_start: 0.6998 (tpp) cc_final: 0.6600 (tpt) REVERT: E 138 ASN cc_start: 0.8040 (t0) cc_final: 0.7654 (t0) REVERT: E 203 TYR cc_start: 0.8086 (t80) cc_final: 0.7584 (t80) REVERT: F 83 LEU cc_start: 0.8850 (mp) cc_final: 0.8525 (mp) REVERT: F 87 THR cc_start: 0.8837 (p) cc_final: 0.8276 (t) REVERT: F 94 MET cc_start: 0.9385 (tpp) cc_final: 0.9149 (tpp) REVERT: F 115 TYR cc_start: 0.8628 (p90) cc_final: 0.8273 (p90) REVERT: G 1 MET cc_start: 0.8728 (tmm) cc_final: 0.8464 (tmm) REVERT: G 60 GLN cc_start: 0.8566 (mm110) cc_final: 0.8340 (mm110) REVERT: G 101 ILE cc_start: 0.8678 (tp) cc_final: 0.8316 (tp) REVERT: G 104 MET cc_start: 0.7422 (tmm) cc_final: 0.6500 (tmm) REVERT: G 156 ASP cc_start: 0.6908 (m-30) cc_final: 0.6494 (m-30) REVERT: H 103 GLU cc_start: 0.7414 (mp0) cc_final: 0.7199 (mp0) REVERT: H 111 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7162 (mtp85) REVERT: H 130 ASN cc_start: 0.8355 (t0) cc_final: 0.8056 (t0) REVERT: I 71 ASP cc_start: 0.9006 (m-30) cc_final: 0.8622 (m-30) REVERT: I 109 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.7992 (ttm-80) REVERT: I 125 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8002 (mt-10) REVERT: K 7 PHE cc_start: 0.8798 (p90) cc_final: 0.8464 (p90) REVERT: K 8 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8724 (pt0) REVERT: K 26 LYS cc_start: 0.8759 (mttt) cc_final: 0.8518 (mtpp) REVERT: K 38 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8025 (mm-30) REVERT: K 93 ASP cc_start: 0.7094 (p0) cc_final: 0.6796 (p0) REVERT: K 111 ASP cc_start: 0.8426 (m-30) cc_final: 0.8217 (m-30) REVERT: L 15 MET cc_start: 0.8006 (tpp) cc_final: 0.7581 (tpp) REVERT: O 652 LEU cc_start: -0.1503 (OUTLIER) cc_final: -0.2128 (pp) REVERT: O 659 ARG cc_start: 0.2664 (tpt90) cc_final: 0.2284 (tmt170) REVERT: Q 125 MET cc_start: -0.2668 (mtt) cc_final: -0.3032 (ttm) REVERT: Q 604 MET cc_start: 0.7557 (mtt) cc_final: 0.7167 (mtt) REVERT: Q 803 MET cc_start: 0.7798 (pmm) cc_final: 0.7475 (pmm) REVERT: Q 881 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6946 (m-80) REVERT: Q 890 MET cc_start: 0.1155 (ptt) cc_final: 0.0840 (ptt) REVERT: R 372 TRP cc_start: 0.7555 (m-90) cc_final: 0.6944 (m100) REVERT: U 448 MET cc_start: 0.3146 (ptt) cc_final: 0.2471 (tpt) REVERT: V 45 ASP cc_start: 0.5619 (p0) cc_final: 0.5339 (p0) REVERT: V 47 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8083 (mmmt) REVERT: V 122 GLN cc_start: 0.8761 (tt0) cc_final: 0.8365 (tm-30) REVERT: V 183 PHE cc_start: 0.1775 (m-80) cc_final: 0.1520 (m-80) REVERT: V 205 MET cc_start: -0.1553 (tpt) cc_final: -0.1815 (tpt) REVERT: W 237 ASN cc_start: 0.8696 (t0) cc_final: 0.8325 (t0) REVERT: X 228 GLU cc_start: 0.8772 (pp20) cc_final: 0.8569 (pp20) REVERT: Z 307 MET cc_start: 0.2209 (tpt) cc_final: 0.1944 (ptp) REVERT: Z 378 MET cc_start: -0.1127 (mmt) cc_final: -0.1390 (mpp) REVERT: Z 460 MET cc_start: 0.0237 (mmt) cc_final: -0.0959 (mtm) REVERT: a 45 THR cc_start: 0.9411 (m) cc_final: 0.9129 (p) REVERT: a 50 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8897 (mp0) REVERT: a 59 GLU cc_start: 0.8011 (pm20) cc_final: 0.7742 (pm20) REVERT: a 93 GLN cc_start: 0.8879 (tt0) cc_final: 0.8592 (tp40) REVERT: a 97 GLU cc_start: 0.8989 (tt0) cc_final: 0.8705 (tp30) REVERT: a 105 GLU cc_start: 0.8944 (tp30) cc_final: 0.8698 (tp30) REVERT: a 129 ARG cc_start: 0.9200 (tpt90) cc_final: 0.8659 (tpm170) REVERT: b 74 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8641 (mm-30) REVERT: b 77 LYS cc_start: 0.9531 (mttm) cc_final: 0.9224 (mmtt) REVERT: b 98 TYR cc_start: 0.9192 (m-10) cc_final: 0.8948 (m-10) REVERT: c 36 LYS cc_start: 0.6974 (pttt) cc_final: 0.6724 (pttm) REVERT: c 91 GLU cc_start: 0.8708 (pm20) cc_final: 0.8045 (pp20) REVERT: c 104 GLN cc_start: 0.8571 (mm-40) cc_final: 0.7872 (tp-100) REVERT: d 93 GLU cc_start: 0.8508 (mp0) cc_final: 0.8070 (mp0) REVERT: d 108 LYS cc_start: 0.9390 (mmtt) cc_final: 0.9171 (ttpp) REVERT: e 45 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8539 (p) REVERT: e 50 GLU cc_start: 0.8985 (tt0) cc_final: 0.7713 (tp30) REVERT: e 97 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7717 (mm-30) REVERT: e 106 ASP cc_start: 0.9007 (m-30) cc_final: 0.8657 (m-30) REVERT: e 110 CYS cc_start: 0.9547 (m) cc_final: 0.8829 (t) REVERT: e 123 ASP cc_start: 0.9293 (m-30) cc_final: 0.8816 (m-30) REVERT: f 30 THR cc_start: 0.8518 (p) cc_final: 0.7843 (t) REVERT: f 53 GLU cc_start: 0.8446 (mp0) cc_final: 0.8062 (mp0) REVERT: f 79 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7684 (mmtp) REVERT: f 84 MET cc_start: 0.8220 (mmm) cc_final: 0.7663 (mmm) REVERT: f 96 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8142 (p) REVERT: g 41 GLU cc_start: 0.7867 (mp0) cc_final: 0.7651 (mp0) REVERT: g 92 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8634 (mt-10) REVERT: g 99 ARG cc_start: 0.8667 (mmm160) cc_final: 0.8458 (mmm-85) REVERT: g 104 GLN cc_start: 0.9013 (mt0) cc_final: 0.8498 (mp10) REVERT: h 68 ASP cc_start: 0.9054 (t0) cc_final: 0.8599 (t0) REVERT: h 85 LYS cc_start: 0.9386 (mmtp) cc_final: 0.9133 (mmtm) REVERT: l 1627 MET cc_start: 0.6249 (tpp) cc_final: 0.4834 (tpp) outliers start: 144 outliers final: 92 residues processed: 849 average time/residue: 0.6778 time to fit residues: 990.0161 Evaluate side-chains 777 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 673 time to evaluate : 5.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1210 TRP Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1539 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 1039 SER Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain O residue 652 LEU Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 169 LYS Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 262 TYR Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain Q residue 510 MET Chi-restraints excluded: chain Q residue 790 HIS Chi-restraints excluded: chain Q residue 851 LEU Chi-restraints excluded: chain Q residue 881 TYR Chi-restraints excluded: chain R residue 490 GLN Chi-restraints excluded: chain V residue 31 CYS Chi-restraints excluded: chain V residue 123 GLN Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain Z residue 500 VAL Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain d residue 64 SER Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 103 LEU Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain f residue 37 LEU Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 86 VAL Chi-restraints excluded: chain f residue 96 THR Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain g residue 85 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain l residue 2024 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 902 optimal weight: 30.0000 chunk 887 optimal weight: 9.9990 chunk 590 optimal weight: 3.9990 chunk 641 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 454 optimal weight: 30.0000 chunk 359 optimal weight: 0.0020 chunk 107 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 265 optimal weight: 0.0870 chunk 780 optimal weight: 50.0000 overall best weight: 1.3370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN A 757 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 ASN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 256 GLN Q 827 HIS ** Q 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 427 GLN ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 254 GLN h 84 ASN ** l1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.123642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.083265 restraints weight = 301006.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.085047 restraints weight = 145806.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 74)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.085904 restraints weight = 96761.706| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 75528 Z= 0.206 Angle : 0.555 11.705 103343 Z= 0.293 Chirality : 0.041 0.296 11031 Planarity : 0.004 0.061 12367 Dihedral : 18.382 175.337 13722 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.17 % Rotamer: Outliers : 2.00 % Allowed : 12.48 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.09), residues: 8646 helix: 1.49 (0.09), residues: 3545 sheet: -1.61 (0.17), residues: 858 loop : -1.58 (0.09), residues: 4243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP X 231 HIS 0.010 0.001 HIS I 60 PHE 0.024 0.001 PHE K 13 TYR 0.019 0.001 TYR b 88 ARG 0.007 0.000 ARG I 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 726 time to evaluate : 5.930 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: A 19 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8754 (mtmt) REVERT: A 58 MET cc_start: 0.7602 (tpp) cc_final: 0.7025 (tpp) REVERT: A 78 MET cc_start: 0.8949 (tpp) cc_final: 0.7457 (tpp) REVERT: A 85 PHE cc_start: 0.6390 (OUTLIER) cc_final: 0.6023 (t80) REVERT: A 104 MET cc_start: 0.8487 (tpp) cc_final: 0.7780 (tpt) REVERT: A 278 HIS cc_start: 0.8795 (m170) cc_final: 0.8332 (m-70) REVERT: A 438 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7828 (tt) REVERT: A 483 ARG cc_start: 0.7767 (mtt90) cc_final: 0.7372 (mtt90) REVERT: A 500 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7600 (mm-30) REVERT: A 539 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6669 (tp40) REVERT: A 561 MET cc_start: 0.8344 (mtt) cc_final: 0.7902 (mtt) REVERT: A 683 GLU cc_start: 0.8293 (tp30) cc_final: 0.7949 (tp30) REVERT: A 782 SER cc_start: 0.9235 (t) cc_final: 0.8996 (p) REVERT: A 792 ASN cc_start: 0.8937 (m-40) cc_final: 0.8537 (m-40) REVERT: A 845 GLU cc_start: 0.8616 (tt0) cc_final: 0.8313 (tt0) REVERT: A 900 SER cc_start: 0.9316 (m) cc_final: 0.8770 (p) REVERT: A 902 GLU cc_start: 0.7422 (tt0) cc_final: 0.6982 (tt0) REVERT: A 928 ARG cc_start: 0.9087 (mtp85) cc_final: 0.8803 (mtp85) REVERT: A 1038 THR cc_start: 0.8894 (m) cc_final: 0.8654 (t) REVERT: A 1078 GLN cc_start: 0.9057 (mt0) cc_final: 0.8816 (mm-40) REVERT: A 1094 SER cc_start: 0.8985 (m) cc_final: 0.8558 (p) REVERT: A 1210 TRP cc_start: 0.6594 (p90) cc_final: 0.5477 (p90) REVERT: A 1378 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8711 (tp) REVERT: A 1405 MET cc_start: 0.8772 (mtt) cc_final: 0.8434 (mtm) REVERT: A 1428 MET cc_start: 0.8866 (ttt) cc_final: 0.8553 (mtp) REVERT: A 1440 MET cc_start: 0.9189 (mmt) cc_final: 0.8689 (mmt) REVERT: A 1459 MET cc_start: 0.8681 (mtp) cc_final: 0.8372 (mtm) REVERT: B 65 ILE cc_start: 0.5836 (OUTLIER) cc_final: 0.5620 (tt) REVERT: B 108 MET cc_start: 0.8597 (ptm) cc_final: 0.8336 (ptp) REVERT: B 508 MET cc_start: 0.8195 (mpp) cc_final: 0.7436 (mpp) REVERT: B 603 MET cc_start: 0.7983 (mtm) cc_final: 0.7724 (mtm) REVERT: B 728 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8078 (ttm) REVERT: B 731 GLN cc_start: 0.8650 (mp-120) cc_final: 0.8341 (mp10) REVERT: B 751 LEU cc_start: 0.9025 (tp) cc_final: 0.8825 (mt) REVERT: B 767 LEU cc_start: 0.9455 (tp) cc_final: 0.9117 (tt) REVERT: B 791 GLU cc_start: 0.7813 (tp30) cc_final: 0.7488 (tp30) REVERT: B 890 ARG cc_start: 0.8980 (ttm170) cc_final: 0.8686 (ttp-170) REVERT: B 1015 LEU cc_start: 0.9602 (tp) cc_final: 0.9308 (tt) REVERT: B 1039 SER cc_start: 0.9146 (OUTLIER) cc_final: 0.8833 (p) REVERT: B 1054 MET cc_start: 0.8469 (mmm) cc_final: 0.8084 (mtp) REVERT: B 1089 MET cc_start: 0.7756 (mtm) cc_final: 0.7472 (mtp) REVERT: B 1090 GLU cc_start: 0.8778 (mp0) cc_final: 0.8146 (mp0) REVERT: B 1135 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: B 1172 MET cc_start: 0.8092 (mmt) cc_final: 0.7643 (mmm) REVERT: C 185 GLU cc_start: 0.7419 (tt0) cc_final: 0.7132 (mt-10) REVERT: D 19 GLN cc_start: 0.9352 (mm-40) cc_final: 0.9043 (mm-40) REVERT: D 61 PHE cc_start: 0.8971 (m-10) cc_final: 0.8453 (m-80) REVERT: D 62 MET cc_start: 0.9021 (mmm) cc_final: 0.8793 (mpp) REVERT: D 74 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.8015 (p90) REVERT: D 132 ASP cc_start: 0.9150 (m-30) cc_final: 0.8866 (t0) REVERT: D 138 ARG cc_start: 0.8359 (mtp180) cc_final: 0.7909 (mtp180) REVERT: E 121 MET cc_start: 0.6711 (tpp) cc_final: 0.6364 (tpt) REVERT: E 138 ASN cc_start: 0.8041 (t0) cc_final: 0.7803 (t0) REVERT: E 203 TYR cc_start: 0.8094 (t80) cc_final: 0.7653 (t80) REVERT: F 83 LEU cc_start: 0.8547 (mp) cc_final: 0.8071 (tp) REVERT: F 87 THR cc_start: 0.8721 (p) cc_final: 0.8234 (t) REVERT: F 91 LEU cc_start: 0.9251 (tp) cc_final: 0.9029 (tp) REVERT: F 115 TYR cc_start: 0.8643 (p90) cc_final: 0.8345 (p90) REVERT: G 1 MET cc_start: 0.8383 (tmm) cc_final: 0.7394 (tmm) REVERT: G 35 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7552 (mm-30) REVERT: G 60 GLN cc_start: 0.8633 (mm110) cc_final: 0.8384 (mm110) REVERT: G 101 ILE cc_start: 0.8580 (tp) cc_final: 0.8225 (tp) REVERT: G 104 MET cc_start: 0.7261 (tmm) cc_final: 0.6563 (tmm) REVERT: G 156 ASP cc_start: 0.6735 (m-30) cc_final: 0.6359 (m-30) REVERT: H 20 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8698 (ttmm) REVERT: H 24 ARG cc_start: 0.8829 (mtt90) cc_final: 0.8615 (mpp80) REVERT: H 36 LYS cc_start: 0.9223 (mmmt) cc_final: 0.9022 (mmmt) REVERT: H 74 GLU cc_start: 0.7713 (pm20) cc_final: 0.7462 (pm20) REVERT: H 103 GLU cc_start: 0.7456 (mp0) cc_final: 0.7217 (mp0) REVERT: H 111 ARG cc_start: 0.7793 (mtp85) cc_final: 0.6989 (mtp85) REVERT: H 130 ASN cc_start: 0.8406 (t0) cc_final: 0.8087 (t0) REVERT: I 71 ASP cc_start: 0.8956 (m-30) cc_final: 0.8615 (m-30) REVERT: I 78 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8575 (mt) REVERT: K 26 LYS cc_start: 0.8735 (mttt) cc_final: 0.8512 (mtpp) REVERT: K 38 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8010 (mm-30) REVERT: K 93 ASP cc_start: 0.6988 (p0) cc_final: 0.6708 (p0) REVERT: L 15 MET cc_start: 0.8019 (tpp) cc_final: 0.7790 (tpp) REVERT: M 1347 MET cc_start: -0.1428 (mtt) cc_final: -0.1863 (ptp) REVERT: O 563 MET cc_start: -0.0689 (tmm) cc_final: -0.1505 (tmm) REVERT: O 652 LEU cc_start: -0.0789 (OUTLIER) cc_final: -0.1616 (pp) REVERT: O 659 ARG cc_start: 0.2647 (tpt90) cc_final: 0.2332 (tmt170) REVERT: Q 125 MET cc_start: -0.2605 (mtt) cc_final: -0.2963 (ttt) REVERT: Q 604 MET cc_start: 0.7562 (mtt) cc_final: 0.7168 (mtt) REVERT: Q 703 MET cc_start: 0.5749 (ttt) cc_final: 0.5508 (ttt) REVERT: Q 803 MET cc_start: 0.7934 (pmm) cc_final: 0.7654 (pmm) REVERT: Q 890 MET cc_start: 0.1660 (ptt) cc_final: 0.1254 (ptt) REVERT: U 448 MET cc_start: 0.2885 (ptt) cc_final: 0.2220 (tpt) REVERT: V 45 ASP cc_start: 0.6105 (p0) cc_final: 0.5644 (p0) REVERT: V 47 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8145 (mmmt) REVERT: V 51 TYR cc_start: 0.7712 (t80) cc_final: 0.6644 (t80) REVERT: V 126 LYS cc_start: 0.8791 (tppt) cc_final: 0.8368 (mmtt) REVERT: V 183 PHE cc_start: 0.1598 (m-80) cc_final: 0.1359 (m-80) REVERT: V 205 MET cc_start: -0.1805 (tpt) cc_final: -0.2039 (tpt) REVERT: W 237 ASN cc_start: 0.8794 (t0) cc_final: 0.8394 (t0) REVERT: Z 460 MET cc_start: 0.0205 (mmt) cc_final: -0.0968 (mtm) REVERT: Z 635 MET cc_start: -0.2640 (ttp) cc_final: -0.2984 (tmm) REVERT: a 36 MET cc_start: 0.2003 (mmm) cc_final: 0.1778 (tpp) REVERT: a 45 THR cc_start: 0.9469 (m) cc_final: 0.9256 (p) REVERT: a 46 VAL cc_start: 0.9289 (t) cc_final: 0.8673 (t) REVERT: a 50 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8894 (mp0) REVERT: a 59 GLU cc_start: 0.7882 (pm20) cc_final: 0.7643 (pm20) REVERT: a 93 GLN cc_start: 0.8830 (tt0) cc_final: 0.8566 (tp40) REVERT: a 120 MET cc_start: 0.7963 (mtt) cc_final: 0.7531 (mtt) REVERT: a 129 ARG cc_start: 0.9163 (tpt90) cc_final: 0.8791 (tpt90) REVERT: b 74 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8624 (mm-30) REVERT: b 77 LYS cc_start: 0.9480 (mttm) cc_final: 0.9122 (mmtt) REVERT: b 84 MET cc_start: 0.8410 (ppp) cc_final: 0.8172 (tmm) REVERT: b 88 TYR cc_start: 0.8662 (m-80) cc_final: 0.8053 (m-10) REVERT: b 98 TYR cc_start: 0.9167 (m-10) cc_final: 0.8937 (m-10) REVERT: c 36 LYS cc_start: 0.7177 (pttt) cc_final: 0.6946 (pttm) REVERT: c 104 GLN cc_start: 0.8504 (mm-40) cc_final: 0.7867 (tp-100) REVERT: d 59 MET cc_start: 0.8910 (tpp) cc_final: 0.8471 (tpp) REVERT: d 71 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8198 (tp30) REVERT: d 93 GLU cc_start: 0.8592 (mp0) cc_final: 0.7930 (mp0) REVERT: e 45 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8748 (p) REVERT: e 97 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7918 (mm-30) REVERT: e 106 ASP cc_start: 0.8978 (m-30) cc_final: 0.8766 (m-30) REVERT: e 110 CYS cc_start: 0.9521 (m) cc_final: 0.8865 (t) REVERT: e 123 ASP cc_start: 0.9250 (m-30) cc_final: 0.8671 (m-30) REVERT: f 30 THR cc_start: 0.8700 (p) cc_final: 0.8028 (t) REVERT: f 79 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7773 (mmtp) REVERT: f 84 MET cc_start: 0.8181 (mmm) cc_final: 0.7531 (mmm) REVERT: f 92 ARG cc_start: 0.9046 (tpt-90) cc_final: 0.8734 (tpt-90) REVERT: f 96 THR cc_start: 0.8587 (m) cc_final: 0.8347 (p) REVERT: g 41 GLU cc_start: 0.7980 (mp0) cc_final: 0.7780 (mp0) REVERT: g 56 GLU cc_start: 0.8655 (tt0) cc_final: 0.8422 (tt0) REVERT: g 92 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8564 (mt-10) REVERT: g 104 GLN cc_start: 0.8932 (mt0) cc_final: 0.8468 (mp10) REVERT: h 68 ASP cc_start: 0.8979 (t0) cc_final: 0.8514 (t0) REVERT: l 1469 MET cc_start: 0.1285 (mmp) cc_final: 0.1058 (mmp) REVERT: l 1627 MET cc_start: 0.6031 (tpp) cc_final: 0.4761 (tpp) outliers start: 131 outliers final: 77 residues processed: 816 average time/residue: 0.6809 time to fit residues: 956.0690 Evaluate side-chains 749 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 660 time to evaluate : 5.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain A residue 1539 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 1039 SER Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain O residue 652 LEU Chi-restraints excluded: chain Q residue 262 TYR Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain Q residue 510 MET Chi-restraints excluded: chain Q residue 667 ARG Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 790 HIS Chi-restraints excluded: chain Q residue 881 TYR Chi-restraints excluded: chain R residue 381 THR Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain V residue 31 CYS Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 123 GLN Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 154 ILE Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 101 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 23 optimal weight: 6.9990 chunk 699 optimal weight: 3.9990 chunk 376 optimal weight: 1.9990 chunk 665 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 866 optimal weight: 0.0270 chunk 757 optimal weight: 50.0000 chunk 737 optimal weight: 50.0000 chunk 576 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 474 optimal weight: 6.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 HIS A 995 HIS ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 ASN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 529 ASN ** Q 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 877 GLN Z 234 HIS Z 337 GLN g 24 GLN ** l1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.122051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.082445 restraints weight = 300412.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.083193 restraints weight = 147356.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.084222 restraints weight = 96014.901| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 75528 Z= 0.266 Angle : 0.579 13.169 103343 Z= 0.305 Chirality : 0.041 0.298 11031 Planarity : 0.004 0.057 12367 Dihedral : 18.408 176.744 13722 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.32 % Favored : 94.63 % Rotamer: Outliers : 2.71 % Allowed : 13.00 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.09), residues: 8646 helix: 1.48 (0.09), residues: 3562 sheet: -1.54 (0.17), residues: 860 loop : -1.55 (0.09), residues: 4224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 130 HIS 0.007 0.001 HIS d 82 PHE 0.018 0.001 PHE h 65 TYR 0.025 0.001 TYR A 145 ARG 0.008 0.000 ARG c 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 688 time to evaluate : 5.971 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: A 19 LYS cc_start: 0.9046 (mmtt) cc_final: 0.8806 (mtmt) REVERT: A 58 MET cc_start: 0.7706 (tpp) cc_final: 0.7125 (tpp) REVERT: A 85 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.6090 (t80) REVERT: A 104 MET cc_start: 0.8581 (tpp) cc_final: 0.7600 (mmm) REVERT: A 278 HIS cc_start: 0.8781 (m170) cc_final: 0.8306 (m-70) REVERT: A 329 MET cc_start: 0.8044 (tpp) cc_final: 0.7505 (tpp) REVERT: A 483 ARG cc_start: 0.7708 (mtt90) cc_final: 0.7245 (mtt90) REVERT: A 501 MET cc_start: 0.7753 (mtp) cc_final: 0.7485 (mtm) REVERT: A 535 MET cc_start: 0.8015 (ptp) cc_final: 0.7025 (mtp) REVERT: A 561 MET cc_start: 0.8394 (mtt) cc_final: 0.8010 (mtt) REVERT: A 683 GLU cc_start: 0.8384 (tp30) cc_final: 0.7990 (tp30) REVERT: A 735 GLN cc_start: 0.8939 (mt0) cc_final: 0.8393 (mt0) REVERT: A 792 ASN cc_start: 0.8976 (m-40) cc_final: 0.8575 (m-40) REVERT: A 872 MET cc_start: 0.8787 (ptm) cc_final: 0.8473 (ptm) REVERT: A 900 SER cc_start: 0.9251 (m) cc_final: 0.8682 (p) REVERT: A 902 GLU cc_start: 0.7566 (tt0) cc_final: 0.7109 (tt0) REVERT: A 928 ARG cc_start: 0.9210 (mtp85) cc_final: 0.8879 (mtp85) REVERT: A 1038 THR cc_start: 0.8937 (m) cc_final: 0.8729 (t) REVERT: A 1086 MET cc_start: 0.8891 (mmm) cc_final: 0.8677 (mmm) REVERT: A 1094 SER cc_start: 0.8915 (m) cc_final: 0.8460 (p) REVERT: A 1210 TRP cc_start: 0.6926 (OUTLIER) cc_final: 0.5435 (p90) REVERT: A 1309 MET cc_start: 0.8171 (ttm) cc_final: 0.7415 (ttt) REVERT: A 1378 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8764 (tp) REVERT: A 1412 MET cc_start: 0.8207 (ppp) cc_final: 0.7662 (tmm) REVERT: A 1428 MET cc_start: 0.8869 (ttt) cc_final: 0.8535 (mtp) REVERT: A 1440 MET cc_start: 0.9134 (mmt) cc_final: 0.8670 (mmt) REVERT: A 1459 MET cc_start: 0.8768 (mtp) cc_final: 0.8442 (mtm) REVERT: B 108 MET cc_start: 0.8670 (ptm) cc_final: 0.8418 (ptp) REVERT: B 204 THR cc_start: 0.8884 (m) cc_final: 0.8569 (p) REVERT: B 508 MET cc_start: 0.8270 (mpp) cc_final: 0.7558 (mpp) REVERT: B 603 MET cc_start: 0.8198 (mtm) cc_final: 0.7685 (mtm) REVERT: B 728 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8292 (ttm) REVERT: B 751 LEU cc_start: 0.9179 (tp) cc_final: 0.8933 (mt) REVERT: B 767 LEU cc_start: 0.9519 (tp) cc_final: 0.9121 (tt) REVERT: B 890 ARG cc_start: 0.9006 (ttm170) cc_final: 0.8687 (ttp-170) REVERT: B 1015 LEU cc_start: 0.9614 (tp) cc_final: 0.9356 (tt) REVERT: B 1025 ASN cc_start: 0.8618 (m-40) cc_final: 0.8351 (m-40) REVERT: B 1039 SER cc_start: 0.9092 (OUTLIER) cc_final: 0.8658 (p) REVERT: B 1054 MET cc_start: 0.8611 (mmm) cc_final: 0.8364 (mtp) REVERT: B 1135 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.7621 (m-80) REVERT: B 1172 MET cc_start: 0.8089 (mmt) cc_final: 0.7585 (mmt) REVERT: C 185 GLU cc_start: 0.7514 (tt0) cc_final: 0.7208 (mt-10) REVERT: D 61 PHE cc_start: 0.8981 (m-10) cc_final: 0.8477 (m-80) REVERT: D 74 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8294 (p90) REVERT: D 138 ARG cc_start: 0.8282 (mtp180) cc_final: 0.7760 (mtp180) REVERT: E 121 MET cc_start: 0.7128 (tpp) cc_final: 0.6713 (tpp) REVERT: E 138 ASN cc_start: 0.8178 (t0) cc_final: 0.7880 (t0) REVERT: E 203 TYR cc_start: 0.8202 (t80) cc_final: 0.7694 (t80) REVERT: F 87 THR cc_start: 0.8787 (p) cc_final: 0.8283 (t) REVERT: F 91 LEU cc_start: 0.9273 (tp) cc_final: 0.9072 (tp) REVERT: F 115 TYR cc_start: 0.8640 (p90) cc_final: 0.8344 (p90) REVERT: G 35 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7550 (mm-30) REVERT: G 60 GLN cc_start: 0.8523 (mm110) cc_final: 0.8295 (mm110) REVERT: G 101 ILE cc_start: 0.8476 (tp) cc_final: 0.8012 (tp) REVERT: G 104 MET cc_start: 0.7232 (tmm) cc_final: 0.6556 (tmm) REVERT: G 156 ASP cc_start: 0.6768 (m-30) cc_final: 0.6426 (m-30) REVERT: H 13 LYS cc_start: 0.9162 (mmtp) cc_final: 0.8765 (mmmm) REVERT: H 20 LYS cc_start: 0.9008 (ttmm) cc_final: 0.8675 (ttmm) REVERT: H 103 GLU cc_start: 0.7582 (mp0) cc_final: 0.7329 (mp0) REVERT: H 111 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7664 (mtp85) REVERT: H 130 ASN cc_start: 0.8729 (t0) cc_final: 0.8350 (t0) REVERT: I 71 ASP cc_start: 0.8997 (m-30) cc_final: 0.8622 (m-30) REVERT: K 8 GLU cc_start: 0.8808 (pt0) cc_final: 0.8568 (mp0) REVERT: K 13 PHE cc_start: 0.7586 (t80) cc_final: 0.7279 (t80) REVERT: K 26 LYS cc_start: 0.8867 (mttt) cc_final: 0.8601 (mtpp) REVERT: K 38 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8089 (mm-30) REVERT: K 85 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7714 (pp20) REVERT: K 93 ASP cc_start: 0.7286 (p0) cc_final: 0.7034 (p0) REVERT: L 44 MET cc_start: 0.8219 (mtt) cc_final: 0.7903 (mmt) REVERT: O 652 LEU cc_start: -0.2004 (OUTLIER) cc_final: -0.2589 (pp) REVERT: O 659 ARG cc_start: 0.2711 (tpt90) cc_final: 0.2312 (tmt170) REVERT: Q 83 MET cc_start: 0.1794 (ppp) cc_final: 0.1232 (ttm) REVERT: Q 125 MET cc_start: -0.2389 (mtt) cc_final: -0.2837 (ttt) REVERT: Q 604 MET cc_start: 0.7623 (mtt) cc_final: 0.7234 (mtt) REVERT: Q 703 MET cc_start: 0.6007 (ttt) cc_final: 0.5691 (ttt) REVERT: Q 762 GLN cc_start: 0.5479 (OUTLIER) cc_final: 0.4888 (tt0) REVERT: Q 890 MET cc_start: 0.1865 (ptt) cc_final: 0.1664 (ptt) REVERT: U 448 MET cc_start: 0.3053 (ptt) cc_final: 0.2357 (tpt) REVERT: V 45 ASP cc_start: 0.6261 (p0) cc_final: 0.5931 (p0) REVERT: V 47 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8355 (mmmt) REVERT: V 51 TYR cc_start: 0.7709 (t80) cc_final: 0.6665 (t80) REVERT: V 183 PHE cc_start: 0.1566 (m-80) cc_final: 0.1319 (m-80) REVERT: W 237 ASN cc_start: 0.8920 (t0) cc_final: 0.8482 (t0) REVERT: X 228 GLU cc_start: 0.8750 (pp20) cc_final: 0.8466 (pp20) REVERT: Y 63 MET cc_start: -0.1587 (mmm) cc_final: -0.2280 (ptt) REVERT: Z 635 MET cc_start: -0.3541 (ttp) cc_final: -0.3889 (tmm) REVERT: a 93 GLN cc_start: 0.8888 (tt0) cc_final: 0.8578 (tp40) REVERT: a 105 GLU cc_start: 0.9053 (tp30) cc_final: 0.8665 (tp30) REVERT: a 120 MET cc_start: 0.7851 (mtt) cc_final: 0.7432 (mtt) REVERT: a 129 ARG cc_start: 0.9242 (tpt90) cc_final: 0.8921 (tpt90) REVERT: b 74 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8647 (mm-30) REVERT: b 84 MET cc_start: 0.8371 (ppp) cc_final: 0.8089 (tmm) REVERT: b 98 TYR cc_start: 0.9152 (m-10) cc_final: 0.8912 (m-10) REVERT: c 36 LYS cc_start: 0.7338 (pttt) cc_final: 0.7129 (pttm) REVERT: c 104 GLN cc_start: 0.8500 (mm-40) cc_final: 0.7885 (tp-100) REVERT: d 71 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8230 (tp30) REVERT: d 93 GLU cc_start: 0.8604 (mp0) cc_final: 0.7930 (mp0) REVERT: e 45 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8773 (p) REVERT: e 110 CYS cc_start: 0.9553 (m) cc_final: 0.8950 (t) REVERT: e 123 ASP cc_start: 0.9310 (m-30) cc_final: 0.8849 (m-30) REVERT: f 79 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7901 (mmtp) REVERT: f 84 MET cc_start: 0.8234 (mmm) cc_final: 0.7193 (mmm) REVERT: f 92 ARG cc_start: 0.9137 (tpt-90) cc_final: 0.8824 (tpt90) REVERT: f 96 THR cc_start: 0.8518 (m) cc_final: 0.8259 (p) REVERT: g 56 GLU cc_start: 0.8763 (tt0) cc_final: 0.8511 (tt0) REVERT: g 64 GLU cc_start: 0.8995 (tt0) cc_final: 0.8194 (mm-30) REVERT: g 92 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8801 (mt-10) REVERT: g 99 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.7764 (mmm-85) REVERT: g 104 GLN cc_start: 0.9017 (mt0) cc_final: 0.8627 (mp10) REVERT: h 68 ASP cc_start: 0.9073 (t0) cc_final: 0.8580 (t0) REVERT: l 1627 MET cc_start: 0.6145 (tpp) cc_final: 0.5053 (tpp) outliers start: 178 outliers final: 118 residues processed: 820 average time/residue: 0.6756 time to fit residues: 959.2422 Evaluate side-chains 772 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 643 time to evaluate : 5.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1210 TRP Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain A residue 1539 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 1039 SER Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain O residue 613 MET Chi-restraints excluded: chain O residue 652 LEU Chi-restraints excluded: chain Q residue 208 PHE Chi-restraints excluded: chain Q residue 262 TYR Chi-restraints excluded: chain Q residue 510 MET Chi-restraints excluded: chain Q residue 647 LEU Chi-restraints excluded: chain Q residue 667 ARG Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 753 LEU Chi-restraints excluded: chain Q residue 762 GLN Chi-restraints excluded: chain Q residue 790 HIS Chi-restraints excluded: chain Q residue 851 LEU Chi-restraints excluded: chain Q residue 881 TYR Chi-restraints excluded: chain R residue 381 THR Chi-restraints excluded: chain R residue 485 TYR Chi-restraints excluded: chain V residue 31 CYS Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 123 GLN Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 154 ILE Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain X residue 243 LYS Chi-restraints excluded: chain Z residue 444 ASP Chi-restraints excluded: chain Z residue 500 VAL Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain d residue 64 SER Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 90 THR Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 37 LEU Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 86 VAL Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain l residue 1514 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 583 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 527 optimal weight: 30.0000 chunk 798 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 514 optimal weight: 6.9990 chunk 566 optimal weight: 8.9990 chunk 730 optimal weight: 10.0000 chunk 379 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS H 131 ASN ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 244 ASN ** Q 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 575 HIS ** Q 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 473 ASN ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l1466 GLN ** l1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l1601 ASN ** l1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.119926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.081143 restraints weight = 302790.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.083177 restraints weight = 151890.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.083007 restraints weight = 102840.900| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 75528 Z= 0.377 Angle : 0.651 15.149 103343 Z= 0.343 Chirality : 0.043 0.340 11031 Planarity : 0.004 0.060 12367 Dihedral : 18.603 177.474 13721 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.88 % Rotamer: Outliers : 2.94 % Allowed : 13.84 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.09), residues: 8646 helix: 1.28 (0.09), residues: 3580 sheet: -1.50 (0.17), residues: 859 loop : -1.60 (0.09), residues: 4207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 581 HIS 0.010 0.001 HIS J 52 PHE 0.024 0.002 PHE B 935 TYR 0.037 0.002 TYR d 83 ARG 0.008 0.001 ARG V 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 660 time to evaluate : 6.004 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: A 58 MET cc_start: 0.7889 (tpp) cc_final: 0.7153 (tpp) REVERT: A 85 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.6319 (t80) REVERT: A 104 MET cc_start: 0.8663 (tpp) cc_final: 0.7718 (mmm) REVERT: A 278 HIS cc_start: 0.8809 (m170) cc_final: 0.8355 (m90) REVERT: A 500 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7453 (mm-30) REVERT: A 539 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7069 (tp-100) REVERT: A 559 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8683 (mm-30) REVERT: A 683 GLU cc_start: 0.8404 (tp30) cc_final: 0.7904 (tp30) REVERT: A 792 ASN cc_start: 0.8854 (m-40) cc_final: 0.8467 (m-40) REVERT: A 794 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8301 (mm-30) REVERT: A 845 GLU cc_start: 0.8692 (tt0) cc_final: 0.7872 (tm-30) REVERT: A 872 MET cc_start: 0.8748 (ptm) cc_final: 0.8469 (ptm) REVERT: A 900 SER cc_start: 0.9198 (m) cc_final: 0.8599 (p) REVERT: A 902 GLU cc_start: 0.7622 (tt0) cc_final: 0.7144 (tt0) REVERT: A 928 ARG cc_start: 0.9223 (mtp85) cc_final: 0.8960 (mmm-85) REVERT: A 1035 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8240 (tm-30) REVERT: A 1038 THR cc_start: 0.8989 (m) cc_final: 0.8746 (t) REVERT: A 1094 SER cc_start: 0.8999 (m) cc_final: 0.8533 (p) REVERT: A 1210 TRP cc_start: 0.6991 (OUTLIER) cc_final: 0.5960 (p90) REVERT: A 1309 MET cc_start: 0.8260 (ttm) cc_final: 0.7568 (ttt) REVERT: A 1378 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8834 (tp) REVERT: A 1412 MET cc_start: 0.8433 (ppp) cc_final: 0.7943 (tmm) REVERT: A 1428 MET cc_start: 0.8859 (ttt) cc_final: 0.8543 (mtp) REVERT: A 1440 MET cc_start: 0.9200 (mmt) cc_final: 0.8669 (mmt) REVERT: A 1459 MET cc_start: 0.8815 (mtp) cc_final: 0.8531 (mtm) REVERT: B 108 MET cc_start: 0.8790 (ptm) cc_final: 0.8432 (ptm) REVERT: B 204 THR cc_start: 0.8868 (m) cc_final: 0.8579 (p) REVERT: B 298 MET cc_start: 0.8877 (ttm) cc_final: 0.8639 (ttp) REVERT: B 407 MET cc_start: 0.7962 (mtt) cc_final: 0.7507 (mtt) REVERT: B 508 MET cc_start: 0.8108 (mpp) cc_final: 0.7203 (mpp) REVERT: B 728 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8154 (ttm) REVERT: B 751 LEU cc_start: 0.9277 (tp) cc_final: 0.8970 (mt) REVERT: B 789 ASN cc_start: 0.8502 (p0) cc_final: 0.7722 (p0) REVERT: B 890 ARG cc_start: 0.9021 (ttm170) cc_final: 0.8740 (ttp-170) REVERT: B 983 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 1025 ASN cc_start: 0.8534 (m-40) cc_final: 0.8252 (m-40) REVERT: B 1039 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8674 (p) REVERT: B 1125 MET cc_start: 0.9092 (mtm) cc_final: 0.8852 (mtm) REVERT: B 1135 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: B 1172 MET cc_start: 0.8229 (mmt) cc_final: 0.7683 (mmm) REVERT: C 185 GLU cc_start: 0.7653 (tt0) cc_final: 0.7371 (mt-10) REVERT: C 214 ASP cc_start: 0.8598 (m-30) cc_final: 0.8247 (m-30) REVERT: D 61 PHE cc_start: 0.8930 (m-10) cc_final: 0.8675 (m-80) REVERT: D 74 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8440 (p90) REVERT: D 132 ASP cc_start: 0.9207 (m-30) cc_final: 0.8983 (t0) REVERT: D 138 ARG cc_start: 0.8311 (mtp180) cc_final: 0.7882 (mtp180) REVERT: E 18 MET cc_start: 0.9448 (mmp) cc_final: 0.9215 (mmp) REVERT: E 121 MET cc_start: 0.7833 (tpp) cc_final: 0.7590 (tpp) REVERT: E 138 ASN cc_start: 0.8189 (t0) cc_final: 0.7884 (t0) REVERT: E 203 TYR cc_start: 0.8297 (t80) cc_final: 0.7848 (t80) REVERT: F 83 LEU cc_start: 0.8868 (mp) cc_final: 0.8340 (tp) REVERT: F 91 LEU cc_start: 0.9302 (tp) cc_final: 0.9073 (tp) REVERT: F 115 TYR cc_start: 0.8684 (p90) cc_final: 0.8379 (p90) REVERT: G 27 LYS cc_start: 0.9322 (mttp) cc_final: 0.9077 (mtmm) REVERT: G 35 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7789 (mm-30) REVERT: G 60 GLN cc_start: 0.8549 (mm110) cc_final: 0.8290 (mm110) REVERT: G 83 GLU cc_start: 0.8300 (pt0) cc_final: 0.7783 (mp0) REVERT: G 101 ILE cc_start: 0.8488 (tp) cc_final: 0.8005 (tp) REVERT: G 104 MET cc_start: 0.7293 (tmm) cc_final: 0.6778 (tmm) REVERT: G 156 ASP cc_start: 0.6526 (m-30) cc_final: 0.6146 (m-30) REVERT: H 13 LYS cc_start: 0.9155 (mmtp) cc_final: 0.8707 (mmmm) REVERT: H 20 LYS cc_start: 0.8965 (ttmm) cc_final: 0.8634 (ttmm) REVERT: H 103 GLU cc_start: 0.7663 (mp0) cc_final: 0.7428 (mp0) REVERT: H 111 ARG cc_start: 0.8100 (mtp85) cc_final: 0.7221 (mtp85) REVERT: H 123 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7396 (ptt) REVERT: H 130 ASN cc_start: 0.8767 (t0) cc_final: 0.8363 (t0) REVERT: I 23 MET cc_start: 0.8749 (mmm) cc_final: 0.8532 (tpt) REVERT: I 71 ASP cc_start: 0.9042 (m-30) cc_final: 0.8695 (m-30) REVERT: K 13 PHE cc_start: 0.7411 (t80) cc_final: 0.7197 (t80) REVERT: K 26 LYS cc_start: 0.8938 (mttt) cc_final: 0.8660 (mtpp) REVERT: K 38 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8049 (mm-30) REVERT: K 85 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7756 (pp20) REVERT: K 93 ASP cc_start: 0.7224 (p0) cc_final: 0.6920 (p0) REVERT: L 29 LYS cc_start: 0.9311 (mppt) cc_final: 0.8890 (mmmm) REVERT: O 652 LEU cc_start: -0.3102 (OUTLIER) cc_final: -0.3419 (pp) REVERT: O 659 ARG cc_start: 0.2996 (tpt90) cc_final: 0.2439 (tmt170) REVERT: Q 83 MET cc_start: 0.2712 (ppp) cc_final: 0.1990 (ttm) REVERT: Q 125 MET cc_start: -0.2609 (mtt) cc_final: -0.3321 (ttm) REVERT: Q 204 MET cc_start: 0.2826 (OUTLIER) cc_final: 0.2372 (mpp) REVERT: Q 540 MET cc_start: 0.8060 (ttt) cc_final: 0.7184 (tmm) REVERT: Q 604 MET cc_start: 0.7967 (mtt) cc_final: 0.7579 (mtt) REVERT: Q 633 LEU cc_start: 0.9224 (tp) cc_final: 0.8935 (pp) REVERT: Q 703 MET cc_start: 0.6191 (ttt) cc_final: 0.5938 (ttt) REVERT: Q 890 MET cc_start: 0.2326 (ptt) cc_final: 0.1430 (ptt) REVERT: U 448 MET cc_start: 0.3099 (ptt) cc_final: 0.2310 (tpt) REVERT: V 45 ASP cc_start: 0.6524 (p0) cc_final: 0.6091 (p0) REVERT: V 47 LYS cc_start: 0.8784 (mmmt) cc_final: 0.8480 (mmmt) REVERT: V 183 PHE cc_start: 0.1160 (m-80) cc_final: 0.0952 (m-80) REVERT: V 205 MET cc_start: -0.2481 (tpt) cc_final: -0.2921 (tpt) REVERT: W 191 MET cc_start: 0.9126 (mmt) cc_final: 0.8905 (mmm) REVERT: W 237 ASN cc_start: 0.9036 (t0) cc_final: 0.8586 (t0) REVERT: X 232 ARG cc_start: 0.8979 (mmm160) cc_final: 0.8779 (mmm160) REVERT: Z 460 MET cc_start: -0.0829 (OUTLIER) cc_final: -0.2211 (mtm) REVERT: Z 635 MET cc_start: -0.3948 (ttp) cc_final: -0.4322 (tmm) REVERT: a 50 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8818 (mt-10) REVERT: a 57 SER cc_start: 0.9198 (p) cc_final: 0.8942 (p) REVERT: a 105 GLU cc_start: 0.8940 (tp30) cc_final: 0.8702 (tp30) REVERT: a 120 MET cc_start: 0.8058 (mtt) cc_final: 0.7466 (mtt) REVERT: a 129 ARG cc_start: 0.9226 (tpt90) cc_final: 0.8875 (tpt90) REVERT: b 74 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8684 (mm-30) REVERT: b 98 TYR cc_start: 0.9108 (m-10) cc_final: 0.8895 (m-10) REVERT: c 36 LYS cc_start: 0.7426 (pttt) cc_final: 0.7208 (pttm) REVERT: c 104 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8021 (tp-100) REVERT: d 71 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8200 (tp30) REVERT: d 93 GLU cc_start: 0.8591 (mp0) cc_final: 0.7900 (mp0) REVERT: d 105 GLU cc_start: 0.8470 (pm20) cc_final: 0.8239 (pm20) REVERT: e 45 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8893 (p) REVERT: e 96 SER cc_start: 0.9593 (m) cc_final: 0.9348 (p) REVERT: e 110 CYS cc_start: 0.9528 (m) cc_final: 0.9096 (t) REVERT: e 123 ASP cc_start: 0.9295 (m-30) cc_final: 0.8898 (m-30) REVERT: f 44 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7419 (mtpt) REVERT: f 53 GLU cc_start: 0.8682 (mp0) cc_final: 0.8070 (mp0) REVERT: f 79 LYS cc_start: 0.8291 (mmtm) cc_final: 0.7975 (mmtp) REVERT: f 84 MET cc_start: 0.8192 (mmm) cc_final: 0.7882 (mmm) REVERT: f 92 ARG cc_start: 0.9188 (tpt-90) cc_final: 0.8987 (tpt-90) REVERT: f 96 THR cc_start: 0.8595 (m) cc_final: 0.8353 (p) REVERT: g 41 GLU cc_start: 0.8177 (mp0) cc_final: 0.7847 (pm20) REVERT: g 56 GLU cc_start: 0.8803 (tt0) cc_final: 0.8503 (tt0) REVERT: g 64 GLU cc_start: 0.9086 (tt0) cc_final: 0.8440 (mm-30) REVERT: g 92 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8742 (mt-10) REVERT: g 99 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.7874 (mmm160) REVERT: g 104 GLN cc_start: 0.9059 (mt0) cc_final: 0.8749 (mp10) REVERT: h 68 ASP cc_start: 0.9063 (t0) cc_final: 0.8469 (t0) REVERT: l 1526 MET cc_start: 0.7318 (tpt) cc_final: 0.7008 (tpt) REVERT: l 1627 MET cc_start: 0.6178 (tpp) cc_final: 0.5080 (tpp) outliers start: 193 outliers final: 127 residues processed: 799 average time/residue: 0.6897 time to fit residues: 951.6865 Evaluate side-chains 764 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 623 time to evaluate : 5.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1210 TRP Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 1039 SER Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain O residue 613 MET Chi-restraints excluded: chain O residue 652 LEU Chi-restraints excluded: chain Q residue 200 VAL Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 208 PHE Chi-restraints excluded: chain Q residue 232 VAL Chi-restraints excluded: chain Q residue 262 TYR Chi-restraints excluded: chain Q residue 510 MET Chi-restraints excluded: chain Q residue 667 ARG Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 753 LEU Chi-restraints excluded: chain Q residue 790 HIS Chi-restraints excluded: chain Q residue 881 TYR Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain V residue 31 CYS Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 123 GLN Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain X residue 243 LYS Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain Z residue 444 ASP Chi-restraints excluded: chain Z residue 460 MET Chi-restraints excluded: chain Z residue 500 VAL Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 130 ILE Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain d residue 35 GLU Chi-restraints excluded: chain d residue 64 SER Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 90 THR Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain f residue 86 VAL Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain l residue 1514 ILE Chi-restraints excluded: chain l residue 1677 LYS Chi-restraints excluded: chain l residue 2024 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 286 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 728 optimal weight: 9.9990 chunk 784 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 622 optimal weight: 6.9990 chunk 299 optimal weight: 0.9990 chunk 819 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 HIS e 108 ASN ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.120951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.083214 restraints weight = 301982.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.085012 restraints weight = 159248.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.084723 restraints weight = 100617.258| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 75528 Z= 0.242 Angle : 0.586 13.727 103343 Z= 0.307 Chirality : 0.041 0.300 11031 Planarity : 0.004 0.063 12367 Dihedral : 18.622 178.880 13721 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.93 % Rotamer: Outliers : 2.36 % Allowed : 14.80 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.09), residues: 8646 helix: 1.43 (0.09), residues: 3584 sheet: -1.38 (0.17), residues: 864 loop : -1.50 (0.09), residues: 4198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Q 581 HIS 0.006 0.001 HIS J 52 PHE 0.019 0.001 PHE D 122 TYR 0.039 0.001 TYR Y 85 ARG 0.012 0.000 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 681 time to evaluate : 6.016 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: A 58 MET cc_start: 0.7889 (tpp) cc_final: 0.7543 (tpp) REVERT: A 85 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6421 (t80) REVERT: A 104 MET cc_start: 0.8639 (tpp) cc_final: 0.8413 (tpp) REVERT: A 278 HIS cc_start: 0.8801 (m170) cc_final: 0.8365 (m90) REVERT: A 329 MET cc_start: 0.8124 (tpp) cc_final: 0.7721 (tpp) REVERT: A 354 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8703 (mm) REVERT: A 535 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.6916 (mtp) REVERT: A 538 VAL cc_start: 0.8355 (p) cc_final: 0.7989 (t) REVERT: A 539 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6756 (tp-100) REVERT: A 559 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8545 (mm-30) REVERT: A 561 MET cc_start: 0.8248 (mtt) cc_final: 0.7916 (mtt) REVERT: A 683 GLU cc_start: 0.8403 (tp30) cc_final: 0.7883 (tp30) REVERT: A 872 MET cc_start: 0.8635 (ptm) cc_final: 0.8358 (ptm) REVERT: A 900 SER cc_start: 0.9208 (m) cc_final: 0.8573 (p) REVERT: A 902 GLU cc_start: 0.7664 (tt0) cc_final: 0.7252 (tt0) REVERT: A 928 ARG cc_start: 0.9183 (mtp85) cc_final: 0.8894 (mtp85) REVERT: A 1094 SER cc_start: 0.8859 (m) cc_final: 0.8385 (p) REVERT: A 1210 TRP cc_start: 0.6990 (OUTLIER) cc_final: 0.6539 (p90) REVERT: A 1309 MET cc_start: 0.8211 (ttm) cc_final: 0.7702 (ttt) REVERT: A 1378 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8933 (tp) REVERT: A 1412 MET cc_start: 0.8448 (ppp) cc_final: 0.7972 (tmm) REVERT: A 1428 MET cc_start: 0.8885 (ttt) cc_final: 0.8560 (mtp) REVERT: A 1440 MET cc_start: 0.9181 (mmt) cc_final: 0.8735 (mmt) REVERT: A 1459 MET cc_start: 0.8743 (mtp) cc_final: 0.8446 (mtm) REVERT: B 204 THR cc_start: 0.8820 (m) cc_final: 0.8547 (p) REVERT: B 298 MET cc_start: 0.8815 (ttm) cc_final: 0.8497 (ttp) REVERT: B 407 MET cc_start: 0.7917 (mtt) cc_final: 0.7418 (mtt) REVERT: B 508 MET cc_start: 0.8102 (mpp) cc_final: 0.7258 (mpp) REVERT: B 751 LEU cc_start: 0.9220 (tp) cc_final: 0.8960 (mt) REVERT: B 789 ASN cc_start: 0.8418 (p0) cc_final: 0.7602 (p0) REVERT: B 890 ARG cc_start: 0.9104 (ttm170) cc_final: 0.8757 (ttp-170) REVERT: B 1025 ASN cc_start: 0.8517 (m-40) cc_final: 0.8279 (m-40) REVERT: B 1039 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8834 (p) REVERT: B 1135 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: B 1172 MET cc_start: 0.8260 (mmt) cc_final: 0.7818 (mmm) REVERT: C 185 GLU cc_start: 0.7496 (tt0) cc_final: 0.7235 (mt-10) REVERT: C 268 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8413 (tm-30) REVERT: D 61 PHE cc_start: 0.8972 (m-10) cc_final: 0.8424 (m-80) REVERT: D 74 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8350 (p90) REVERT: D 132 ASP cc_start: 0.9259 (m-30) cc_final: 0.9040 (t0) REVERT: D 138 ARG cc_start: 0.8234 (mtp180) cc_final: 0.7671 (mtp180) REVERT: E 18 MET cc_start: 0.9445 (mmp) cc_final: 0.9204 (mmp) REVERT: E 121 MET cc_start: 0.7339 (tpp) cc_final: 0.7040 (tpp) REVERT: E 138 ASN cc_start: 0.8113 (t0) cc_final: 0.7859 (t0) REVERT: E 203 TYR cc_start: 0.8184 (t80) cc_final: 0.7648 (t80) REVERT: F 83 LEU cc_start: 0.8874 (mp) cc_final: 0.8488 (tp) REVERT: F 91 LEU cc_start: 0.9258 (tp) cc_final: 0.9030 (tp) REVERT: F 115 TYR cc_start: 0.8675 (p90) cc_final: 0.8365 (p90) REVERT: G 35 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7504 (mm-30) REVERT: G 60 GLN cc_start: 0.8534 (mm110) cc_final: 0.8316 (mm110) REVERT: G 83 GLU cc_start: 0.8157 (pt0) cc_final: 0.7659 (mp0) REVERT: G 101 ILE cc_start: 0.8368 (tp) cc_final: 0.7884 (tp) REVERT: G 104 MET cc_start: 0.7118 (tmm) cc_final: 0.6605 (tmm) REVERT: G 156 ASP cc_start: 0.6534 (m-30) cc_final: 0.6176 (m-30) REVERT: H 13 LYS cc_start: 0.9144 (mmtp) cc_final: 0.8695 (mmmm) REVERT: H 20 LYS cc_start: 0.9038 (ttmm) cc_final: 0.8648 (ttmm) REVERT: H 36 LYS cc_start: 0.9228 (mmmt) cc_final: 0.8538 (mmpt) REVERT: H 106 THR cc_start: 0.9138 (p) cc_final: 0.8570 (p) REVERT: H 111 ARG cc_start: 0.7961 (mtp85) cc_final: 0.7083 (mtp85) REVERT: H 130 ASN cc_start: 0.8705 (t0) cc_final: 0.8279 (t0) REVERT: I 23 MET cc_start: 0.8693 (mmm) cc_final: 0.8481 (tpt) REVERT: I 71 ASP cc_start: 0.8985 (m-30) cc_final: 0.8638 (m-30) REVERT: K 13 PHE cc_start: 0.7343 (t80) cc_final: 0.7120 (t80) REVERT: K 26 LYS cc_start: 0.8947 (mttt) cc_final: 0.8609 (mtpp) REVERT: K 38 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8142 (mm-30) REVERT: K 93 ASP cc_start: 0.7165 (p0) cc_final: 0.6866 (p0) REVERT: L 15 MET cc_start: 0.7407 (tpp) cc_final: 0.6605 (tpp) REVERT: L 29 LYS cc_start: 0.9314 (mppt) cc_final: 0.8884 (mmmm) REVERT: L 38 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8678 (mp0) REVERT: O 652 LEU cc_start: -0.3133 (OUTLIER) cc_final: -0.3438 (pp) REVERT: O 659 ARG cc_start: 0.2990 (tpt90) cc_final: 0.2453 (tmt170) REVERT: Q 83 MET cc_start: 0.2766 (ppp) cc_final: 0.2032 (ttm) REVERT: Q 125 MET cc_start: -0.2812 (mtt) cc_final: -0.3995 (ttp) REVERT: Q 204 MET cc_start: 0.1923 (OUTLIER) cc_final: 0.1669 (mpp) REVERT: Q 350 MET cc_start: 0.4556 (mmm) cc_final: 0.4042 (mmm) REVERT: Q 604 MET cc_start: 0.7899 (mtt) cc_final: 0.7540 (mtt) REVERT: Q 633 LEU cc_start: 0.9277 (tp) cc_final: 0.9013 (pp) REVERT: Q 703 MET cc_start: 0.6339 (ttt) cc_final: 0.6122 (ttt) REVERT: Q 762 GLN cc_start: 0.5458 (OUTLIER) cc_final: 0.4886 (tt0) REVERT: U 448 MET cc_start: 0.3148 (ptt) cc_final: 0.2351 (tpt) REVERT: V 38 SER cc_start: 0.8875 (t) cc_final: 0.8504 (p) REVERT: V 47 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8027 (mtmt) REVERT: V 51 TYR cc_start: 0.7610 (t80) cc_final: 0.6503 (t80) REVERT: V 126 LYS cc_start: 0.8880 (tppt) cc_final: 0.8648 (mttt) REVERT: V 205 MET cc_start: -0.2091 (tpt) cc_final: -0.2509 (tpt) REVERT: W 191 MET cc_start: 0.9118 (mmt) cc_final: 0.8818 (mmm) REVERT: X 257 LYS cc_start: 0.8615 (ptpt) cc_final: 0.8409 (pttt) REVERT: Z 635 MET cc_start: -0.4134 (OUTLIER) cc_final: -0.4498 (tmm) REVERT: a 50 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8802 (mt-10) REVERT: a 59 GLU cc_start: 0.8226 (pm20) cc_final: 0.7967 (pm20) REVERT: a 97 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8822 (tp30) REVERT: a 105 GLU cc_start: 0.8928 (tp30) cc_final: 0.8648 (tp30) REVERT: a 120 MET cc_start: 0.8002 (mtt) cc_final: 0.7541 (mtm) REVERT: a 129 ARG cc_start: 0.9168 (tpt90) cc_final: 0.8802 (tpt90) REVERT: b 74 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8679 (mm-30) REVERT: b 84 MET cc_start: 0.8445 (ppp) cc_final: 0.8154 (tmm) REVERT: c 36 LYS cc_start: 0.7555 (pttt) cc_final: 0.7337 (pttm) REVERT: c 104 GLN cc_start: 0.8532 (mm-40) cc_final: 0.7982 (tp-100) REVERT: d 71 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8168 (tp30) REVERT: d 93 GLU cc_start: 0.8625 (mp0) cc_final: 0.7892 (mp0) REVERT: d 105 GLU cc_start: 0.8547 (pm20) cc_final: 0.8230 (pm20) REVERT: e 45 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.8956 (p) REVERT: e 110 CYS cc_start: 0.9470 (m) cc_final: 0.9116 (t) REVERT: e 115 LYS cc_start: 0.9414 (mtmt) cc_final: 0.9183 (ptmt) REVERT: e 123 ASP cc_start: 0.9221 (m-30) cc_final: 0.8889 (m-30) REVERT: f 53 GLU cc_start: 0.8621 (mp0) cc_final: 0.8073 (mp0) REVERT: f 92 ARG cc_start: 0.9115 (tpt-90) cc_final: 0.8658 (tpt-90) REVERT: f 96 THR cc_start: 0.8652 (m) cc_final: 0.8385 (p) REVERT: g 56 GLU cc_start: 0.8896 (tt0) cc_final: 0.8556 (tt0) REVERT: g 64 GLU cc_start: 0.9064 (tt0) cc_final: 0.8441 (mm-30) REVERT: g 92 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8781 (mt-10) REVERT: g 104 GLN cc_start: 0.9003 (mt0) cc_final: 0.8698 (mp10) REVERT: h 68 ASP cc_start: 0.9023 (t0) cc_final: 0.8506 (t0) REVERT: h 79 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8753 (mtm-85) REVERT: l 1526 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7205 (tpt) REVERT: l 1627 MET cc_start: 0.6287 (tpp) cc_final: 0.5259 (tpp) outliers start: 155 outliers final: 108 residues processed: 781 average time/residue: 0.6726 time to fit residues: 906.8563 Evaluate side-chains 767 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 642 time to evaluate : 5.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1210 TRP Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain A residue 1539 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 1039 SER Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain O residue 596 MET Chi-restraints excluded: chain O residue 613 MET Chi-restraints excluded: chain O residue 652 LEU Chi-restraints excluded: chain Q residue 200 VAL Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 208 PHE Chi-restraints excluded: chain Q residue 262 TYR Chi-restraints excluded: chain Q residue 510 MET Chi-restraints excluded: chain Q residue 667 ARG Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 753 LEU Chi-restraints excluded: chain Q residue 762 GLN Chi-restraints excluded: chain Q residue 790 HIS Chi-restraints excluded: chain Q residue 881 TYR Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 123 GLN Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 154 ILE Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain X residue 243 LYS Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain Z residue 444 ASP Chi-restraints excluded: chain Z residue 500 VAL Chi-restraints excluded: chain Z residue 635 MET Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 130 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 90 THR Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain l residue 1514 ILE Chi-restraints excluded: chain l residue 1526 MET Chi-restraints excluded: chain l residue 2024 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 570 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 598 optimal weight: 5.9990 chunk 592 optimal weight: 0.0770 chunk 844 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 768 optimal weight: 10.0000 chunk 249 optimal weight: 9.9990 chunk 436 optimal weight: 9.9990 chunk 532 optimal weight: 2.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 55 GLN e 108 ASN ** l1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.121209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.082469 restraints weight = 301024.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.084029 restraints weight = 150422.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.084405 restraints weight = 97869.375| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 75528 Z= 0.211 Angle : 0.578 13.132 103343 Z= 0.301 Chirality : 0.041 0.331 11031 Planarity : 0.004 0.061 12367 Dihedral : 18.575 178.977 13721 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.00 % Rotamer: Outliers : 2.32 % Allowed : 15.27 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.09), residues: 8646 helix: 1.51 (0.09), residues: 3586 sheet: -1.31 (0.17), residues: 846 loop : -1.41 (0.09), residues: 4214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 653 HIS 0.005 0.001 HIS f 75 PHE 0.021 0.001 PHE D 26 TYR 0.053 0.001 TYR G 3 ARG 0.013 0.000 ARG Q 866 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 661 time to evaluate : 5.955 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: A 58 MET cc_start: 0.7997 (tpp) cc_final: 0.7616 (tpp) REVERT: A 85 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6561 (t80) REVERT: A 104 MET cc_start: 0.8770 (tpp) cc_final: 0.7927 (mmm) REVERT: A 248 MET cc_start: 0.7649 (ttp) cc_final: 0.7447 (ttp) REVERT: A 278 HIS cc_start: 0.8803 (m170) cc_final: 0.8337 (m90) REVERT: A 329 MET cc_start: 0.8111 (tpp) cc_final: 0.7810 (tpp) REVERT: A 354 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8750 (mm) REVERT: A 500 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7571 (mm-30) REVERT: A 535 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7197 (mtm) REVERT: A 538 VAL cc_start: 0.8305 (p) cc_final: 0.7963 (t) REVERT: A 539 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.6981 (tp-100) REVERT: A 683 GLU cc_start: 0.8398 (tp30) cc_final: 0.7901 (tp30) REVERT: A 872 MET cc_start: 0.8712 (ptm) cc_final: 0.8363 (ptm) REVERT: A 900 SER cc_start: 0.9175 (m) cc_final: 0.8486 (p) REVERT: A 902 GLU cc_start: 0.7638 (tt0) cc_final: 0.7244 (tt0) REVERT: A 928 ARG cc_start: 0.9215 (mtp85) cc_final: 0.8900 (mtp85) REVERT: A 1094 SER cc_start: 0.8781 (m) cc_final: 0.8361 (p) REVERT: A 1378 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8903 (tp) REVERT: A 1412 MET cc_start: 0.8462 (ppp) cc_final: 0.7998 (tmm) REVERT: A 1428 MET cc_start: 0.8901 (ttt) cc_final: 0.8584 (mtp) REVERT: A 1459 MET cc_start: 0.8706 (mtp) cc_final: 0.8415 (mtm) REVERT: B 204 THR cc_start: 0.8841 (m) cc_final: 0.8571 (p) REVERT: B 298 MET cc_start: 0.8795 (ttm) cc_final: 0.8503 (ttp) REVERT: B 368 MET cc_start: 0.9313 (tpp) cc_final: 0.8826 (tpt) REVERT: B 407 MET cc_start: 0.7943 (mtt) cc_final: 0.7505 (mtt) REVERT: B 422 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7400 (t80) REVERT: B 508 MET cc_start: 0.8057 (mpp) cc_final: 0.7247 (mpp) REVERT: B 603 MET cc_start: 0.8210 (mtm) cc_final: 0.7757 (mtm) REVERT: B 751 LEU cc_start: 0.9225 (tp) cc_final: 0.8882 (mt) REVERT: B 789 ASN cc_start: 0.8497 (p0) cc_final: 0.7717 (p0) REVERT: B 890 ARG cc_start: 0.9013 (ttm170) cc_final: 0.8645 (ttp-170) REVERT: B 1015 LEU cc_start: 0.9611 (tp) cc_final: 0.9359 (tt) REVERT: B 1025 ASN cc_start: 0.8564 (m-40) cc_final: 0.8306 (m-40) REVERT: B 1039 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.8832 (p) REVERT: B 1135 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: B 1172 MET cc_start: 0.8268 (mmt) cc_final: 0.7865 (mmt) REVERT: C 185 GLU cc_start: 0.7432 (tt0) cc_final: 0.7192 (mt-10) REVERT: D 61 PHE cc_start: 0.8900 (m-10) cc_final: 0.8352 (m-80) REVERT: D 74 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8216 (p90) REVERT: D 132 ASP cc_start: 0.9153 (m-30) cc_final: 0.8899 (t0) REVERT: D 138 ARG cc_start: 0.8227 (mtp180) cc_final: 0.7660 (mtp180) REVERT: E 18 MET cc_start: 0.9480 (mmp) cc_final: 0.9266 (mmp) REVERT: E 121 MET cc_start: 0.7313 (tpp) cc_final: 0.6985 (tpp) REVERT: E 138 ASN cc_start: 0.8148 (t0) cc_final: 0.7895 (t0) REVERT: E 203 TYR cc_start: 0.8201 (t80) cc_final: 0.7684 (t80) REVERT: F 91 LEU cc_start: 0.9284 (tp) cc_final: 0.9055 (tp) REVERT: F 115 TYR cc_start: 0.8678 (p90) cc_final: 0.8395 (p90) REVERT: F 122 GLU cc_start: 0.9034 (tt0) cc_final: 0.8492 (tt0) REVERT: G 35 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7592 (mm-30) REVERT: G 60 GLN cc_start: 0.8510 (mm110) cc_final: 0.8298 (mm110) REVERT: G 83 GLU cc_start: 0.7936 (pt0) cc_final: 0.7642 (mp0) REVERT: G 101 ILE cc_start: 0.8429 (tp) cc_final: 0.7914 (tp) REVERT: G 104 MET cc_start: 0.7174 (tmm) cc_final: 0.6683 (tmm) REVERT: G 156 ASP cc_start: 0.6478 (m-30) cc_final: 0.6104 (m-30) REVERT: H 13 LYS cc_start: 0.9151 (mmtp) cc_final: 0.8682 (mmmm) REVERT: H 20 LYS cc_start: 0.9031 (ttmm) cc_final: 0.8708 (ttmm) REVERT: H 36 LYS cc_start: 0.9230 (mmmt) cc_final: 0.8579 (mmpt) REVERT: H 74 GLU cc_start: 0.7997 (pm20) cc_final: 0.7476 (pm20) REVERT: H 106 THR cc_start: 0.9138 (p) cc_final: 0.8567 (p) REVERT: H 111 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7624 (mtp85) REVERT: H 130 ASN cc_start: 0.8681 (t0) cc_final: 0.8238 (t0) REVERT: H 136 GLU cc_start: 0.8244 (mp0) cc_final: 0.7935 (mp0) REVERT: I 23 MET cc_start: 0.8643 (mmm) cc_final: 0.8439 (tpt) REVERT: I 71 ASP cc_start: 0.9030 (m-30) cc_final: 0.8671 (m-30) REVERT: K 1 MET cc_start: 0.8360 (ptp) cc_final: 0.7449 (pmm) REVERT: K 13 PHE cc_start: 0.7490 (t80) cc_final: 0.6871 (t80) REVERT: K 26 LYS cc_start: 0.8910 (mttt) cc_final: 0.8593 (mtpp) REVERT: K 38 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8164 (mm-30) REVERT: K 93 ASP cc_start: 0.7116 (p0) cc_final: 0.6813 (p0) REVERT: L 15 MET cc_start: 0.7336 (tpp) cc_final: 0.6577 (tpp) REVERT: L 29 LYS cc_start: 0.9309 (mppt) cc_final: 0.8886 (mmmm) REVERT: O 652 LEU cc_start: -0.3066 (OUTLIER) cc_final: -0.3562 (pt) REVERT: O 659 ARG cc_start: 0.2946 (tpt90) cc_final: 0.2468 (tmt170) REVERT: Q 83 MET cc_start: 0.2638 (ppp) cc_final: 0.1913 (ttm) REVERT: Q 125 MET cc_start: -0.2841 (mtt) cc_final: -0.3809 (ttp) REVERT: Q 204 MET cc_start: 0.1578 (OUTLIER) cc_final: 0.1296 (mpp) REVERT: Q 350 MET cc_start: 0.4498 (mmm) cc_final: 0.4180 (mmm) REVERT: Q 540 MET cc_start: 0.8080 (ttt) cc_final: 0.7205 (tmm) REVERT: Q 604 MET cc_start: 0.7878 (mtt) cc_final: 0.7482 (mtt) REVERT: Q 633 LEU cc_start: 0.9218 (tp) cc_final: 0.8979 (pp) REVERT: Q 703 MET cc_start: 0.6457 (ttt) cc_final: 0.6152 (ttt) REVERT: Q 762 GLN cc_start: 0.5377 (OUTLIER) cc_final: 0.4771 (tt0) REVERT: U 378 LEU cc_start: 0.1535 (tt) cc_final: 0.1221 (tp) REVERT: U 448 MET cc_start: 0.3193 (ptt) cc_final: 0.2413 (tpt) REVERT: V 38 SER cc_start: 0.8775 (t) cc_final: 0.8383 (p) REVERT: V 47 LYS cc_start: 0.8445 (mmmt) cc_final: 0.7918 (mtmt) REVERT: V 51 TYR cc_start: 0.7616 (t80) cc_final: 0.6410 (t80) REVERT: V 205 MET cc_start: -0.2216 (tpt) cc_final: -0.2828 (tpt) REVERT: W 191 MET cc_start: 0.9177 (mmt) cc_final: 0.8892 (mmm) REVERT: W 237 ASN cc_start: 0.9080 (t0) cc_final: 0.8676 (t0) REVERT: X 257 LYS cc_start: 0.8421 (ptpt) cc_final: 0.8211 (pttt) REVERT: Y 42 MET cc_start: 0.4076 (pmm) cc_final: 0.3358 (ptm) REVERT: Z 460 MET cc_start: -0.0407 (mmt) cc_final: -0.1906 (mtm) REVERT: Z 635 MET cc_start: -0.4017 (OUTLIER) cc_final: -0.4433 (tmm) REVERT: a 50 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8873 (mt-10) REVERT: a 93 GLN cc_start: 0.9069 (tt0) cc_final: 0.8522 (tp40) REVERT: a 97 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8892 (tp30) REVERT: a 105 GLU cc_start: 0.9043 (tp30) cc_final: 0.8829 (tp30) REVERT: a 120 MET cc_start: 0.8014 (mtt) cc_final: 0.7563 (mtt) REVERT: a 125 GLN cc_start: 0.9349 (mt0) cc_final: 0.9014 (mt0) REVERT: a 129 ARG cc_start: 0.9233 (tpt90) cc_final: 0.8851 (tpt90) REVERT: b 74 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8756 (mm-30) REVERT: b 98 TYR cc_start: 0.9149 (m-10) cc_final: 0.8920 (m-10) REVERT: c 36 LYS cc_start: 0.7615 (pttt) cc_final: 0.7399 (pttm) REVERT: c 104 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8006 (tp-100) REVERT: d 71 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8177 (tp30) REVERT: d 93 GLU cc_start: 0.8654 (mp0) cc_final: 0.7916 (mp0) REVERT: e 45 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.8931 (p) REVERT: e 110 CYS cc_start: 0.9485 (m) cc_final: 0.9123 (t) REVERT: e 115 LYS cc_start: 0.9438 (mtmt) cc_final: 0.9227 (ptmt) REVERT: e 123 ASP cc_start: 0.9235 (m-30) cc_final: 0.8941 (m-30) REVERT: f 53 GLU cc_start: 0.8755 (mp0) cc_final: 0.8037 (mp0) REVERT: f 92 ARG cc_start: 0.9120 (tpt-90) cc_final: 0.8642 (ttt90) REVERT: f 96 THR cc_start: 0.8676 (m) cc_final: 0.8440 (p) REVERT: g 56 GLU cc_start: 0.8863 (tt0) cc_final: 0.8532 (tt0) REVERT: g 64 GLU cc_start: 0.9088 (tt0) cc_final: 0.8431 (mm-30) REVERT: g 92 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8823 (mp0) REVERT: g 104 GLN cc_start: 0.9009 (mt0) cc_final: 0.8657 (mp10) REVERT: h 59 MET cc_start: 0.5970 (ttm) cc_final: 0.5610 (tpp) REVERT: h 68 ASP cc_start: 0.9100 (t0) cc_final: 0.8581 (t0) REVERT: h 79 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8814 (mtm-85) REVERT: h 105 GLU cc_start: 0.7578 (tp30) cc_final: 0.7237 (tp30) REVERT: l 1526 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7176 (tpt) REVERT: l 1627 MET cc_start: 0.6205 (tpp) cc_final: 0.5200 (tpp) outliers start: 152 outliers final: 112 residues processed: 764 average time/residue: 0.6626 time to fit residues: 877.2401 Evaluate side-chains 761 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 633 time to evaluate : 5.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain A residue 1539 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 1039 SER Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain O residue 596 MET Chi-restraints excluded: chain O residue 613 MET Chi-restraints excluded: chain O residue 652 LEU Chi-restraints excluded: chain Q residue 200 VAL Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 208 PHE Chi-restraints excluded: chain Q residue 262 TYR Chi-restraints excluded: chain Q residue 510 MET Chi-restraints excluded: chain Q residue 667 ARG Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 753 LEU Chi-restraints excluded: chain Q residue 762 GLN Chi-restraints excluded: chain Q residue 790 HIS Chi-restraints excluded: chain Q residue 881 TYR Chi-restraints excluded: chain R residue 563 ILE Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 123 GLN Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain X residue 243 LYS Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain Z residue 444 ASP Chi-restraints excluded: chain Z residue 500 VAL Chi-restraints excluded: chain Z residue 635 MET Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 130 ILE Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 90 THR Chi-restraints excluded: chain d residue 108 LYS Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 55 GLN Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain l residue 1514 ILE Chi-restraints excluded: chain l residue 1526 MET Chi-restraints excluded: chain l residue 1694 ARG Chi-restraints excluded: chain l residue 2024 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 175 optimal weight: 1.9990 chunk 803 optimal weight: 0.9990 chunk 675 optimal weight: 8.9990 chunk 523 optimal weight: 20.0000 chunk 854 optimal weight: 3.9990 chunk 820 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 482 optimal weight: 8.9990 chunk 478 optimal weight: 20.0000 chunk 710 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 GLN ** Q 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 374 HIS ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 55 GLN e 108 ASN ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l1629 HIS ** l1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.120145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.081756 restraints weight = 301985.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.083327 restraints weight = 161303.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.083416 restraints weight = 102848.228| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 75528 Z= 0.267 Angle : 0.616 15.552 103343 Z= 0.320 Chirality : 0.042 0.311 11031 Planarity : 0.004 0.062 12367 Dihedral : 18.614 179.530 13721 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.32 % Favored : 94.66 % Rotamer: Outliers : 2.26 % Allowed : 15.44 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.09), residues: 8646 helix: 1.47 (0.09), residues: 3585 sheet: -1.22 (0.17), residues: 852 loop : -1.39 (0.09), residues: 4209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 27 HIS 0.006 0.001 HIS Q 659 PHE 0.021 0.001 PHE A 496 TYR 0.068 0.002 TYR d 83 ARG 0.011 0.000 ARG c 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 639 time to evaluate : 6.200 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: A 58 MET cc_start: 0.7977 (tpp) cc_final: 0.7663 (tpp) REVERT: A 85 PHE cc_start: 0.6794 (OUTLIER) cc_final: 0.6377 (t80) REVERT: A 104 MET cc_start: 0.8731 (tpp) cc_final: 0.7946 (mmm) REVERT: A 278 HIS cc_start: 0.8805 (m170) cc_final: 0.8358 (m90) REVERT: A 329 MET cc_start: 0.8021 (tpp) cc_final: 0.7793 (tpp) REVERT: A 500 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7756 (mm-30) REVERT: A 535 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7311 (mtm) REVERT: A 538 VAL cc_start: 0.8420 (p) cc_final: 0.8111 (t) REVERT: A 539 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7073 (tp-100) REVERT: A 559 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8642 (mm-30) REVERT: A 683 GLU cc_start: 0.8438 (tp30) cc_final: 0.7946 (tp30) REVERT: A 845 GLU cc_start: 0.8641 (tt0) cc_final: 0.7873 (tm-30) REVERT: A 872 MET cc_start: 0.8721 (ptm) cc_final: 0.8406 (ptm) REVERT: A 900 SER cc_start: 0.9155 (m) cc_final: 0.8447 (p) REVERT: A 902 GLU cc_start: 0.7691 (tt0) cc_final: 0.7281 (tt0) REVERT: A 928 ARG cc_start: 0.9190 (mtp85) cc_final: 0.8956 (mmm-85) REVERT: A 1094 SER cc_start: 0.8817 (m) cc_final: 0.8291 (p) REVERT: A 1378 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8917 (tp) REVERT: A 1412 MET cc_start: 0.8418 (ppp) cc_final: 0.8031 (tmm) REVERT: A 1428 MET cc_start: 0.8899 (ttt) cc_final: 0.8575 (mtp) REVERT: A 1459 MET cc_start: 0.8659 (mtp) cc_final: 0.8415 (mtm) REVERT: B 204 THR cc_start: 0.8869 (m) cc_final: 0.8629 (p) REVERT: B 298 MET cc_start: 0.8846 (ttm) cc_final: 0.8541 (ttp) REVERT: B 368 MET cc_start: 0.9149 (tpp) cc_final: 0.8724 (tpt) REVERT: B 407 MET cc_start: 0.7938 (mtt) cc_final: 0.7499 (mtt) REVERT: B 508 MET cc_start: 0.8006 (mpp) cc_final: 0.7218 (mpp) REVERT: B 603 MET cc_start: 0.8306 (mtm) cc_final: 0.7795 (mtm) REVERT: B 751 LEU cc_start: 0.9264 (tp) cc_final: 0.8965 (mt) REVERT: B 789 ASN cc_start: 0.8647 (p0) cc_final: 0.7874 (p0) REVERT: B 890 ARG cc_start: 0.9088 (ttm170) cc_final: 0.8779 (ttp-170) REVERT: B 1025 ASN cc_start: 0.8582 (m-40) cc_final: 0.8333 (m-40) REVERT: B 1039 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8820 (p) REVERT: B 1135 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: B 1172 MET cc_start: 0.8250 (mmt) cc_final: 0.7801 (mmt) REVERT: C 185 GLU cc_start: 0.7501 (tt0) cc_final: 0.7268 (mt-10) REVERT: D 61 PHE cc_start: 0.8937 (m-10) cc_final: 0.8384 (m-80) REVERT: D 74 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8234 (p90) REVERT: D 132 ASP cc_start: 0.9205 (m-30) cc_final: 0.8956 (t0) REVERT: D 138 ARG cc_start: 0.8250 (mtp180) cc_final: 0.7686 (mtp180) REVERT: E 121 MET cc_start: 0.7594 (tpp) cc_final: 0.7218 (tpp) REVERT: E 138 ASN cc_start: 0.8180 (t0) cc_final: 0.7922 (t0) REVERT: E 203 TYR cc_start: 0.8230 (t80) cc_final: 0.7695 (t80) REVERT: F 83 LEU cc_start: 0.8770 (mp) cc_final: 0.8466 (tp) REVERT: F 91 LEU cc_start: 0.9300 (tp) cc_final: 0.9068 (tp) REVERT: F 115 TYR cc_start: 0.8689 (p90) cc_final: 0.8406 (p90) REVERT: F 122 GLU cc_start: 0.9031 (tt0) cc_final: 0.8786 (tt0) REVERT: G 35 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7596 (mm-30) REVERT: G 60 GLN cc_start: 0.8541 (mm110) cc_final: 0.8315 (mm110) REVERT: G 83 GLU cc_start: 0.8075 (pt0) cc_final: 0.7653 (mp0) REVERT: G 101 ILE cc_start: 0.8415 (tp) cc_final: 0.7876 (tp) REVERT: G 104 MET cc_start: 0.7210 (tmm) cc_final: 0.6780 (tmm) REVERT: G 156 ASP cc_start: 0.6563 (m-30) cc_final: 0.6223 (m-30) REVERT: H 13 LYS cc_start: 0.9119 (mmtp) cc_final: 0.8664 (mmmm) REVERT: H 20 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8590 (ttmm) REVERT: H 36 LYS cc_start: 0.9216 (mmmt) cc_final: 0.8571 (mmpt) REVERT: H 111 ARG cc_start: 0.8167 (mtp85) cc_final: 0.7818 (mtp85) REVERT: H 130 ASN cc_start: 0.8720 (t0) cc_final: 0.8256 (t0) REVERT: I 23 MET cc_start: 0.8626 (mmm) cc_final: 0.8283 (tpt) REVERT: I 71 ASP cc_start: 0.9030 (m-30) cc_final: 0.8672 (m-30) REVERT: K 1 MET cc_start: 0.8443 (ptp) cc_final: 0.7431 (pmm) REVERT: K 26 LYS cc_start: 0.8967 (mttt) cc_final: 0.8629 (mtpp) REVERT: K 38 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8173 (mm-30) REVERT: K 93 ASP cc_start: 0.7157 (p0) cc_final: 0.6876 (p0) REVERT: L 15 MET cc_start: 0.7334 (tpp) cc_final: 0.6513 (tpp) REVERT: L 29 LYS cc_start: 0.9331 (mppt) cc_final: 0.8920 (mmmm) REVERT: O 652 LEU cc_start: -0.3295 (OUTLIER) cc_final: -0.3719 (pt) REVERT: O 659 ARG cc_start: 0.3011 (tpt90) cc_final: 0.2501 (tmt170) REVERT: Q 83 MET cc_start: 0.2883 (ppp) cc_final: 0.2144 (ttm) REVERT: Q 125 MET cc_start: -0.3325 (mtt) cc_final: -0.4267 (ttp) REVERT: Q 204 MET cc_start: 0.2136 (OUTLIER) cc_final: 0.1899 (mpp) REVERT: Q 350 MET cc_start: 0.4555 (mmm) cc_final: 0.4269 (mmm) REVERT: Q 540 MET cc_start: 0.8192 (ttt) cc_final: 0.7299 (tmm) REVERT: Q 604 MET cc_start: 0.7959 (mtt) cc_final: 0.7547 (mtt) REVERT: Q 633 LEU cc_start: 0.9300 (tp) cc_final: 0.9038 (pp) REVERT: Q 703 MET cc_start: 0.6613 (ttt) cc_final: 0.6366 (ttt) REVERT: Q 762 GLN cc_start: 0.5483 (OUTLIER) cc_final: 0.4880 (tt0) REVERT: Q 881 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7169 (t80) REVERT: U 378 LEU cc_start: 0.1399 (tt) cc_final: 0.1044 (tp) REVERT: U 448 MET cc_start: 0.3168 (ptt) cc_final: 0.2381 (tpt) REVERT: V 38 SER cc_start: 0.8927 (t) cc_final: 0.8529 (p) REVERT: V 47 LYS cc_start: 0.8475 (mmmt) cc_final: 0.7952 (mtmt) REVERT: V 122 GLN cc_start: 0.8866 (tt0) cc_final: 0.8403 (mm110) REVERT: V 126 LYS cc_start: 0.8975 (tppt) cc_final: 0.8738 (mttt) REVERT: V 205 MET cc_start: -0.1836 (tpt) cc_final: -0.2480 (tpt) REVERT: W 191 MET cc_start: 0.9177 (mmt) cc_final: 0.8909 (mmm) REVERT: W 237 ASN cc_start: 0.9108 (t0) cc_final: 0.8697 (t0) REVERT: Y 42 MET cc_start: 0.4001 (pmm) cc_final: 0.2810 (ptm) REVERT: Z 635 MET cc_start: -0.4144 (OUTLIER) cc_final: -0.4520 (tmm) REVERT: a 50 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8788 (mt-10) REVERT: a 105 GLU cc_start: 0.8960 (tp30) cc_final: 0.8755 (tp30) REVERT: a 120 MET cc_start: 0.8111 (mtt) cc_final: 0.7626 (mtt) REVERT: a 125 GLN cc_start: 0.9303 (mt0) cc_final: 0.8925 (mt0) REVERT: a 129 ARG cc_start: 0.9186 (tpt90) cc_final: 0.8815 (tpt90) REVERT: b 74 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8718 (mm-30) REVERT: b 98 TYR cc_start: 0.9143 (m-10) cc_final: 0.8906 (m-10) REVERT: c 36 LYS cc_start: 0.7641 (pttt) cc_final: 0.7415 (pttm) REVERT: c 104 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8090 (tp-100) REVERT: d 62 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.9036 (mpp) REVERT: d 71 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8197 (tp30) REVERT: d 87 SER cc_start: 0.8089 (m) cc_final: 0.7717 (p) REVERT: d 88 THR cc_start: 0.9203 (p) cc_final: 0.8986 (p) REVERT: d 93 GLU cc_start: 0.8635 (mp0) cc_final: 0.7856 (mp0) REVERT: e 45 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8941 (p) REVERT: e 110 CYS cc_start: 0.9432 (m) cc_final: 0.9083 (t) REVERT: e 123 ASP cc_start: 0.9234 (m-30) cc_final: 0.8931 (m-30) REVERT: f 53 GLU cc_start: 0.8762 (mp0) cc_final: 0.8062 (mp0) REVERT: f 96 THR cc_start: 0.8697 (m) cc_final: 0.8461 (p) REVERT: g 41 GLU cc_start: 0.7965 (pm20) cc_final: 0.7687 (pm20) REVERT: g 56 GLU cc_start: 0.8905 (tt0) cc_final: 0.8614 (tt0) REVERT: g 64 GLU cc_start: 0.9110 (tt0) cc_final: 0.8491 (mm-30) REVERT: g 92 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8907 (mp0) REVERT: g 104 GLN cc_start: 0.9033 (mt0) cc_final: 0.8729 (mp10) REVERT: h 68 ASP cc_start: 0.9051 (t0) cc_final: 0.8494 (t0) REVERT: h 79 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8727 (mtm-85) REVERT: h 105 GLU cc_start: 0.7628 (tp30) cc_final: 0.7241 (tp30) REVERT: l 1526 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7162 (mmm) REVERT: l 1627 MET cc_start: 0.6292 (tpp) cc_final: 0.5413 (tpp) outliers start: 148 outliers final: 120 residues processed: 745 average time/residue: 0.6753 time to fit residues: 873.6618 Evaluate side-chains 758 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 622 time to evaluate : 5.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1210 TRP Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain A residue 1539 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 1039 SER Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain O residue 652 LEU Chi-restraints excluded: chain Q residue 200 VAL Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 208 PHE Chi-restraints excluded: chain Q residue 262 TYR Chi-restraints excluded: chain Q residue 510 MET Chi-restraints excluded: chain Q residue 667 ARG Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 753 LEU Chi-restraints excluded: chain Q residue 762 GLN Chi-restraints excluded: chain Q residue 790 HIS Chi-restraints excluded: chain Q residue 881 TYR Chi-restraints excluded: chain R residue 563 ILE Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 123 GLN Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 154 ILE Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain X residue 243 LYS Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain Z residue 444 ASP Chi-restraints excluded: chain Z residue 500 VAL Chi-restraints excluded: chain Z residue 635 MET Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 130 ILE Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 90 THR Chi-restraints excluded: chain d residue 108 LYS Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 55 GLN Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain l residue 1514 ILE Chi-restraints excluded: chain l residue 1526 MET Chi-restraints excluded: chain l residue 1694 ARG Chi-restraints excluded: chain l residue 2024 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 494 optimal weight: 20.0000 chunk 181 optimal weight: 0.9990 chunk 621 optimal weight: 50.0000 chunk 736 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 312 optimal weight: 0.6980 chunk 447 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 763 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 245 ASN ** Q 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 490 HIS ** Q 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 55 GLN e 108 ASN ** l1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.119525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.080807 restraints weight = 303319.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.082866 restraints weight = 166306.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.082895 restraints weight = 101133.317| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 75528 Z= 0.297 Angle : 0.636 14.181 103343 Z= 0.331 Chirality : 0.042 0.298 11031 Planarity : 0.004 0.072 12367 Dihedral : 18.706 179.727 13721 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.68 % Favored : 94.31 % Rotamer: Outliers : 2.21 % Allowed : 15.72 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.06 % Twisted Proline : 0.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.09), residues: 8646 helix: 1.39 (0.09), residues: 3597 sheet: -1.22 (0.17), residues: 864 loop : -1.40 (0.10), residues: 4185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q 684 HIS 0.006 0.001 HIS I 84 PHE 0.036 0.002 PHE K 58 TYR 0.061 0.002 TYR f 88 ARG 0.018 0.000 ARG f 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 644 time to evaluate : 6.322 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: A 58 MET cc_start: 0.8062 (tpp) cc_final: 0.7771 (tpp) REVERT: A 85 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6531 (t80) REVERT: A 104 MET cc_start: 0.8734 (tpp) cc_final: 0.7967 (mmm) REVERT: A 278 HIS cc_start: 0.8824 (m170) cc_final: 0.8399 (m90) REVERT: A 329 MET cc_start: 0.7971 (tpp) cc_final: 0.7754 (tpp) REVERT: A 500 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 535 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7249 (mtm) REVERT: A 538 VAL cc_start: 0.8458 (p) cc_final: 0.8157 (t) REVERT: A 539 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7172 (tp-100) REVERT: A 559 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8563 (mm-30) REVERT: A 561 MET cc_start: 0.8873 (mtt) cc_final: 0.8124 (mtt) REVERT: A 565 MET cc_start: 0.9247 (mmm) cc_final: 0.8959 (mmm) REVERT: A 683 GLU cc_start: 0.8410 (tp30) cc_final: 0.7896 (tp30) REVERT: A 835 GLU cc_start: 0.8561 (mp0) cc_final: 0.8355 (pm20) REVERT: A 845 GLU cc_start: 0.8685 (tt0) cc_final: 0.8340 (tt0) REVERT: A 872 MET cc_start: 0.8694 (ptm) cc_final: 0.8352 (ptm) REVERT: A 900 SER cc_start: 0.9165 (m) cc_final: 0.8468 (p) REVERT: A 902 GLU cc_start: 0.7598 (tt0) cc_final: 0.7169 (tt0) REVERT: A 928 ARG cc_start: 0.9174 (mtp85) cc_final: 0.8955 (mmm-85) REVERT: A 1094 SER cc_start: 0.8824 (m) cc_final: 0.8316 (p) REVERT: A 1378 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8963 (tp) REVERT: A 1412 MET cc_start: 0.8459 (ppp) cc_final: 0.8105 (tmm) REVERT: A 1428 MET cc_start: 0.8919 (ttt) cc_final: 0.8564 (mtp) REVERT: A 1459 MET cc_start: 0.8636 (mtp) cc_final: 0.8431 (mtm) REVERT: B 108 MET cc_start: 0.8697 (ptm) cc_final: 0.8167 (ptm) REVERT: B 204 THR cc_start: 0.8764 (m) cc_final: 0.8557 (p) REVERT: B 298 MET cc_start: 0.8864 (ttm) cc_final: 0.8588 (ttp) REVERT: B 368 MET cc_start: 0.9097 (tpp) cc_final: 0.8689 (tpt) REVERT: B 407 MET cc_start: 0.7951 (mtt) cc_final: 0.7517 (mtt) REVERT: B 422 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7583 (t80) REVERT: B 508 MET cc_start: 0.7999 (mpp) cc_final: 0.7261 (mpp) REVERT: B 751 LEU cc_start: 0.9202 (tp) cc_final: 0.8973 (mt) REVERT: B 890 ARG cc_start: 0.9109 (ttm170) cc_final: 0.8793 (ttp-170) REVERT: B 1039 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8805 (p) REVERT: B 1135 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: B 1172 MET cc_start: 0.8315 (mmt) cc_final: 0.7824 (mmm) REVERT: C 185 GLU cc_start: 0.7561 (tt0) cc_final: 0.7344 (mt-10) REVERT: D 61 PHE cc_start: 0.8968 (m-10) cc_final: 0.8341 (m-80) REVERT: D 74 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8305 (p90) REVERT: D 138 ARG cc_start: 0.8209 (mtp180) cc_final: 0.7736 (mtp180) REVERT: E 121 MET cc_start: 0.7702 (tpp) cc_final: 0.7349 (tpp) REVERT: E 138 ASN cc_start: 0.8237 (t0) cc_final: 0.7971 (t0) REVERT: E 203 TYR cc_start: 0.8240 (t80) cc_final: 0.7738 (t80) REVERT: F 80 MET cc_start: 0.8726 (mmp) cc_final: 0.8392 (mmt) REVERT: F 91 LEU cc_start: 0.9272 (tp) cc_final: 0.9033 (tp) REVERT: F 94 MET cc_start: 0.9240 (tpp) cc_final: 0.9033 (tpp) REVERT: F 115 TYR cc_start: 0.8687 (p90) cc_final: 0.8407 (p90) REVERT: F 122 GLU cc_start: 0.9028 (tt0) cc_final: 0.8786 (tt0) REVERT: G 17 TYR cc_start: 0.8556 (m-10) cc_final: 0.8170 (m-10) REVERT: G 35 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7602 (mm-30) REVERT: G 60 GLN cc_start: 0.8507 (mm110) cc_final: 0.8275 (mm110) REVERT: G 83 GLU cc_start: 0.8020 (pt0) cc_final: 0.7569 (mp0) REVERT: G 101 ILE cc_start: 0.8402 (tp) cc_final: 0.7855 (tp) REVERT: G 104 MET cc_start: 0.7191 (tmm) cc_final: 0.6831 (tmm) REVERT: G 156 ASP cc_start: 0.6522 (m-30) cc_final: 0.6301 (m-30) REVERT: H 13 LYS cc_start: 0.9123 (mmtp) cc_final: 0.8670 (mmmm) REVERT: H 20 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8586 (ttmm) REVERT: H 36 LYS cc_start: 0.9222 (mmmt) cc_final: 0.8558 (mmpt) REVERT: H 92 MET cc_start: 0.7878 (mtm) cc_final: 0.7653 (ptp) REVERT: H 111 ARG cc_start: 0.8168 (mtp85) cc_final: 0.7828 (mtp85) REVERT: H 123 MET cc_start: 0.7665 (tmm) cc_final: 0.7384 (tmm) REVERT: H 130 ASN cc_start: 0.8724 (t0) cc_final: 0.8235 (t0) REVERT: H 136 GLU cc_start: 0.8245 (mp0) cc_final: 0.7944 (mp0) REVERT: I 71 ASP cc_start: 0.8996 (m-30) cc_final: 0.8657 (m-30) REVERT: K 1 MET cc_start: 0.8362 (ptp) cc_final: 0.7542 (pmm) REVERT: K 26 LYS cc_start: 0.8948 (mttt) cc_final: 0.8632 (mtpp) REVERT: K 38 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8118 (mm-30) REVERT: K 93 ASP cc_start: 0.7059 (p0) cc_final: 0.6769 (p0) REVERT: L 29 LYS cc_start: 0.9361 (mppt) cc_final: 0.8966 (mmmm) REVERT: O 652 LEU cc_start: -0.3310 (OUTLIER) cc_final: -0.3721 (pt) REVERT: O 659 ARG cc_start: 0.3111 (tpt90) cc_final: 0.2601 (tmt170) REVERT: Q 83 MET cc_start: 0.2900 (ppp) cc_final: 0.2167 (ttm) REVERT: Q 125 MET cc_start: -0.3463 (mtt) cc_final: -0.4420 (ttp) REVERT: Q 204 MET cc_start: 0.1812 (OUTLIER) cc_final: 0.1556 (mpp) REVERT: Q 350 MET cc_start: 0.5367 (mmm) cc_final: 0.5102 (mmm) REVERT: Q 510 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8634 (ptm) REVERT: Q 540 MET cc_start: 0.8246 (ttt) cc_final: 0.7345 (tmm) REVERT: Q 604 MET cc_start: 0.8067 (mtt) cc_final: 0.7661 (mtt) REVERT: Q 633 LEU cc_start: 0.9328 (tp) cc_final: 0.9071 (pp) REVERT: Q 703 MET cc_start: 0.6704 (ttt) cc_final: 0.6436 (ttt) REVERT: Q 762 GLN cc_start: 0.5544 (OUTLIER) cc_final: 0.4973 (tt0) REVERT: Q 881 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7335 (t80) REVERT: R 464 MET cc_start: 0.3047 (mpp) cc_final: 0.2653 (pmm) REVERT: U 378 LEU cc_start: 0.1480 (tt) cc_final: 0.1120 (tp) REVERT: U 448 MET cc_start: 0.3224 (ptt) cc_final: 0.2419 (tpt) REVERT: V 38 SER cc_start: 0.8902 (t) cc_final: 0.8479 (p) REVERT: V 47 LYS cc_start: 0.8469 (mmmt) cc_final: 0.7983 (mtmt) REVERT: V 122 GLN cc_start: 0.8876 (tt0) cc_final: 0.8440 (mm110) REVERT: V 126 LYS cc_start: 0.8969 (tppt) cc_final: 0.8682 (mttt) REVERT: V 183 PHE cc_start: 0.1092 (m-80) cc_final: 0.0852 (m-10) REVERT: V 205 MET cc_start: -0.1609 (tpt) cc_final: -0.2176 (tpt) REVERT: W 191 MET cc_start: 0.9194 (mmt) cc_final: 0.8924 (mmm) REVERT: W 237 ASN cc_start: 0.9129 (t0) cc_final: 0.8733 (t0) REVERT: Y 42 MET cc_start: 0.4207 (pmm) cc_final: 0.2899 (ptm) REVERT: Y 63 MET cc_start: -0.0926 (ptt) cc_final: -0.2561 (mtm) REVERT: Z 460 MET cc_start: 0.1105 (mmp) cc_final: -0.0968 (mtt) REVERT: Z 508 MET cc_start: 0.5509 (tpp) cc_final: 0.5308 (tpp) REVERT: a 50 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8786 (mt-10) REVERT: a 53 ARG cc_start: 0.9132 (tmt90) cc_final: 0.8437 (tmm-80) REVERT: a 105 GLU cc_start: 0.8958 (tp30) cc_final: 0.8751 (tp30) REVERT: a 120 MET cc_start: 0.8261 (mtt) cc_final: 0.7723 (mtt) REVERT: a 125 GLN cc_start: 0.9272 (mt0) cc_final: 0.8885 (mt0) REVERT: a 129 ARG cc_start: 0.9186 (tpt90) cc_final: 0.8803 (tpt90) REVERT: b 74 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8696 (mm-30) REVERT: b 98 TYR cc_start: 0.9153 (m-10) cc_final: 0.8893 (m-10) REVERT: c 36 LYS cc_start: 0.7699 (pttt) cc_final: 0.7492 (pttm) REVERT: d 62 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.9081 (mpp) REVERT: d 71 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8211 (tp30) REVERT: d 87 SER cc_start: 0.8258 (m) cc_final: 0.7839 (p) REVERT: d 88 THR cc_start: 0.9234 (p) cc_final: 0.8997 (p) REVERT: d 93 GLU cc_start: 0.8612 (mp0) cc_final: 0.7845 (mp0) REVERT: e 45 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.8977 (p) REVERT: e 110 CYS cc_start: 0.9418 (m) cc_final: 0.9163 (t) REVERT: e 123 ASP cc_start: 0.9220 (m-30) cc_final: 0.8920 (m-30) REVERT: f 53 GLU cc_start: 0.8747 (mp0) cc_final: 0.8270 (mp0) REVERT: f 84 MET cc_start: 0.8159 (mmm) cc_final: 0.7847 (tmm) REVERT: f 96 THR cc_start: 0.8717 (m) cc_final: 0.8492 (p) REVERT: g 56 GLU cc_start: 0.8894 (tt0) cc_final: 0.8605 (tt0) REVERT: g 64 GLU cc_start: 0.9168 (tt0) cc_final: 0.8614 (tp30) REVERT: g 92 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8935 (mp0) REVERT: g 99 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.7877 (mmm-85) REVERT: g 104 GLN cc_start: 0.9028 (mt0) cc_final: 0.8739 (mp10) REVERT: h 48 VAL cc_start: 0.9476 (m) cc_final: 0.9137 (m) REVERT: h 68 ASP cc_start: 0.9041 (t0) cc_final: 0.8469 (t0) REVERT: h 79 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8768 (mtm-85) REVERT: h 105 GLU cc_start: 0.7678 (tp30) cc_final: 0.7301 (tp30) REVERT: l 1469 MET cc_start: 0.1522 (mmp) cc_final: 0.1316 (mmt) REVERT: l 1526 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7385 (mmm) REVERT: l 1627 MET cc_start: 0.6222 (tpp) cc_final: 0.5385 (tpp) outliers start: 145 outliers final: 118 residues processed: 747 average time/residue: 0.6745 time to fit residues: 872.2550 Evaluate side-chains 765 residues out of total 7730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 630 time to evaluate : 5.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1210 TRP Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 1039 SER Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain O residue 652 LEU Chi-restraints excluded: chain Q residue 200 VAL Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 208 PHE Chi-restraints excluded: chain Q residue 232 VAL Chi-restraints excluded: chain Q residue 262 TYR Chi-restraints excluded: chain Q residue 510 MET Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 753 LEU Chi-restraints excluded: chain Q residue 762 GLN Chi-restraints excluded: chain Q residue 790 HIS Chi-restraints excluded: chain Q residue 881 TYR Chi-restraints excluded: chain R residue 563 ILE Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 123 GLN Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 154 ILE Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain X residue 243 LYS Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Z residue 444 ASP Chi-restraints excluded: chain Z residue 500 VAL Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 130 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 90 THR Chi-restraints excluded: chain d residue 108 LYS Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 55 GLN Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain l residue 1514 ILE Chi-restraints excluded: chain l residue 1526 MET Chi-restraints excluded: chain l residue 1694 ARG Chi-restraints excluded: chain l residue 2024 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 9 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 314 optimal weight: 3.9990 chunk 346 optimal weight: 0.5980 chunk 789 optimal weight: 20.0000 chunk 186 optimal weight: 3.9990 chunk 836 optimal weight: 0.9990 chunk 780 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 chunk 640 optimal weight: 50.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 55 GLN e 108 ASN ** l1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l1541 ASN ** l1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.120156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.080582 restraints weight = 301782.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.081447 restraints weight = 147115.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.082569 restraints weight = 95111.300| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 75528 Z= 0.227 Angle : 0.607 13.539 103343 Z= 0.314 Chirality : 0.041 0.295 11031 Planarity : 0.004 0.059 12367 Dihedral : 18.709 179.335 13721 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.04 % Allowed : 15.95 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.09), residues: 8646 helix: 1.47 (0.09), residues: 3591 sheet: -1.16 (0.17), residues: 865 loop : -1.32 (0.10), residues: 4190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V 130 HIS 0.005 0.001 HIS Q 659 PHE 0.022 0.001 PHE D 26 TYR 0.085 0.001 TYR f 88 ARG 0.017 0.000 ARG f 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31805.21 seconds wall clock time: 547 minutes 58.09 seconds (32878.09 seconds total)