Starting phenix.real_space_refine on Sat Jan 25 11:15:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eh1_48043/01_2025/9eh1_48043.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eh1_48043/01_2025/9eh1_48043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eh1_48043/01_2025/9eh1_48043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eh1_48043/01_2025/9eh1_48043.map" model { file = "/net/cci-nas-00/data/ceres_data/9eh1_48043/01_2025/9eh1_48043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eh1_48043/01_2025/9eh1_48043.cif" } resolution = 3.1 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= 0.014 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 365 5.49 5 Mg 1 5.21 5 S 316 5.16 5 C 43967 2.51 5 N 13089 2.21 5 O 14496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 72243 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: 3474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3474 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} 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: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 3725 Classifications: {'DNA': 181} Link IDs: {'rna3p': 180} 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: {'CIS': 1, 'PTRANS': 3, 'TRANS': 89} 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: 2149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2149 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain breaks: 1 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 78.755 106.324 153.684 1.00268.96 S ATOM 494 SG CYS A 74 75.766 103.937 153.121 1.00236.94 S ATOM 541 SG CYS A 81 79.045 103.385 151.153 1.00218.51 S ATOM 19805 SG CYS B1119 61.520 107.066 146.535 1.00197.54 S ATOM 19827 SG CYS B1122 63.224 110.100 144.995 1.00213.90 S ATOM 19942 SG CYS B1137 64.198 108.996 148.446 1.00225.05 S ATOM 19963 SG CYS B1140 60.797 110.644 147.755 1.00239.07 S ATOM 20929 SG CYS C 88 122.430 57.047 136.808 1.00139.52 S ATOM 20942 SG CYS C 90 123.772 57.729 139.137 1.00155.51 S ATOM 20999 SG CYS C 97 124.828 58.723 135.280 1.00128.15 S ATOM 28249 SG CYS I 17 99.289 169.138 87.878 1.00173.14 S ATOM 28273 SG CYS I 20 98.651 168.021 90.739 1.00165.56 S ATOM 28434 SG CYS I 39 95.893 167.845 90.420 1.00172.36 S ATOM 28811 SG CYS I 86 118.661 136.630 63.619 1.00158.31 S ATOM 28835 SG CYS I 89 122.376 136.536 63.846 1.00154.36 S ATOM 29039 SG CYS I 114 120.609 134.987 66.675 1.00157.50 S ATOM 29074 SG CYS I 119 120.294 138.784 66.108 1.00173.04 S ATOM 29184 SG CYS J 7 126.778 75.678 107.822 1.00112.56 S ATOM 29472 SG CYS J 44 126.268 74.684 104.046 1.00116.57 S ATOM 29478 SG CYS J 45 129.210 74.227 105.746 1.00117.48 S ATOM 59436 SG CYS Y 19 91.008 167.091 167.600 1.00814.21 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: 30.31, per 1000 atoms: 0.42 Number of scatterers: 72243 At special positions: 0 Unit cell: (218.9, 185.9, 335.5, 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 365 15.00 Mg 1 11.99 O 14496 8.00 N 13089 7.00 C 43967 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: 15.21 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 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " 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 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " 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 16998 Ramachandran restraints generated. 8499 Oldfield, 0 Emsley, 8499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14536 Finding SS restraints... Secondary structure from input PDB file: 322 helices and 89 sheets defined 44.8% alpha, 11.5% beta 179 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 22.14 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: 3.714A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.618A 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: 3.543A pdb=" N VAL A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.875A pdb=" N VAL A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 301 through 319 removed outlier: 4.294A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.822A 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 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.603A pdb=" N LEU A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.716A 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: 4.143A 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 525 removed outlier: 3.710A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.740A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.560A pdb=" N MET A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 4.046A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 3.579A 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: 3.871A pdb=" N ASN A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.961A 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 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.500A pdb=" N SER A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 785 Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.203A pdb=" N GLY A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.567A 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 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.598A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 4.068A 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: 3.509A 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 1079 Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix removed outlier: 3.890A 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 1150 removed outlier: 3.880A pdb=" N ASP A1150 " --> pdb=" O SER A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1162 removed outlier: 4.170A pdb=" N ASP A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 4.233A 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: 3.514A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.683A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1239 removed outlier: 3.586A pdb=" N PHE A1239 " --> pdb=" O ILE A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1295 removed outlier: 3.595A pdb=" N LEU A1285 " --> pdb=" O ASP A1281 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1349 removed outlier: 3.665A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A1349 " --> pdb=" O ARG A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.995A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A1367 " --> pdb=" O VAL A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 4.002A 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: 3.918A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) removed outlier: 3.771A 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 21 through 37 removed outlier: 4.205A pdb=" N ALA B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 removed outlier: 3.516A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 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 removed outlier: 3.560A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.708A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.769A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.555A pdb=" N ALA B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.850A 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 377 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: 3.684A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.884A 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: 3.613A 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: 3.610A 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: 3.675A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.684A 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 705 through 710 removed outlier: 3.997A pdb=" N ILE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 3.988A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 removed outlier: 3.542A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 772 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.275A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.844A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1016 removed outlier: 3.548A 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: 3.893A pdb=" N ILE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 3.694A 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: 3.506A 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 removed outlier: 3.596A pdb=" N TRP C 176 " --> pdb=" O HIS C 173 " (cutoff:3.500A) 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: 3.708A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.722A pdb=" N SER D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 70 removed outlier: 3.604A pdb=" N ARG D 70 " --> pdb=" O ASN D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.615A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.690A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.840A 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: 3.633A 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: 3.770A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 45 Processing helix chain 'E' and resid 83 through 96 removed outlier: 4.282A pdb=" N ILE E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.524A pdb=" N LYS E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.568A 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 163 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: 3.907A 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: 3.791A pdb=" N GLU J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 removed outlier: 4.016A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.622A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG J 47 " --> pdb=" O TYR J 43 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.999A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.506A pdb=" N GLU K 8 " --> pdb=" O PRO K 5 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.665A 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 39 through 53 removed outlier: 3.532A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.627A 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 292 Processing helix chain 'M' and resid 295 through 302 Processing helix chain 'M' and resid 309 through 325 removed outlier: 4.156A pdb=" N GLU M 314 " --> pdb=" O ASP M 310 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU M 315 " --> pdb=" O ASP M 311 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE M 325 " --> pdb=" O TYR M 321 " (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 391 through 429 Processing helix chain 'M' and resid 445 through 453 removed outlier: 4.023A pdb=" N GLU M 449 " --> pdb=" O THR M 445 " (cutoff:3.500A) Processing helix chain 'M' and resid 456 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 Processing helix chain 'M' and resid 599 through 607 Processing helix chain 'M' and resid 621 through 629 removed outlier: 4.298A pdb=" N LYS M 626 " --> pdb=" O LYS M 622 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP M 629 " --> pdb=" O ARG M 625 " (cutoff:3.500A) Processing helix chain 'M' and resid 632 through 637 removed outlier: 4.373A pdb=" N PHE M 637 " --> pdb=" O TYR M 633 " (cutoff:3.500A) Processing helix chain 'M' and resid 644 through 650 removed outlier: 3.881A pdb=" N LEU M 648 " --> pdb=" O PRO M 644 " (cutoff:3.500A) Processing helix chain 'M' and resid 651 through 664 removed outlier: 3.597A pdb=" N LYS M 655 " --> pdb=" O ASP M 651 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU M 664 " --> pdb=" O GLU M 660 " (cutoff:3.500A) Processing helix chain 'M' and resid 685 through 692 removed outlier: 4.080A pdb=" N ILE M 689 " --> pdb=" O TYR M 685 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS M 690 " --> pdb=" O PHE M 686 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN M 691 " --> pdb=" O GLU M 687 " (cutoff:3.500A) removed outlier: 3.579A 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: 3.957A pdb=" N MET M 725 " --> pdb=" O LEU M 721 " (cutoff:3.500A) Processing helix chain 'M' and resid 759 through 763 removed outlier: 3.620A pdb=" N GLN M 763 " --> pdb=" O PRO M 760 " (cutoff:3.500A) Processing helix chain 'M' and resid 830 through 843 removed outlier: 3.561A 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: 3.681A pdb=" N LEU M 892 " --> pdb=" O GLU M 888 " (cutoff:3.500A) removed outlier: 3.838A 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: 4.103A 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: 4.116A pdb=" N GLU M 947 " --> pdb=" O HIS M 943 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS M 948 " --> pdb=" O PRO M 944 " (cutoff:3.500A) Processing helix chain 'M' and resid 950 through 970 removed outlier: 3.931A pdb=" N LEU M 954 " --> pdb=" O VAL M 950 " (cutoff:3.500A) Processing helix chain 'M' and resid 974 through 979 removed outlier: 3.999A pdb=" N ALA M 978 " --> pdb=" O ASN M 974 " (cutoff:3.500A) removed outlier: 3.603A 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: 4.552A pdb=" N GLU M1064 " --> pdb=" O PRO M1060 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TRP M1065 " --> pdb=" O GLU M1061 " (cutoff:3.500A) Processing helix chain 'M' and resid 1086 through 1095 removed outlier: 3.509A 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: 4.131A 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: 3.717A pdb=" N LEU M1245 " --> pdb=" O PRO M1241 " (cutoff:3.500A) Processing helix chain 'M' and resid 1282 through 1287 removed outlier: 3.947A pdb=" N LEU M1286 " --> pdb=" O ARG M1282 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.502A 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: 3.620A pdb=" N LEU M1426 " --> pdb=" O PHE M1422 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU M1427 " --> pdb=" O ALA M1423 " (cutoff:3.500A) Processing helix chain 'M' and resid 1434 through 1439 removed outlier: 3.727A pdb=" N ASP M1439 " --> pdb=" O CYS M1435 " (cutoff:3.500A) Processing helix chain 'M' and resid 1439 through 1452 removed outlier: 3.788A pdb=" N GLU M1444 " --> pdb=" O ARG M1440 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU M1445 " --> pdb=" O LYS M1441 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU M1446 " --> pdb=" O LYS M1442 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU M1447 " --> pdb=" O LEU M1443 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE M1448 " --> pdb=" O GLU M1444 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS M1452 " --> pdb=" O ILE M1448 " (cutoff:3.500A) Processing helix chain 'M' and resid 1503 through 1512 removed outlier: 4.062A pdb=" N LEU M1507 " --> pdb=" O THR M1503 " (cutoff:3.500A) removed outlier: 3.866A 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: 3.641A 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: 3.632A 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: 3.723A pdb=" N GLU O 636 " --> pdb=" O LYS O 632 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS O 639 " --> pdb=" O GLU O 635 " (cutoff:3.500A) Processing helix chain 'O' and resid 648 through 656 removed outlier: 3.577A 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: 3.580A pdb=" N LYS O 675 " --> pdb=" O SER O 671 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET O 677 " --> pdb=" O SER O 673 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 36 removed outlier: 3.986A pdb=" N ILE Q 31 " --> pdb=" O GLY Q 27 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER Q 32 " --> pdb=" O ASP Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 53 removed outlier: 4.156A pdb=" N TRP Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE Q 45 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 64 removed outlier: 4.023A pdb=" N LEU Q 64 " --> pdb=" O PHE Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 69 removed outlier: 3.790A pdb=" N ARG Q 68 " --> pdb=" O GLU Q 65 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.541A pdb=" N GLN Q 82 " --> pdb=" O HIS Q 78 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR Q 88 " --> pdb=" O THR Q 84 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU Q 89 " --> pdb=" O CYS Q 85 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR Q 93 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL Q 94 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG Q 98 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 124 removed outlier: 3.687A pdb=" N LEU Q 109 " --> pdb=" O ASN Q 105 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN Q 112 " --> pdb=" O ASP Q 108 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU Q 116 " --> pdb=" O GLN Q 112 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR Q 118 " --> pdb=" O THR Q 114 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET Q 119 " --> pdb=" O LEU Q 115 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE Q 123 " --> pdb=" O MET Q 119 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE Q 124 " --> pdb=" O ALA Q 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 141 removed outlier: 3.663A pdb=" N PHE Q 137 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N CYS Q 138 " --> pdb=" O ARG Q 134 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU Q 139 " --> pdb=" O ALA Q 135 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 removed outlier: 3.547A pdb=" N PHE Q 154 " --> pdb=" O ALA Q 150 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL Q 155 " --> pdb=" O GLN Q 151 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU Q 156 " --> pdb=" O PHE Q 152 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN Q 157 " --> pdb=" O HIS Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 176 removed outlier: 3.712A pdb=" N GLY Q 168 " --> pdb=" O PRO Q 164 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS Q 169 " --> pdb=" O ALA Q 165 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA Q 170 " --> pdb=" O LEU Q 166 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS Q 171 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) removed outlier: 3.923A 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: 3.707A pdb=" N ARG Q 191 " --> pdb=" O LYS Q 187 " (cutoff:3.500A) removed outlier: 4.066A 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: 3.882A pdb=" N MET Q 204 " --> pdb=" O VAL Q 200 " (cutoff:3.500A) Processing helix chain 'Q' and resid 213 through 228 removed outlier: 3.842A pdb=" N LEU Q 219 " --> pdb=" O GLU Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 242 removed outlier: 4.074A pdb=" N LEU Q 238 " --> pdb=" O ALA Q 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 249 through 255 removed outlier: 3.836A 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: 3.734A pdb=" N PHE Q 281 " --> pdb=" O ASN Q 277 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS Q 282 " --> pdb=" O HIS Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 284 through 298 removed outlier: 3.878A pdb=" N VAL Q 288 " --> pdb=" O ASP Q 284 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU Q 293 " --> pdb=" O GLN Q 289 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS Q 294 " --> pdb=" O HIS Q 290 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN Q 298 " --> pdb=" O HIS Q 294 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 319 removed outlier: 3.787A pdb=" N GLN Q 305 " --> pdb=" O VAL Q 301 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN Q 319 " --> pdb=" O SER Q 315 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 336 removed outlier: 3.758A pdb=" N ALA Q 325 " --> pdb=" O ASP Q 321 " (cutoff:3.500A) removed outlier: 3.620A 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: 3.526A pdb=" N ALA Q 360 " --> pdb=" O ASP Q 356 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS Q 366 " --> pdb=" O GLN Q 362 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL Q 367 " --> pdb=" O CYS Q 363 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU Q 368 " --> pdb=" O PHE Q 364 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS Q 369 " --> pdb=" O GLU Q 365 " (cutoff:3.500A) Processing helix chain 'Q' and resid 373 through 383 removed outlier: 4.390A pdb=" N MET Q 378 " --> pdb=" O ASN Q 374 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS Q 379 " --> pdb=" O TYR Q 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE Q 380 " --> pdb=" O GLU Q 376 " (cutoff:3.500A) Processing helix chain 'Q' and resid 390 through 407 removed outlier: 4.910A pdb=" N ILE Q 396 " --> pdb=" O GLU Q 392 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU Q 406 " --> pdb=" O LYS Q 402 " (cutoff:3.500A) removed outlier: 3.832A 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 441 removed outlier: 3.725A pdb=" N ALA Q 430 " --> pdb=" O ASP Q 426 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG Q 439 " --> pdb=" O GLY Q 435 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU Q 441 " --> pdb=" O ALA Q 437 " (cutoff:3.500A) Processing helix chain 'Q' and resid 450 through 463 removed outlier: 3.795A pdb=" N LEU Q 454 " --> pdb=" O PRO Q 450 " (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: 3.779A pdb=" N GLU Q 526 " --> pdb=" O ASN Q 522 " (cutoff:3.500A) Processing helix chain 'Q' and resid 531 through 545 removed outlier: 3.627A pdb=" N GLY Q 538 " --> pdb=" O TYR Q 534 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS Q 544 " --> pdb=" O MET Q 540 " (cutoff:3.500A) Processing helix chain 'Q' and resid 548 through 561 removed outlier: 4.003A pdb=" N ASP Q 552 " --> pdb=" O TYR Q 548 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS Q 555 " --> pdb=" O SER Q 551 " (cutoff:3.500A) Processing helix chain 'Q' and resid 564 through 575 removed outlier: 3.809A pdb=" N HIS Q 575 " --> pdb=" O ILE Q 571 " (cutoff:3.500A) Processing helix chain 'Q' and resid 576 through 577 No H-bonds generated for 'chain 'Q' and resid 576 through 577' Processing helix chain 'Q' and resid 578 through 583 removed outlier: 3.903A pdb=" N TRP Q 581 " --> pdb=" O LYS Q 578 " (cutoff:3.500A) Proline residue: Q 583 - end of helix Processing helix chain 'Q' and resid 584 through 589 removed outlier: 4.149A pdb=" N PHE Q 588 " --> pdb=" O GLY Q 584 " (cutoff:3.500A) Processing helix chain 'Q' and resid 600 through 614 removed outlier: 3.930A 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 660 removed outlier: 3.917A pdb=" N ALA Q 650 " --> pdb=" O ASN Q 646 " (cutoff:3.500A) Processing helix chain 'Q' and resid 662 through 677 removed outlier: 4.649A pdb=" N ASP Q 668 " --> pdb=" O ARG Q 664 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL Q 669 " --> pdb=" O GLU Q 665 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN Q 672 " --> pdb=" O ASP Q 668 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL Q 673 " --> pdb=" O VAL Q 669 " (cutoff:3.500A) Processing helix chain 'Q' and resid 680 through 694 removed outlier: 3.744A pdb=" N TRP Q 684 " --> pdb=" O ILE Q 680 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU Q 685 " --> pdb=" O SER Q 681 " (cutoff:3.500A) Processing helix chain 'Q' and resid 697 through 709 removed outlier: 4.214A pdb=" N GLN Q 702 " --> pdb=" O ILE Q 698 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N MET Q 703 " --> pdb=" O SER Q 699 " (cutoff:3.500A) Processing helix chain 'Q' and resid 716 through 724 removed outlier: 3.585A 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: 3.697A pdb=" N VAL Q 746 " --> pdb=" O LYS Q 742 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA Q 747 " --> pdb=" O ALA Q 743 " (cutoff:3.500A) Processing helix chain 'Q' and resid 750 through 770 removed outlier: 3.774A pdb=" N MET Q 754 " --> pdb=" O ASP Q 750 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA Q 758 " --> pdb=" O MET Q 754 " (cutoff:3.500A) Processing helix chain 'Q' and resid 775 through 797 removed outlier: 3.594A pdb=" N VAL Q 779 " --> pdb=" O ASN Q 775 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL Q 783 " --> pdb=" O VAL Q 779 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS Q 784 " --> pdb=" O LEU Q 780 " (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: 4.259A pdb=" N ALA Q 829 " --> pdb=" O GLN Q 825 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG Q 830 " --> pdb=" O TYR Q 826 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU Q 848 " --> pdb=" O LYS Q 844 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU Q 883 " --> pdb=" O ALA Q 879 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS Q 886 " --> pdb=" O VAL Q 882 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN Q 887 " --> pdb=" O GLU Q 883 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR Q 892 " --> pdb=" O ILE Q 888 " (cutoff:3.500A) Processing helix chain 'R' and resid 355 through 360 removed outlier: 3.613A 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: 4.065A pdb=" N LEU R 477 " --> pdb=" O ASN R 473 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER R 478 " --> pdb=" O LYS R 474 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE R 479 " --> pdb=" O LYS R 475 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS R 480 " --> pdb=" O GLU R 476 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN R 484 " --> pdb=" O LYS R 480 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 503 removed outlier: 3.712A 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: 3.827A 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: 3.591A 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: 4.206A 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: 3.586A 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 69 removed outlier: 3.895A pdb=" N GLN V 69 " --> pdb=" O SER V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 107 removed outlier: 3.816A pdb=" N LEU V 107 " --> pdb=" O ALA V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 126 removed outlier: 4.130A pdb=" N HIS V 124 " --> pdb=" O SER V 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS V 126 " --> pdb=" O GLN V 123 " (cutoff:3.500A) Processing helix chain 'V' and resid 172 through 186 removed outlier: 3.717A pdb=" N THR V 177 " --> pdb=" O ASP V 173 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE V 183 " --> pdb=" O ILE V 179 " (cutoff:3.500A) 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: 3.642A pdb=" N ALA X 251 " --> pdb=" O LYS X 247 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE X 252 " --> pdb=" O ASN X 248 " (cutoff:3.500A) removed outlier: 3.724A 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 69 through 76 Processing helix chain 'Y' and resid 97 through 104 removed outlier: 3.848A pdb=" N LEU Y 101 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS Y 102 " --> pdb=" O VAL Y 98 " (cutoff:3.500A) removed outlier: 3.558A 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: 4.013A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 246 through 250 removed outlier: 4.486A pdb=" N TRP Z 250 " --> pdb=" O LEU Z 247 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 261 removed outlier: 4.146A 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: 3.624A 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 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 24 through 29 removed outlier: 3.728A pdb=" N GLN b 27 " --> pdb=" O ASP b 24 " (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: 3.624A 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: 3.558A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 73 removed outlier: 3.622A pdb=" N LEU c 65 " --> pdb=" O GLU c 61 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 104 through 123 removed outlier: 3.854A pdb=" N LYS d 108 " --> pdb=" O GLY d 104 " (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: 3.550A pdb=" N VAL e 89 " --> pdb=" O GLN e 85 " (cutoff:3.500A) Processing helix chain 'e' and resid 120 through 132 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: 4.043A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 94 removed outlier: 3.583A 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: 3.724A pdb=" N VAL g 30 " --> pdb=" O PRO g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 72 removed outlier: 4.596A 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: 3.559A pdb=" N ASN g 94 " --> pdb=" O ASP g 90 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS g 95 " --> pdb=" O GLU g 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 37 through 49 removed outlier: 3.765A pdb=" N GLN h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL h 48 " --> pdb=" O VAL h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 103 through 123 removed outlier: 3.588A pdb=" N THR h 122 " --> pdb=" O VAL h 118 " (cutoff:3.500A) Processing helix chain 'l' and resid 1520 through 1525 removed outlier: 3.814A pdb=" N LEU l1525 " --> pdb=" O LEU l1521 " (cutoff:3.500A) Processing helix chain 'l' and resid 1535 through 1539 removed outlier: 3.898A pdb=" N CYS l1539 " --> pdb=" O GLY l1536 " (cutoff:3.500A) Processing helix chain 'l' and resid 1585 through 1598 removed outlier: 3.796A pdb=" N PHE l1589 " --> pdb=" O ASP l1585 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS l1590 " --> pdb=" O HIS l1586 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA l1591 " --> pdb=" O LYS l1587 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS l1594 " --> pdb=" O LYS l1590 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG l1598 " --> pdb=" O LYS l1594 " (cutoff:3.500A) Processing helix chain 'l' and resid 1622 through 1627 removed outlier: 3.984A pdb=" N PHE l1626 " --> pdb=" O CYS l1623 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET l1627 " --> pdb=" O SER l1624 " (cutoff:3.500A) Processing helix chain 'l' and resid 2029 through 2039 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 193 removed outlier: 4.685A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.688A 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: 5.862A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET A 501 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 369 removed outlier: 3.805A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.177A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 556 Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 581 removed outlier: 5.709A pdb=" N ILE A 579 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR H 93 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 581 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA H 114 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 5.709A pdb=" N ILE A 579 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR H 93 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 581 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 3.917A 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: 6.556A 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: 3.689A pdb=" N THR A 878 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 6.845A 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 Processing sheet with id=AB5, first strand: chain 'A' and resid 1211 through 1216 removed outlier: 3.590A pdb=" N ALA A1174 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.941A pdb=" N VAL B 132 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 140 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 134 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 87 through 93 removed outlier: 5.460A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC1, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.764A pdb=" N GLU B 198 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS B 524 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 215 through 223 removed outlier: 3.964A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 237 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 531 through 532 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 572 through 577 removed outlier: 4.574A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 749 through 751 removed outlier: 3.703A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B 922 " --> pdb=" O GLN B 906 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET L 44 " --> pdb=" O VAL B 909 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AC8, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 3.629A pdb=" N ALA B 936 " --> pdb=" O GLN B1049 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 965 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 826 through 829 removed outlier: 4.124A pdb=" N GLU B 826 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 837 through 839 Processing sheet with id=AD2, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD3, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.719A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 121 through 122 removed outlier: 7.043A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.471A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 62 through 63 removed outlier: 3.921A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE E 73 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.720A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 2 through 13 removed outlier: 8.721A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 46 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.606A pdb=" N LEU G 67 " --> pdb=" O VAL G 58 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 107 through 109 removed outlier: 7.159A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 128 through 129 Processing sheet with id=AE3, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.783A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 38 through 39 removed outlier: 6.255A pdb=" N ARG H 27 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE H 15 " --> pdb=" O ARG H 27 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS H 146 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 24 through 29 Processing sheet with id=AE6, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE7, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE8, first strand: chain 'M' and resid 804 through 810 removed outlier: 5.529A pdb=" N VAL M 805 " --> pdb=" O ASN M 800 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ASN M 800 " --> pdb=" O VAL M 805 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL M 848 " --> pdb=" O GLU M 883 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 971 through 972 removed outlier: 5.785A pdb=" N VAL M 971 " --> pdb=" O LYS M1036 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'M' and resid 1237 through 1240 removed outlier: 6.635A pdb=" N ARG M1231 " --> pdb=" O VAL M1171 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL M1171 " --> pdb=" O ARG M1231 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG M1266 " --> pdb=" O THR M1280 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 1355 through 1359 removed outlier: 3.844A 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: 4.135A pdb=" N GLN M1379 " --> pdb=" O TRP M1371 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 1461 through 1464 removed outlier: 4.072A pdb=" N PHE M1461 " --> pdb=" O GLY M1475 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY M1475 " --> pdb=" O PHE M1461 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR M1488 " --> pdb=" O ARG M1495 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 5 through 7 removed outlier: 4.411A pdb=" N ILE Q 6 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU Q 19 " --> pdb=" O ILE Q 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'R' and resid 386 through 387 removed outlier: 3.988A pdb=" N VAL R 387 " --> pdb=" O ALA R 403 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA R 403 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N ARG R 421 " --> pdb=" O LYS R 413 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N LYS R 413 " --> pdb=" O ARG R 421 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASN R 423 " --> pdb=" O THR R 411 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL R 409 " --> pdb=" O GLY R 425 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 386 through 387 removed outlier: 3.988A pdb=" N VAL R 387 " --> pdb=" O ALA R 403 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA R 403 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU R 428 " --> pdb=" O ARG R 435 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG R 435 " --> pdb=" O LEU R 428 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 256 through 258 Processing sheet with id=AF8, first strand: chain 'U' and resid 376 through 377 removed outlier: 3.511A pdb=" N PHE V 312 " --> pdb=" O VAL U 376 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 494 through 495 removed outlier: 3.844A pdb=" N HIS U 494 " --> pdb=" O TYR U 460 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR U 460 " --> pdb=" O HIS U 494 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET U 448 " --> pdb=" O VAL U 459 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS U 451 " --> pdb=" O ARG U 439 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG U 439 " --> pdb=" O HIS U 451 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE U 440 " --> pdb=" O VAL V 204 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL V 204 " --> pdb=" O ILE U 440 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS U 442 " --> pdb=" O VAL V 202 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 221 through 222 removed outlier: 3.567A pdb=" N ARG V 331 " --> pdb=" O LYS V 292 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER V 333 " --> pdb=" O LYS V 290 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS V 290 " --> pdb=" O SER V 333 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 250 through 251 removed outlier: 3.664A pdb=" N GLN V 250 " --> pdb=" O VAL V 261 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 6 through 11 removed outlier: 4.889A pdb=" N ILE W 7 " --> pdb=" O ASP W 302 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP W 302 " --> pdb=" O ILE W 7 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 19 through 24 removed outlier: 6.132A pdb=" N VAL W 44 " --> pdb=" O SER W 59 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER W 59 " --> pdb=" O VAL W 44 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL W 46 " --> pdb=" O GLN W 57 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 67 through 72 removed outlier: 7.295A pdb=" N SER W 82 " --> pdb=" O VAL W 68 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL W 70 " --> pdb=" O ALA W 80 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA W 80 " --> pdb=" O VAL W 70 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE W 72 " --> pdb=" O ILE W 78 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE W 78 " --> pdb=" O ILE W 72 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER W 83 " --> pdb=" O HIS W 87 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N HIS W 87 " --> pdb=" O SER W 83 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS W 100 " --> pdb=" O LEU W 90 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASP W 92 " --> pdb=" O GLN W 98 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN W 98 " --> pdb=" O ASP W 92 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 120 through 124 removed outlier: 3.545A pdb=" N VAL W 130 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY W 134 " --> pdb=" O LYS W 140 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LYS W 140 " --> pdb=" O GLY W 134 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 151 through 156 removed outlier: 6.297A pdb=" N GLY W 166 " --> pdb=" O LEU W 152 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE W 154 " --> pdb=" O ALA W 164 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ALA W 164 " --> pdb=" O ILE W 154 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 195 through 198 removed outlier: 3.673A pdb=" N SER W 195 " --> pdb=" O ALA W 208 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR W 197 " --> pdb=" O VAL W 206 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL W 206 " --> pdb=" O THR W 197 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR W 207 " --> pdb=" O LYS W 215 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS W 215 " --> pdb=" O THR W 207 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE W 214 " --> pdb=" O THR W 227 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR W 227 " --> pdb=" O ILE W 214 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE W 216 " --> pdb=" O ALA W 225 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 235 through 240 removed outlier: 3.650A pdb=" N HIS W 268 " --> pdb=" O VAL W 258 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 13 through 15 Processing sheet with id=AH2, first strand: chain 'Y' and resid 57 through 58 Processing sheet with id=AH3, first strand: chain 'Y' and resid 61 through 63 Processing sheet with id=AH4, first strand: chain 'Z' and resid 224 through 229 removed outlier: 3.845A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Z' and resid 290 through 292 Processing sheet with id=AH6, first strand: chain 'Z' and resid 302 through 304 Processing sheet with id=AH7, first strand: chain 'Z' and resid 352 through 354 Processing sheet with id=AH8, first strand: chain 'Z' and resid 367 through 368 Processing sheet with id=AH9, first strand: chain 'Z' and resid 438 through 439 Processing sheet with id=AI1, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.545A pdb=" N VAL Z 478 " --> pdb=" O GLY Z 490 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY Z 490 " --> pdb=" O VAL Z 478 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU Z 491 " --> pdb=" O PHE Z 503 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.328A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL Z 551 " --> pdb=" O GLN Z 559 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN Z 541 " --> pdb=" O THR Z 576 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR Z 576 " --> pdb=" O GLN Z 541 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Z' and resid 622 through 625 removed outlier: 6.957A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY Z 612 " --> pdb=" O VAL Z 600 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL Z 600 " --> pdb=" O GLY Z 612 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.572A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'a' and resid 83 through 84 removed outlier: 7.197A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AI7, first strand: chain 'b' and resid 96 through 98 removed outlier: 6.426A pdb=" N THR b 96 " --> pdb=" O THR g 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.102A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AJ1, first strand: chain 'c' and resid 101 through 102 removed outlier: 6.867A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.912A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AJ4, first strand: chain 'g' and resid 42 through 43 removed outlier: 6.933A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AJ6, first strand: chain 'l' and resid 1554 through 1558 removed outlier: 5.755A pdb=" N LEU l1556 " --> pdb=" O GLY l1563 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY l1563 " --> pdb=" O LEU l1556 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU l1558 " --> pdb=" O GLY l1561 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'l' and resid 1575 through 1578 removed outlier: 6.877A pdb=" N PHE l1650 " --> pdb=" O VAL l1576 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLU l1578 " --> pdb=" O VAL l1648 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL l1648 " --> pdb=" O GLU l1578 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'l' and resid 1582 through 1583 2831 hydrogen bonds defined for protein. 8061 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 454 hydrogen bonds 908 hydrogen bond angles 0 basepair planarities 179 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 50.15 Time building geometry restraints manager: 17.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.55: 73046 1.55 - 1.89: 1233 1.89 - 2.23: 0 2.23 - 2.57: 0 2.57 - 2.91: 1 Bond restraints: 74280 Sorted by residual: bond pdb=" C GLN e 76 " pdb=" N PHE e 78 " ideal model delta sigma weight residual 1.329 2.914 -1.585 1.40e-02 5.10e+03 1.28e+04 bond pdb=" OG1 TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" OG1 TPO Z 775 " pdb=" P TPO Z 775 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" O2P TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+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 1.67e+01 ... (remaining 74275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.98: 101495 12.98 - 25.97: 37 25.97 - 38.95: 0 38.95 - 51.93: 1 51.93 - 64.92: 1 Bond angle restraints: 101534 Sorted by residual: angle pdb=" O GLN e 76 " pdb=" C GLN e 76 " pdb=" N PHE e 78 " ideal model delta sigma weight residual 122.55 76.14 46.41 1.13e+00 7.83e-01 1.69e+03 angle pdb=" O3' DT N 109 " pdb=" P DT N 110 " pdb=" OP1 DT N 110 " ideal model delta sigma weight residual 108.00 43.08 64.92 3.00e+00 1.11e-01 4.68e+02 angle pdb=" C GLN e 76 " pdb=" N PHE e 78 " pdb=" CA PHE e 78 " ideal model delta sigma weight residual 121.70 146.59 -24.89 1.80e+00 3.09e-01 1.91e+02 angle pdb=" CA GLN e 76 " pdb=" C GLN e 76 " pdb=" N PHE e 78 " ideal model delta sigma weight residual 115.25 126.76 -11.51 1.34e+00 5.57e-01 7.37e+01 angle pdb=" O3' DT T -86 " pdb=" P DT T -85 " pdb=" OP1 DT T -85 " ideal model delta sigma weight residual 108.00 129.24 -21.24 3.00e+00 1.11e-01 5.01e+01 ... (remaining 101529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 41504 35.29 - 70.57: 1424 70.57 - 105.86: 41 105.86 - 141.14: 0 141.14 - 176.43: 10 Dihedral angle restraints: 42979 sinusoidal: 19594 harmonic: 23385 Sorted by residual: 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 35.47 -70.47 1 8.00e+00 1.56e-02 9.99e+01 dihedral pdb=" C5' A P 16 " pdb=" C4' A P 16 " pdb=" C3' A P 16 " pdb=" O3' A P 16 " ideal model delta sinusoidal sigma weight residual 147.00 77.68 69.32 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 81.12 65.88 1 8.00e+00 1.56e-02 8.87e+01 ... (remaining 42976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.238: 10450 0.238 - 0.476: 306 0.476 - 0.715: 44 0.715 - 0.953: 1 0.953 - 1.191: 1 Chirality restraints: 10802 Sorted by residual: chirality pdb=" P DT N 110 " pdb=" OP1 DT N 110 " pdb=" OP2 DT N 110 " pdb=" O5' DT N 110 " both_signs ideal model delta sigma weight residual True 2.35 1.15 1.19 2.00e-01 2.50e+01 3.55e+01 chirality pdb=" C1' A P 16 " pdb=" O4' A P 16 " pdb=" C2' A P 16 " pdb=" N9 A P 16 " both_signs ideal model delta sigma weight residual False 2.44 1.56 0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" P DC T -98 " pdb=" OP1 DC T -98 " pdb=" OP2 DC T -98 " pdb=" O5' DC T -98 " both_signs ideal model delta sigma weight residual True 2.35 -3.00 -0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 10799 not shown) Planarity restraints: 12198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN e 76 " 0.179 2.00e-02 2.50e+03 2.32e-01 5.40e+02 pdb=" C GLN e 76 " -0.393 2.00e-02 2.50e+03 pdb=" O GLN e 76 " 0.164 2.00e-02 2.50e+03 pdb=" N PHE e 78 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A P 18 " 0.042 2.00e-02 2.50e+03 1.89e-02 9.85e+00 pdb=" N9 A P 18 " -0.043 2.00e-02 2.50e+03 pdb=" C8 A P 18 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A P 18 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A P 18 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A P 18 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A P 18 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A P 18 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A P 18 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A P 18 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A P 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 6 " -0.037 2.00e-02 2.50e+03 1.85e-02 7.69e+00 pdb=" N1 DC N 6 " 0.037 2.00e-02 2.50e+03 pdb=" C2 DC N 6 " 0.005 2.00e-02 2.50e+03 pdb=" O2 DC N 6 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DC N 6 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC N 6 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC N 6 " -0.012 2.00e-02 2.50e+03 pdb=" C5 DC N 6 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC N 6 " 0.008 2.00e-02 2.50e+03 ... (remaining 12195 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 344 2.41 - 3.03: 47796 3.03 - 3.66: 108332 3.66 - 4.28: 163027 4.28 - 4.90: 261096 Nonbonded interactions: 580595 Sorted by model distance: nonbonded pdb=" OH TYR Q 353 " pdb=" O ARG V 57 " model vdw 1.788 3.040 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 1.823 2.170 nonbonded pdb=" OH TYR Q 534 " pdb=" OE1 GLU Q 556 " model vdw 1.874 3.040 nonbonded pdb=" OD1 ASP E 67 " pdb=" OG1 THR E 69 " model vdw 1.908 3.040 nonbonded pdb=" OD1 ASP B 891 " pdb=" OG SER B 893 " model vdw 1.923 3.040 ... (remaining 580590 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.410 Construct map_model_manager: 0.100 Extract box with map and model: 2.580 Check model and map are aligned: 0.450 Set scattering table: 0.550 Process input model: 174.460 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.390 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: 0.030 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 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 : 0.008 1.585 74280 Z= 0.427 Angle : 1.066 64.918 101534 Z= 0.471 Chirality : 0.085 1.191 10802 Planarity : 0.004 0.232 12198 Dihedral : 14.618 176.429 28443 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Rotamer: Outliers : 0.53 % Allowed : 3.60 % Favored : 95.87 % 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: -0.90 (0.09), residues: 8499 helix: 1.36 (0.09), residues: 3359 sheet: -2.16 (0.18), residues: 798 loop : -1.96 (0.09), residues: 4342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 679 HIS 0.008 0.001 HIS C 66 PHE 0.015 0.001 PHE B 805 TYR 0.015 0.001 TYR K 81 ARG 0.005 0.000 ARG b 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16998 Ramachandran restraints generated. 8499 Oldfield, 0 Emsley, 8499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16998 Ramachandran restraints generated. 8499 Oldfield, 0 Emsley, 8499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 697 time to evaluate : 6.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8175 (mp0) cc_final: 0.7458 (pt0) REVERT: A 58 MET cc_start: 0.8175 (tpp) cc_final: 0.7607 (tpp) REVERT: A 70 ARG cc_start: 0.8333 (mmt180) cc_final: 0.7982 (tpp-160) REVERT: A 266 MET cc_start: -0.0065 (tmm) cc_final: -0.0854 (tpp) REVERT: A 320 ASN cc_start: 0.8001 (t0) cc_final: 0.7595 (p0) REVERT: A 347 GLU cc_start: 0.8258 (mp0) cc_final: 0.7893 (tm-30) REVERT: A 388 MET cc_start: 0.6681 (mtt) cc_final: 0.6424 (mtt) REVERT: A 501 MET cc_start: 0.6941 (mtp) cc_final: 0.6248 (mtm) REVERT: A 552 ASP cc_start: 0.7938 (p0) cc_final: 0.7563 (p0) REVERT: A 900 SER cc_start: 0.8899 (m) cc_final: 0.8632 (t) REVERT: A 1101 GLN cc_start: 0.8335 (mt0) cc_final: 0.7853 (mm110) REVERT: B 108 MET cc_start: 0.8116 (ptm) cc_final: 0.7911 (ptm) REVERT: B 508 MET cc_start: 0.8375 (mmt) cc_final: 0.7783 (mmt) REVERT: B 840 MET cc_start: 0.5619 (ttp) cc_final: 0.5135 (ttm) REVERT: B 1017 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.7960 (t0) REVERT: B 1151 MET cc_start: 0.8442 (ptp) cc_final: 0.7893 (ptm) REVERT: B 1157 LEU cc_start: 0.8616 (tt) cc_final: 0.7708 (tp) REVERT: B 1161 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7590 (mp0) REVERT: B 1163 MET cc_start: 0.7010 (mtm) cc_final: 0.6743 (mtp) REVERT: D 94 LYS cc_start: 0.9290 (mmmt) cc_final: 0.8942 (tttt) REVERT: F 115 TYR cc_start: 0.8143 (p90) cc_final: 0.7536 (p90) REVERT: G 3 TYR cc_start: 0.8604 (m-80) cc_final: 0.7791 (m-80) REVERT: G 83 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8216 (mt-10) REVERT: G 106 CYS cc_start: 0.4840 (m) cc_final: 0.4627 (m) REVERT: G 165 ASP cc_start: 0.8135 (t70) cc_final: 0.7934 (t70) REVERT: I 56 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7672 (m-40) REVERT: M 1346 MET cc_start: 0.5244 (ptt) cc_final: 0.4712 (ppp) REVERT: M 1384 ARG cc_start: 0.2646 (mtt180) cc_final: 0.1486 (mtm180) REVERT: Q 552 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7083 (t0) REVERT: Q 653 ILE cc_start: 0.7369 (mt) cc_final: 0.7097 (mm) REVERT: Q 707 CYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7159 (p) REVERT: U 378 LEU cc_start: 0.1686 (tp) cc_final: 0.1303 (mt) REVERT: V 67 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8680 (tm-30) REVERT: V 69 GLN cc_start: 0.5765 (pt0) cc_final: 0.5058 (pp30) REVERT: V 128 VAL cc_start: 0.6561 (t) cc_final: 0.6312 (p) REVERT: V 137 ILE cc_start: 0.5967 (mp) cc_final: 0.5109 (mp) REVERT: Y 64 MET cc_start: 0.3422 (mtm) cc_final: 0.3022 (mtt) REVERT: Z 260 MET cc_start: 0.5672 (mmt) cc_final: 0.5468 (mtt) REVERT: Z 460 MET cc_start: 0.3124 (mtp) cc_final: 0.1801 (ptt) REVERT: Z 635 MET cc_start: -0.3405 (ttt) cc_final: -0.3734 (ttm) REVERT: a 59 GLU cc_start: 0.4456 (pt0) cc_final: 0.3453 (pm20) REVERT: a 93 GLN cc_start: 0.4106 (tt0) cc_final: 0.3047 (tp40) REVERT: b 78 ARG cc_start: 0.1866 (mtm-85) cc_final: 0.1650 (mtt180) REVERT: b 84 MET cc_start: 0.8149 (mmm) cc_final: 0.7946 (ppp) REVERT: b 93 GLN cc_start: -0.3566 (mp-120) cc_final: -0.3810 (mm-40) REVERT: c 38 ASN cc_start: 0.7144 (m110) cc_final: 0.2786 (p0) REVERT: e 51 ILE cc_start: 0.9103 (mt) cc_final: 0.8731 (mt) REVERT: e 96 SER cc_start: 0.9199 (m) cc_final: 0.8984 (p) REVERT: e 125 GLN cc_start: 0.8556 (mt0) cc_final: 0.8339 (mm-40) REVERT: f 49 LEU cc_start: 0.9233 (mt) cc_final: 0.8971 (tp) REVERT: f 63 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8375 (mm-30) REVERT: f 79 LYS cc_start: 0.8204 (mmtm) cc_final: 0.7983 (tptt) REVERT: g 62 ILE cc_start: 0.9179 (mm) cc_final: 0.8975 (mt) REVERT: h 119 THR cc_start: 0.9183 (m) cc_final: 0.8961 (p) outliers start: 35 outliers final: 7 residues processed: 729 average time/residue: 0.7219 time to fit residues: 885.0724 Evaluate side-chains 402 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 391 time to evaluate : 6.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 1017 ASP Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain I residue 56 ASN 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 707 CYS Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain W residue 272 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 749 optimal weight: 0.0970 chunk 672 optimal weight: 0.8980 chunk 373 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 453 optimal weight: 5.9990 chunk 359 optimal weight: 7.9990 chunk 695 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 chunk 422 optimal weight: 7.9990 chunk 517 optimal weight: 9.9990 chunk 805 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 288 ASN A 341 GLN A 387 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN A 780 ASN A 791 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN A 991 GLN ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN A1457 ASN A1462 GLN B 98 HIS B 227 ASN B 319 ASN B 420 GLN B 452 ASN B 471 ASN B 725 GLN B 790 GLN B1071 ASN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS C 114 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 56 ASN I 98 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1366 HIS Q 38 HIS ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 ASN Q 129 ASN ** Q 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 268 ASN ** Q 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 349 GLN Q 407 GLN ** Q 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 502 ASN Q 527 HIS Q 529 ASN Q 616 HIS Q 628 HIS ** Q 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 734 GLN Q 775 ASN R 430 HIS R 490 GLN ** R 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 69 GLN V 124 HIS V 187 GLN ** W 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 273 HIS Z 446 ASN Z 545 GLN b 93 GLN c 24 GLN d 49 HIS d 109 HIS ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 84 ASN h 95 GLN l1535 ASN l1549 HIS l1603 HIS Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.093114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.071168 restraints weight = 499330.323| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 7.93 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3824 r_free = 0.3824 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 442 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3824 r_free = 0.3824 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 442 | |-----------------------------------------------------------------------------| r_final: 0.3824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 74280 Z= 0.237 Angle : 0.651 27.437 101534 Z= 0.340 Chirality : 0.048 1.991 10802 Planarity : 0.004 0.062 12198 Dihedral : 18.359 179.113 13347 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.11 % Rotamer: Outliers : 1.17 % Allowed : 7.21 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.07 % 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: -0.67 (0.09), residues: 8501 helix: 1.36 (0.09), residues: 3452 sheet: -1.83 (0.17), residues: 865 loop : -1.74 (0.09), residues: 4184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 570 HIS 0.008 0.001 HIS J 52 PHE 0.024 0.002 PHE H 150 TYR 0.023 0.002 TYR H 115 ARG 0.007 0.001 ARG W 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 435 time to evaluate : 6.342 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: A 45 GLU cc_start: 0.8432 (mp0) cc_final: 0.7973 (tt0) REVERT: A 58 MET cc_start: 0.8309 (tpp) cc_final: 0.8013 (mmm) REVERT: A 104 MET cc_start: 0.6845 (ttm) cc_final: 0.6258 (tpt) REVERT: A 266 MET cc_start: 0.0693 (tmm) cc_final: -0.0012 (tpp) REVERT: A 320 ASN cc_start: 0.7626 (t0) cc_final: 0.7377 (p0) REVERT: A 355 MET cc_start: 0.8349 (mmm) cc_final: 0.7605 (mpp) REVERT: A 457 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7964 (mt) REVERT: A 469 MET cc_start: 0.8203 (mtm) cc_final: 0.7781 (mtt) REVERT: A 501 MET cc_start: 0.6904 (mtp) cc_final: 0.6232 (mtm) REVERT: A 535 MET cc_start: 0.7293 (mtp) cc_final: 0.7026 (mtp) REVERT: A 552 ASP cc_start: 0.7865 (p0) cc_final: 0.7627 (p0) REVERT: A 900 SER cc_start: 0.8969 (m) cc_final: 0.8657 (t) REVERT: A 1086 MET cc_start: 0.7981 (mmm) cc_final: 0.7334 (mmp) REVERT: A 1101 GLN cc_start: 0.8227 (mt0) cc_final: 0.7793 (mm110) REVERT: A 1412 MET cc_start: 0.8125 (ptm) cc_final: 0.7130 (ppp) REVERT: B 108 MET cc_start: 0.7751 (ptm) cc_final: 0.7503 (ptp) REVERT: B 200 MET cc_start: 0.7633 (mmm) cc_final: 0.7408 (mmm) REVERT: B 508 MET cc_start: 0.8096 (mmt) cc_final: 0.7557 (mmt) REVERT: B 584 MET cc_start: 0.8458 (tpp) cc_final: 0.8048 (tpp) REVERT: B 840 MET cc_start: 0.5398 (ttp) cc_final: 0.5188 (ttp) REVERT: B 1151 MET cc_start: 0.8028 (ptp) cc_final: 0.7397 (ptm) REVERT: B 1157 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.7747 (tp) REVERT: B 1161 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7672 (mp0) REVERT: B 1172 MET cc_start: 0.7762 (mmm) cc_final: 0.7300 (mmm) REVERT: E 72 MET cc_start: 0.7836 (ptm) cc_final: 0.7579 (mtm) REVERT: F 115 TYR cc_start: 0.8074 (p90) cc_final: 0.7349 (p90) REVERT: H 37 MET cc_start: 0.7472 (mtp) cc_final: 0.6940 (mtm) REVERT: H 145 MET cc_start: 0.7818 (ptm) cc_final: 0.7561 (ptm) REVERT: K 14 GLU cc_start: 0.8014 (mp0) cc_final: 0.7809 (pm20) REVERT: L 44 MET cc_start: 0.7869 (mtp) cc_final: 0.7475 (mmt) REVERT: M 1346 MET cc_start: 0.5161 (ptt) cc_final: 0.4790 (ppp) REVERT: Q 510 MET cc_start: 0.7067 (tmm) cc_final: 0.6675 (tmm) REVERT: Q 540 MET cc_start: 0.6601 (ttm) cc_final: 0.6294 (ttm) REVERT: Q 703 MET cc_start: 0.7260 (mtp) cc_final: 0.6838 (ttt) REVERT: Q 707 CYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7255 (p) REVERT: R 464 MET cc_start: 0.6031 (ptp) cc_final: 0.5161 (pmm) REVERT: V 67 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8854 (tm-30) REVERT: V 69 GLN cc_start: 0.6653 (OUTLIER) cc_final: 0.6186 (pp30) REVERT: V 128 VAL cc_start: 0.6466 (t) cc_final: 0.6206 (p) REVERT: V 137 ILE cc_start: 0.6572 (mp) cc_final: 0.6146 (mm) REVERT: W 191 MET cc_start: 0.8767 (mmm) cc_final: 0.8478 (ttm) REVERT: Z 260 MET cc_start: 0.5249 (mmt) cc_final: 0.5027 (mtp) REVERT: Z 460 MET cc_start: 0.3439 (mtp) cc_final: 0.2418 (ptt) REVERT: Z 635 MET cc_start: -0.3245 (ttt) cc_final: -0.3456 (ttm) REVERT: a 50 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8712 (mp0) REVERT: c 64 GLU cc_start: 0.8598 (tp30) cc_final: 0.8393 (tp30) REVERT: d 59 MET cc_start: 0.8228 (mmm) cc_final: 0.7949 (tpp) REVERT: e 90 MET cc_start: 0.8509 (mmm) cc_final: 0.8197 (mmm) REVERT: e 96 SER cc_start: 0.9247 (m) cc_final: 0.8988 (p) REVERT: e 125 GLN cc_start: 0.8586 (mt0) cc_final: 0.8332 (mm-40) REVERT: f 49 LEU cc_start: 0.9403 (mt) cc_final: 0.8985 (tt) REVERT: f 63 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8324 (mm-30) REVERT: f 79 LYS cc_start: 0.8324 (mmtm) cc_final: 0.8016 (tptt) REVERT: h 105 GLU cc_start: 0.8226 (mp0) cc_final: 0.7945 (mp0) REVERT: l 1497 MET cc_start: 0.7627 (tpp) cc_final: 0.6464 (mmm) outliers start: 77 outliers final: 34 residues processed: 491 average time/residue: 0.6739 time to fit residues: 577.8401 Evaluate side-chains 407 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 368 time to evaluate : 6.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 1539 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain O residue 648 SER Chi-restraints excluded: chain O residue 671 SER Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain Q residue 479 ASP Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 734 GLN Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain Q residue 857 LEU Chi-restraints excluded: chain Q residue 865 LEU Chi-restraints excluded: chain R residue 495 ILE Chi-restraints excluded: chain R residue 563 ILE Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain X residue 241 THR Chi-restraints excluded: chain Z residue 451 MET Chi-restraints excluded: chain a residue 50 GLU Chi-restraints excluded: chain b residue 90 LEU Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain c residue 74 LYS Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain l residue 1463 CYS Chi-restraints excluded: chain l residue 1602 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 270 optimal weight: 4.9990 chunk 456 optimal weight: 0.9990 chunk 457 optimal weight: 9.9990 chunk 583 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 875 optimal weight: 10.0000 chunk 665 optimal weight: 8.9990 chunk 614 optimal weight: 8.9990 chunk 598 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 513 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 700 GLN A 740 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 HIS ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN A1332 GLN B 387 HIS B 452 ASN B 537 GLN B 582 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 HIS B1053 HIS ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN H 29 HIS I 60 HIS I 98 GLN M1366 HIS O 667 HIS ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 289 GLN Q 305 GLN ** Q 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 442 GLN ** Q 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 561 ASN ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 609 ASN Q 689 HIS Q 706 ASN ** Q 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 756 ASN ** Q 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 834 GLN ** Q 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 567 ASN ** R 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 70 HIS ** V 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 184 HIS ** W 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 337 GLN ** Z 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 24 GLN ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 68 GLN ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l1535 ASN l1601 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.088003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.064760 restraints weight = 479945.957| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 7.98 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.135 74280 Z= 0.533 Angle : 0.848 27.448 101534 Z= 0.445 Chirality : 0.053 2.002 10802 Planarity : 0.006 0.083 12198 Dihedral : 19.142 177.369 13333 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.15 % Rotamer: Outliers : 2.27 % Allowed : 9.06 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.07 % Twisted Proline : 0.29 % 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: -1.35 (0.09), residues: 8501 helix: 0.47 (0.09), residues: 3453 sheet: -1.69 (0.17), residues: 856 loop : -1.94 (0.09), residues: 4192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 27 HIS 0.017 0.002 HIS A 839 PHE 0.029 0.003 PHE B 805 TYR 0.038 0.003 TYR L 41 ARG 0.020 0.001 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 396 time to evaluate : 6.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7074 (ttm) cc_final: 0.6499 (tpp) REVERT: A 266 MET cc_start: 0.0505 (tmm) cc_final: -0.0287 (tpp) REVERT: A 320 ASN cc_start: 0.7549 (t0) cc_final: 0.7247 (p0) REVERT: A 347 GLU cc_start: 0.8325 (mp0) cc_final: 0.8056 (tm-30) REVERT: A 355 MET cc_start: 0.8441 (mmm) cc_final: 0.8014 (mpp) REVERT: A 535 MET cc_start: 0.7694 (mtp) cc_final: 0.7479 (mtp) REVERT: A 561 MET cc_start: 0.8149 (mtm) cc_final: 0.7619 (mtt) REVERT: A 943 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8211 (mm) REVERT: A 1102 MET cc_start: 0.7254 (mmm) cc_final: 0.6239 (mmm) REVERT: A 1135 LYS cc_start: 0.8618 (ttmt) cc_final: 0.8408 (mtmt) REVERT: B 200 MET cc_start: 0.8262 (mmm) cc_final: 0.7783 (mmm) REVERT: B 508 MET cc_start: 0.7759 (mmt) cc_final: 0.7381 (mmt) REVERT: B 529 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.6480 (mpt) REVERT: B 677 MET cc_start: 0.8621 (tpp) cc_final: 0.8355 (tpp) REVERT: B 702 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.5017 (tpp) REVERT: B 840 MET cc_start: 0.5348 (ttp) cc_final: 0.4911 (ttm) REVERT: B 1151 MET cc_start: 0.8126 (ptp) cc_final: 0.7846 (ptp) REVERT: B 1172 MET cc_start: 0.8079 (mmm) cc_final: 0.7676 (mmm) REVERT: C 61 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7986 (t0) REVERT: D 84 ARG cc_start: 0.9352 (mtp85) cc_final: 0.9144 (mtp180) REVERT: H 37 MET cc_start: 0.8166 (mtp) cc_final: 0.7622 (mtm) REVERT: H 145 MET cc_start: 0.7755 (ptm) cc_final: 0.7346 (ptm) REVERT: K 14 GLU cc_start: 0.8038 (mp0) cc_final: 0.7799 (pm20) REVERT: L 15 MET cc_start: 0.7582 (tpp) cc_final: 0.7335 (tmm) REVERT: L 44 MET cc_start: 0.8207 (mtp) cc_final: 0.7563 (mmm) REVERT: M 1346 MET cc_start: 0.4948 (ptt) cc_final: 0.4627 (ppp) REVERT: M 1347 MET cc_start: -0.3991 (ptt) cc_final: -0.4319 (ptt) REVERT: Q 510 MET cc_start: 0.7609 (tmm) cc_final: 0.7205 (tmm) REVERT: Q 540 MET cc_start: 0.7324 (ttm) cc_final: 0.6996 (ttm) REVERT: Q 703 MET cc_start: 0.7837 (mtp) cc_final: 0.7346 (ttt) REVERT: Q 755 PHE cc_start: 0.7091 (t80) cc_final: 0.6881 (t80) REVERT: R 464 MET cc_start: 0.6400 (ptp) cc_final: 0.5414 (pmm) REVERT: V 122 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8182 (tm-30) REVERT: V 132 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7043 (mtm180) REVERT: W 191 MET cc_start: 0.8801 (mmm) cc_final: 0.8498 (tpp) REVERT: W 277 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7820 (p) REVERT: Z 460 MET cc_start: 0.3133 (mtp) cc_final: 0.1967 (ptt) REVERT: Z 635 MET cc_start: -0.2462 (ttt) cc_final: -0.2749 (ttm) REVERT: d 105 GLU cc_start: 0.8441 (tp30) cc_final: 0.8236 (tp30) REVERT: e 90 MET cc_start: 0.8760 (mmm) cc_final: 0.8472 (mmm) REVERT: e 125 GLN cc_start: 0.8750 (mt0) cc_final: 0.8480 (mm-40) REVERT: f 43 VAL cc_start: 0.9340 (t) cc_final: 0.9133 (m) REVERT: f 63 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8473 (tp30) REVERT: f 79 LYS cc_start: 0.8191 (mmtm) cc_final: 0.7978 (tptt) REVERT: h 62 MET cc_start: 0.8864 (mmm) cc_final: 0.8608 (mmp) REVERT: h 105 GLU cc_start: 0.8610 (mp0) cc_final: 0.8295 (mp0) REVERT: l 1526 MET cc_start: 0.8512 (mmm) cc_final: 0.8223 (mmm) outliers start: 149 outliers final: 77 residues processed: 521 average time/residue: 0.6944 time to fit residues: 641.5553 Evaluate side-chains 431 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 349 time to evaluate : 6.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 42 TYR Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 115 TYR Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain M residue 815 THR Chi-restraints excluded: chain M residue 1381 VAL Chi-restraints excluded: chain O residue 648 SER Chi-restraints excluded: chain O residue 652 LEU Chi-restraints excluded: chain O residue 671 SER Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain Q residue 479 ASP Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain Q residue 837 GLU Chi-restraints excluded: chain Q residue 857 LEU Chi-restraints excluded: chain Q residue 865 LEU Chi-restraints excluded: chain R residue 495 ILE Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 73 ASP Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 277 VAL Chi-restraints excluded: chain X residue 241 THR Chi-restraints excluded: chain a residue 50 GLU Chi-restraints excluded: chain b residue 87 VAL Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain c residue 74 LYS Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain f residue 96 THR Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain h residue 57 LYS Chi-restraints excluded: chain l residue 1463 CYS Chi-restraints excluded: chain l residue 1602 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 381 optimal weight: 30.0000 chunk 497 optimal weight: 7.9990 chunk 660 optimal weight: 0.6980 chunk 506 optimal weight: 6.9990 chunk 317 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 286 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 450 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 A 740 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1163 HIS B 387 HIS ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 GLN C 66 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN I 41 ASN I 100 HIS M1366 HIS O 667 HIS ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 245 ASN ** Q 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 305 GLN ** Q 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 734 GLN Q 827 HIS Q 880 GLN Q 887 ASN ** V 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 ASN a 93 GLN ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l1629 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.090199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.066261 restraints weight = 480538.489| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 8.78 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 74280 Z= 0.177 Angle : 0.589 27.122 101534 Z= 0.308 Chirality : 0.046 2.038 10802 Planarity : 0.004 0.101 12198 Dihedral : 19.056 178.744 13330 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.26 % Favored : 95.71 % Rotamer: Outliers : 1.59 % Allowed : 10.45 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.07 % Twisted Proline : 0.29 % 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: -0.73 (0.09), residues: 8501 helix: 1.12 (0.09), residues: 3449 sheet: -1.63 (0.17), residues: 896 loop : -1.64 (0.09), residues: 4156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 49 HIS 0.009 0.001 HIS I 100 PHE 0.019 0.001 PHE Z 200 TYR 0.027 0.001 TYR b 88 ARG 0.013 0.000 ARG B 608 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 380 time to evaluate : 6.283 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: A 104 MET cc_start: 0.7029 (ttm) cc_final: 0.6543 (tpt) REVERT: A 266 MET cc_start: -0.0056 (tmm) cc_final: -0.0697 (tpp) REVERT: A 347 GLU cc_start: 0.8175 (mp0) cc_final: 0.7832 (tm-30) REVERT: A 355 MET cc_start: 0.8254 (mmm) cc_final: 0.7657 (mpp) REVERT: A 457 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7823 (tt) REVERT: A 469 MET cc_start: 0.8372 (mtt) cc_final: 0.7925 (mtt) REVERT: A 535 MET cc_start: 0.7498 (mtp) cc_final: 0.7278 (mtp) REVERT: A 868 MET cc_start: 0.7958 (mtp) cc_final: 0.7737 (mtm) REVERT: A 872 MET cc_start: 0.7826 (ptm) cc_final: 0.7575 (ttp) REVERT: A 943 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8358 (mm) REVERT: A 1102 MET cc_start: 0.7109 (mmm) cc_final: 0.6583 (mmm) REVERT: A 1135 LYS cc_start: 0.8634 (ttmt) cc_final: 0.8299 (mtmm) REVERT: B 200 MET cc_start: 0.8045 (mmm) cc_final: 0.7654 (mmp) REVERT: B 508 MET cc_start: 0.7849 (mmt) cc_final: 0.7325 (mmt) REVERT: B 790 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6713 (mt0) REVERT: B 840 MET cc_start: 0.5546 (ttp) cc_final: 0.5188 (ttm) REVERT: B 954 MET cc_start: 0.8274 (tpp) cc_final: 0.7706 (tpp) REVERT: B 1006 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8448 (m) REVERT: B 1151 MET cc_start: 0.8133 (ptp) cc_final: 0.7903 (ptp) REVERT: B 1165 MET cc_start: 0.7300 (mtp) cc_final: 0.7070 (mtp) REVERT: B 1172 MET cc_start: 0.7859 (mmm) cc_final: 0.7341 (mmm) REVERT: D 84 ARG cc_start: 0.9366 (mtp85) cc_final: 0.9035 (mtp180) REVERT: E 18 MET cc_start: 0.9109 (mmp) cc_final: 0.8871 (mmp) REVERT: F 115 TYR cc_start: 0.8202 (p90) cc_final: 0.7371 (p90) REVERT: H 145 MET cc_start: 0.7639 (ptm) cc_final: 0.7184 (ttp) REVERT: K 14 GLU cc_start: 0.8072 (mp0) cc_final: 0.7799 (pm20) REVERT: L 15 MET cc_start: 0.7387 (tpp) cc_final: 0.6836 (tmm) REVERT: M 1346 MET cc_start: 0.4816 (ptt) cc_final: 0.4531 (ppp) REVERT: O 604 LYS cc_start: 0.4335 (OUTLIER) cc_final: 0.3959 (tppt) REVERT: Q 314 ARG cc_start: 0.9252 (tpm170) cc_final: 0.8832 (ptm-80) REVERT: Q 350 MET cc_start: 0.8270 (mmp) cc_final: 0.7645 (mmp) REVERT: Q 510 MET cc_start: 0.7663 (tmm) cc_final: 0.7397 (tmm) REVERT: Q 703 MET cc_start: 0.7673 (mtp) cc_final: 0.7249 (ttt) REVERT: R 465 GLN cc_start: 0.7518 (pm20) cc_final: 0.7001 (tm-30) REVERT: V 132 ARG cc_start: 0.7516 (mtp180) cc_final: 0.7104 (mtm180) REVERT: V 137 ILE cc_start: 0.6581 (mm) cc_final: 0.6202 (tt) REVERT: W 191 MET cc_start: 0.8926 (mmm) cc_final: 0.8310 (pmm) REVERT: Z 460 MET cc_start: 0.2937 (mtp) cc_final: 0.2033 (ptt) REVERT: Z 635 MET cc_start: 0.2568 (ttt) cc_final: 0.2089 (ttm) REVERT: a 50 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8798 (mp0) REVERT: b 84 MET cc_start: 0.8589 (ppp) cc_final: 0.8330 (tmm) REVERT: e 90 MET cc_start: 0.8475 (mmm) cc_final: 0.8163 (mmm) REVERT: e 110 CYS cc_start: 0.9466 (m) cc_final: 0.9058 (m) REVERT: e 125 GLN cc_start: 0.8713 (mt0) cc_final: 0.8378 (mm-40) REVERT: f 63 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8443 (mm-30) REVERT: h 57 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8346 (pttm) REVERT: h 62 MET cc_start: 0.8853 (mmm) cc_final: 0.8639 (mmm) REVERT: h 105 GLU cc_start: 0.8388 (mp0) cc_final: 0.8093 (mp0) REVERT: l 1497 MET cc_start: 0.7527 (mmm) cc_final: 0.6443 (mmm) REVERT: l 1526 MET cc_start: 0.8259 (mmm) cc_final: 0.7940 (mmm) REVERT: l 1607 MET cc_start: 0.8377 (tmm) cc_final: 0.7064 (mmp) REVERT: l 1627 MET cc_start: 0.6274 (mmm) cc_final: 0.5875 (mmm) outliers start: 104 outliers final: 56 residues processed: 458 average time/residue: 0.6422 time to fit residues: 520.3061 Evaluate side-chains 414 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 351 time to evaluate : 6.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain O residue 604 LYS Chi-restraints excluded: chain O residue 648 SER Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 337 SER Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain Q residue 479 ASP Chi-restraints excluded: chain Q residue 610 VAL Chi-restraints excluded: chain Q residue 698 ILE Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 734 GLN Chi-restraints excluded: chain Q residue 768 VAL Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain R residue 495 ILE Chi-restraints excluded: chain V residue 73 ASP Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 196 LEU Chi-restraints excluded: chain X residue 241 THR Chi-restraints excluded: chain Z residue 396 PHE Chi-restraints excluded: chain Z residue 451 MET Chi-restraints excluded: chain Z residue 509 HIS Chi-restraints excluded: chain a residue 50 GLU Chi-restraints excluded: chain c residue 74 LYS Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 57 LYS Chi-restraints excluded: chain l residue 1516 CYS Chi-restraints excluded: chain l residue 1602 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 740 optimal weight: 10.0000 chunk 841 optimal weight: 0.0870 chunk 71 optimal weight: 0.3980 chunk 536 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 703 optimal weight: 9.9990 chunk 317 optimal weight: 7.9990 chunk 275 optimal weight: 0.4980 chunk 13 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 chunk 397 optimal weight: 7.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN M1366 HIS ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 442 GLN ** Q 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 734 GLN Q 854 GLN ** V 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 GLN ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1498 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 = 0.4400 r_free = 0.4400 target = 0.090287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.066833 restraints weight = 472589.485| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 8.61 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 74280 Z= 0.161 Angle : 0.550 26.898 101534 Z= 0.288 Chirality : 0.045 2.030 10802 Planarity : 0.004 0.049 12198 Dihedral : 18.825 178.704 13330 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.67 % Favored : 95.32 % Rotamer: Outliers : 1.36 % Allowed : 11.53 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.07 % 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: -0.44 (0.09), residues: 8501 helix: 1.38 (0.09), residues: 3460 sheet: -1.41 (0.17), residues: 904 loop : -1.53 (0.09), residues: 4137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 684 HIS 0.005 0.001 HIS A 839 PHE 0.020 0.001 PHE H 150 TYR 0.024 0.001 TYR L 41 ARG 0.005 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 366 time to evaluate : 6.459 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: A 104 MET cc_start: 0.7069 (ttm) cc_final: 0.6755 (tpp) REVERT: A 266 MET cc_start: 0.0011 (tmm) cc_final: -0.0606 (tpp) REVERT: A 347 GLU cc_start: 0.8231 (mp0) cc_final: 0.7851 (tm-30) REVERT: A 355 MET cc_start: 0.8255 (mmm) cc_final: 0.7644 (mpp) REVERT: A 457 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7840 (tt) REVERT: A 469 MET cc_start: 0.8408 (mtt) cc_final: 0.7890 (mtt) REVERT: A 501 MET cc_start: 0.6254 (mtm) cc_final: 0.6025 (mtm) REVERT: A 535 MET cc_start: 0.7596 (mtp) cc_final: 0.7307 (mtp) REVERT: A 552 ASP cc_start: 0.7198 (p0) cc_final: 0.6461 (p0) REVERT: A 637 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7859 (mtp) REVERT: A 868 MET cc_start: 0.7852 (mtp) cc_final: 0.7631 (mtm) REVERT: A 943 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8327 (mm) REVERT: A 1102 MET cc_start: 0.7176 (mmm) cc_final: 0.6669 (mmm) REVERT: A 1135 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8330 (mtmm) REVERT: A 1412 MET cc_start: 0.8370 (ptm) cc_final: 0.7874 (ppp) REVERT: B 297 MET cc_start: 0.8661 (ttt) cc_final: 0.8286 (tpt) REVERT: B 508 MET cc_start: 0.7936 (mmt) cc_final: 0.7388 (mmt) REVERT: B 529 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7777 (mpp) REVERT: B 790 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6584 (mt0) REVERT: B 840 MET cc_start: 0.5498 (ttp) cc_final: 0.5116 (ttm) REVERT: B 1151 MET cc_start: 0.8037 (ptp) cc_final: 0.7793 (ptp) REVERT: D 84 ARG cc_start: 0.9314 (mtp85) cc_final: 0.9062 (mtp180) REVERT: E 18 MET cc_start: 0.9112 (mmp) cc_final: 0.8895 (mmp) REVERT: E 121 MET cc_start: 0.5784 (tpp) cc_final: 0.5569 (tmm) REVERT: F 88 ASP cc_start: 0.8083 (t0) cc_final: 0.7841 (t70) REVERT: F 115 TYR cc_start: 0.8176 (p90) cc_final: 0.7404 (p90) REVERT: H 37 MET cc_start: 0.7538 (mtp) cc_final: 0.7177 (mtm) REVERT: H 87 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: H 145 MET cc_start: 0.7755 (ptm) cc_final: 0.7249 (ttp) REVERT: K 14 GLU cc_start: 0.8046 (mp0) cc_final: 0.7759 (pm20) REVERT: K 77 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8738 (p) REVERT: L 15 MET cc_start: 0.7177 (tpp) cc_final: 0.6860 (tpp) REVERT: L 43 ILE cc_start: 0.9269 (mt) cc_final: 0.8997 (tp) REVERT: M 1346 MET cc_start: 0.4732 (ptt) cc_final: 0.4461 (ppp) REVERT: O 604 LYS cc_start: 0.3931 (OUTLIER) cc_final: 0.3646 (tppt) REVERT: O 677 MET cc_start: 0.6274 (ptt) cc_final: 0.6040 (tmm) REVERT: Q 314 ARG cc_start: 0.9237 (tpm170) cc_final: 0.8805 (ptm-80) REVERT: Q 350 MET cc_start: 0.8250 (mmp) cc_final: 0.7825 (mmp) REVERT: Q 510 MET cc_start: 0.7895 (tmm) cc_final: 0.7496 (tmm) REVERT: Q 703 MET cc_start: 0.7845 (mtp) cc_final: 0.7350 (ttt) REVERT: R 465 GLN cc_start: 0.7397 (pm20) cc_final: 0.6863 (tm-30) REVERT: V 132 ARG cc_start: 0.7493 (mtp85) cc_final: 0.7109 (mtm180) REVERT: W 191 MET cc_start: 0.9024 (mmm) cc_final: 0.8691 (ttm) REVERT: Y 63 MET cc_start: 0.1978 (ppp) cc_final: 0.1601 (ptm) REVERT: Z 460 MET cc_start: 0.2927 (mtp) cc_final: 0.1931 (ptt) REVERT: Z 635 MET cc_start: 0.0867 (ttt) cc_final: 0.0365 (ttm) REVERT: b 84 MET cc_start: 0.8654 (ppp) cc_final: 0.8423 (tmm) REVERT: c 64 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8252 (pp20) REVERT: d 111 VAL cc_start: 0.9229 (m) cc_final: 0.8946 (p) REVERT: e 90 MET cc_start: 0.8430 (mmm) cc_final: 0.8101 (mmm) REVERT: e 110 CYS cc_start: 0.9452 (m) cc_final: 0.8752 (t) REVERT: e 125 GLN cc_start: 0.8697 (mt0) cc_final: 0.8347 (mm-40) REVERT: f 63 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8355 (mm-30) REVERT: f 79 LYS cc_start: 0.7573 (tptt) cc_final: 0.7328 (tptt) REVERT: h 57 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8362 (pttm) REVERT: h 105 GLU cc_start: 0.8345 (mp0) cc_final: 0.8058 (mp0) REVERT: l 1497 MET cc_start: 0.7849 (mmm) cc_final: 0.6833 (mmm) REVERT: l 1526 MET cc_start: 0.8447 (mmm) cc_final: 0.8077 (mmm) REVERT: l 1607 MET cc_start: 0.8356 (tmm) cc_final: 0.7901 (tmm) REVERT: l 1627 MET cc_start: 0.6116 (mmm) cc_final: 0.5761 (mmm) outliers start: 89 outliers final: 50 residues processed: 435 average time/residue: 0.6596 time to fit residues: 506.3862 Evaluate side-chains 405 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 346 time to evaluate : 6.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain O residue 604 LYS Chi-restraints excluded: chain O residue 652 LEU Chi-restraints excluded: chain Q residue 267 SER Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain Q residue 479 ASP Chi-restraints excluded: chain Q residue 482 LYS Chi-restraints excluded: chain Q residue 610 VAL Chi-restraints excluded: chain Q residue 768 VAL Chi-restraints excluded: chain U residue 459 VAL Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 73 ASP Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 196 LEU Chi-restraints excluded: chain X residue 241 THR Chi-restraints excluded: chain Z residue 451 MET Chi-restraints excluded: chain Z residue 509 HIS Chi-restraints excluded: chain a residue 50 GLU Chi-restraints excluded: chain b residue 90 LEU Chi-restraints excluded: chain c residue 74 LYS Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 57 LYS Chi-restraints excluded: chain l residue 1516 CYS Chi-restraints excluded: chain l residue 1602 ILE Chi-restraints excluded: chain l residue 1695 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 196 optimal weight: 1.9990 chunk 342 optimal weight: 0.5980 chunk 735 optimal weight: 50.0000 chunk 307 optimal weight: 6.9990 chunk 673 optimal weight: 0.0170 chunk 793 optimal weight: 2.9990 chunk 548 optimal weight: 3.9990 chunk 449 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 661 optimal weight: 6.9990 chunk 358 optimal weight: 10.0000 overall best weight: 1.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1366 HIS ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 466 ASN Q 573 ASN ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 756 ASN ** Q 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 567 ASN V 69 GLN W 173 ASN W 221 HIS ** Z 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1498 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 = 0.4381 r_free = 0.4381 target = 0.089406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.066034 restraints weight = 476223.959| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 7.93 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 74280 Z= 0.216 Angle : 0.562 26.718 101534 Z= 0.293 Chirality : 0.045 2.022 10802 Planarity : 0.004 0.126 12198 Dihedral : 18.828 177.892 13329 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.94 % Favored : 95.05 % Rotamer: Outliers : 1.81 % Allowed : 11.54 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.07 % Twisted Proline : 0.29 % 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: 8501 helix: 1.46 (0.09), residues: 3454 sheet: -1.35 (0.17), residues: 896 loop : -1.48 (0.09), residues: 4151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 27 HIS 0.007 0.001 HIS A 839 PHE 0.013 0.001 PHE W 133 TYR 0.019 0.001 TYR L 41 ARG 0.004 0.000 ARG V 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 355 time to evaluate : 6.352 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: A 104 MET cc_start: 0.7254 (ttm) cc_final: 0.6889 (tpp) REVERT: A 266 MET cc_start: 0.0323 (tmm) cc_final: -0.0420 (tpp) REVERT: A 343 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7809 (pp) REVERT: A 347 GLU cc_start: 0.8154 (mp0) cc_final: 0.7903 (tm-30) REVERT: A 350 VAL cc_start: 0.7525 (OUTLIER) cc_final: 0.7156 (m) REVERT: A 496 PHE cc_start: 0.7871 (m-80) cc_final: 0.7411 (m-80) REVERT: A 535 MET cc_start: 0.7578 (mtp) cc_final: 0.7307 (mtp) REVERT: A 561 MET cc_start: 0.8731 (mtt) cc_final: 0.8456 (mtt) REVERT: A 868 MET cc_start: 0.7931 (mtp) cc_final: 0.7545 (mtm) REVERT: A 943 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8309 (mm) REVERT: A 1102 MET cc_start: 0.7245 (mmm) cc_final: 0.6724 (mmm) REVERT: A 1135 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8361 (mtmm) REVERT: A 1412 MET cc_start: 0.8352 (ptm) cc_final: 0.7800 (ppp) REVERT: B 200 MET cc_start: 0.7905 (mmp) cc_final: 0.7504 (mmm) REVERT: B 297 MET cc_start: 0.8716 (ttt) cc_final: 0.8144 (tpt) REVERT: B 508 MET cc_start: 0.7854 (mmt) cc_final: 0.7357 (mmt) REVERT: B 529 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7913 (tpp) REVERT: B 790 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6739 (mt0) REVERT: B 840 MET cc_start: 0.5538 (ttp) cc_final: 0.5142 (ttm) REVERT: B 1151 MET cc_start: 0.8041 (ptp) cc_final: 0.7839 (ptp) REVERT: D 84 ARG cc_start: 0.9281 (mtp85) cc_final: 0.8836 (mtp180) REVERT: E 18 MET cc_start: 0.9098 (mmp) cc_final: 0.8888 (mmp) REVERT: E 37 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8941 (tt) REVERT: F 115 TYR cc_start: 0.8170 (p90) cc_final: 0.7382 (p90) REVERT: G 131 MET cc_start: 0.6422 (mmp) cc_final: 0.5583 (ptp) REVERT: H 37 MET cc_start: 0.7721 (mtp) cc_final: 0.7128 (mtm) REVERT: H 87 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: H 145 MET cc_start: 0.7896 (ptm) cc_final: 0.7595 (ptm) REVERT: K 14 GLU cc_start: 0.8000 (mp0) cc_final: 0.7739 (pm20) REVERT: K 77 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8654 (p) REVERT: L 15 MET cc_start: 0.7331 (tpp) cc_final: 0.6790 (tpt) REVERT: M 1346 MET cc_start: 0.5052 (ptt) cc_final: 0.4755 (ppp) REVERT: Q 145 MET cc_start: 0.0635 (tpp) cc_final: 0.0160 (tpp) REVERT: Q 314 ARG cc_start: 0.9258 (tpm170) cc_final: 0.8792 (ptm-80) REVERT: Q 350 MET cc_start: 0.8346 (mmp) cc_final: 0.7954 (mmp) REVERT: Q 510 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7669 (tmm) REVERT: Q 703 MET cc_start: 0.8042 (mtp) cc_final: 0.7515 (ttt) REVERT: R 465 GLN cc_start: 0.7415 (pm20) cc_final: 0.6769 (tm-30) REVERT: V 132 ARG cc_start: 0.7514 (mtp85) cc_final: 0.7016 (mtm180) REVERT: W 191 MET cc_start: 0.9163 (mmm) cc_final: 0.8595 (mpp) REVERT: W 221 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7952 (p90) REVERT: Y 63 MET cc_start: 0.1864 (ppp) cc_final: 0.1628 (ptm) REVERT: Z 460 MET cc_start: 0.2822 (mtp) cc_final: 0.1757 (ptt) REVERT: Z 602 VAL cc_start: 0.0814 (OUTLIER) cc_final: 0.0494 (t) REVERT: Z 635 MET cc_start: -0.1463 (ttt) cc_final: -0.1775 (ttp) REVERT: b 84 MET cc_start: 0.8691 (ppp) cc_final: 0.8436 (tmm) REVERT: d 111 VAL cc_start: 0.9242 (m) cc_final: 0.8984 (p) REVERT: e 90 MET cc_start: 0.8484 (mmm) cc_final: 0.8060 (mmm) REVERT: e 110 CYS cc_start: 0.9430 (m) cc_final: 0.8816 (t) REVERT: e 125 GLN cc_start: 0.8687 (mt0) cc_final: 0.8344 (mm-40) REVERT: f 63 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8386 (mm-30) REVERT: f 79 LYS cc_start: 0.7633 (tptt) cc_final: 0.7381 (tptt) REVERT: h 57 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8378 (pttm) REVERT: h 89 ILE cc_start: 0.7074 (mt) cc_final: 0.6649 (pt) REVERT: h 105 GLU cc_start: 0.8355 (mp0) cc_final: 0.8065 (mp0) REVERT: l 1497 MET cc_start: 0.7959 (mmm) cc_final: 0.6979 (mmm) REVERT: l 1526 MET cc_start: 0.8562 (mmm) cc_final: 0.8118 (mmm) REVERT: l 1607 MET cc_start: 0.8360 (tmm) cc_final: 0.7981 (tmm) REVERT: l 1627 MET cc_start: 0.6234 (mmm) cc_final: 0.5881 (mmm) outliers start: 119 outliers final: 62 residues processed: 450 average time/residue: 0.6581 time to fit residues: 528.3712 Evaluate side-chains 419 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 345 time to evaluate : 6.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain O residue 671 SER Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain Q residue 479 ASP Chi-restraints excluded: chain Q residue 510 MET Chi-restraints excluded: chain Q residue 610 VAL Chi-restraints excluded: chain Q residue 768 VAL Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain U residue 459 VAL Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 73 ASP Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 196 LEU Chi-restraints excluded: chain W residue 221 HIS Chi-restraints excluded: chain X residue 241 THR Chi-restraints excluded: chain Z residue 182 VAL Chi-restraints excluded: chain Z residue 296 VAL Chi-restraints excluded: chain Z residue 509 HIS Chi-restraints excluded: chain Z residue 602 VAL Chi-restraints excluded: chain a residue 50 GLU Chi-restraints excluded: chain b residue 87 VAL Chi-restraints excluded: chain c residue 74 LYS Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 57 LYS Chi-restraints excluded: chain l residue 1516 CYS Chi-restraints excluded: chain l residue 1602 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 543 optimal weight: 0.0570 chunk 596 optimal weight: 7.9990 chunk 337 optimal weight: 7.9990 chunk 357 optimal weight: 0.8980 chunk 715 optimal weight: 7.9990 chunk 619 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 167 optimal weight: 6.9990 chunk 804 optimal weight: 9.9990 chunk 436 optimal weight: 20.0000 chunk 541 optimal weight: 9.9990 overall best weight: 4.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 387 HIS ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 157 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1366 HIS O 654 HIS O 667 HIS ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 GLN Q 245 ASN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 305 GLN ** Q 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 442 GLN ** Q 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 781 ASN Q 816 GLN ** Q 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 632 ASN ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 113 HIS ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 95 GLN ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 27 GLN ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.086730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.063748 restraints weight = 473060.765| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 7.92 r_work: 0.3483 rms_B_bonded: 7.67 restraints_weight: 2.0000 r_work: 0.3577 rms_B_bonded: 5.73 restraints_weight: 4.0000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 74280 Z= 0.428 Angle : 0.727 26.766 101534 Z= 0.380 Chirality : 0.049 2.013 10802 Planarity : 0.005 0.070 12198 Dihedral : 19.297 178.762 13329 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.78 % Favored : 93.19 % Rotamer: Outliers : 2.06 % Allowed : 12.06 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.07 % Twisted Proline : 0.29 % 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: -0.83 (0.09), residues: 8501 helix: 0.97 (0.09), residues: 3460 sheet: -1.62 (0.17), residues: 894 loop : -1.66 (0.09), residues: 4147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 27 HIS 0.041 0.002 HIS W 221 PHE 0.023 0.002 PHE B 805 TYR 0.036 0.002 TYR B 648 ARG 0.010 0.001 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 349 time to evaluate : 6.383 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: A 104 MET cc_start: 0.7480 (ttm) cc_final: 0.6938 (tpp) REVERT: A 266 MET cc_start: 0.0573 (tmm) cc_final: -0.0469 (tpp) REVERT: A 343 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8015 (pp) REVERT: A 347 GLU cc_start: 0.8267 (mp0) cc_final: 0.7922 (tm-30) REVERT: A 469 MET cc_start: 0.8718 (mtp) cc_final: 0.8143 (mtp) REVERT: A 470 MET cc_start: 0.8109 (mpp) cc_final: 0.7566 (mtt) REVERT: A 565 MET cc_start: 0.8554 (tpt) cc_final: 0.8097 (tpt) REVERT: A 943 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8324 (mm) REVERT: A 1086 MET cc_start: 0.8458 (mmp) cc_final: 0.7785 (mmt) REVERT: A 1102 MET cc_start: 0.7199 (mmm) cc_final: 0.6588 (mmm) REVERT: A 1135 LYS cc_start: 0.8642 (ttmt) cc_final: 0.8416 (mtmm) REVERT: A 1451 MET cc_start: 0.8581 (tpp) cc_final: 0.8136 (tpp) REVERT: B 508 MET cc_start: 0.7972 (mmt) cc_final: 0.7635 (mmt) REVERT: B 790 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7077 (mt0) REVERT: B 840 MET cc_start: 0.5089 (ttp) cc_final: 0.4443 (ttm) REVERT: D 84 ARG cc_start: 0.9527 (mtp85) cc_final: 0.9216 (mtp180) REVERT: E 59 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8104 (t) REVERT: H 37 MET cc_start: 0.8129 (mtp) cc_final: 0.7715 (mtm) REVERT: H 87 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7870 (mp10) REVERT: H 145 MET cc_start: 0.7916 (ptm) cc_final: 0.7568 (ptm) REVERT: J 26 GLN cc_start: 0.9030 (tt0) cc_final: 0.8507 (tp-100) REVERT: M 1346 MET cc_start: 0.5205 (ptt) cc_final: 0.4896 (ppp) REVERT: Q 145 MET cc_start: 0.1970 (tpp) cc_final: 0.1485 (tpp) REVERT: Q 244 ASN cc_start: 0.6337 (p0) cc_final: 0.6113 (p0) REVERT: Q 510 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7974 (tmm) REVERT: Q 703 MET cc_start: 0.8320 (mtp) cc_final: 0.7788 (ttt) REVERT: R 465 GLN cc_start: 0.7477 (pm20) cc_final: 0.6873 (tm-30) REVERT: W 191 MET cc_start: 0.9191 (mmm) cc_final: 0.8517 (mpp) REVERT: Y 63 MET cc_start: 0.1092 (ppp) cc_final: 0.0773 (ptm) REVERT: Z 460 MET cc_start: 0.2608 (mtp) cc_final: 0.1312 (ptt) REVERT: Z 635 MET cc_start: -0.1408 (ttt) cc_final: -0.1718 (ttp) REVERT: b 84 MET cc_start: 0.8746 (ppp) cc_final: 0.8447 (tmm) REVERT: d 111 VAL cc_start: 0.9350 (m) cc_final: 0.9095 (p) REVERT: e 90 MET cc_start: 0.8525 (mmm) cc_final: 0.8305 (mmm) REVERT: e 125 GLN cc_start: 0.8829 (mt0) cc_final: 0.8521 (mm-40) REVERT: f 79 LYS cc_start: 0.7878 (tptt) cc_final: 0.7644 (tptt) REVERT: h 52 THR cc_start: 0.6324 (OUTLIER) cc_final: 0.6028 (t) REVERT: h 57 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8426 (pttm) REVERT: h 62 MET cc_start: 0.8909 (mmm) cc_final: 0.8705 (mmm) REVERT: h 93 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8603 (pt0) REVERT: h 105 GLU cc_start: 0.8870 (mp0) cc_final: 0.8458 (mp0) REVERT: l 1497 MET cc_start: 0.8042 (mmm) cc_final: 0.7352 (mmm) REVERT: l 1526 MET cc_start: 0.8771 (mmm) cc_final: 0.8212 (mmm) outliers start: 135 outliers final: 82 residues processed: 458 average time/residue: 0.6517 time to fit residues: 528.3288 Evaluate side-chains 428 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 337 time to evaluate : 6.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 115 TYR Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain M residue 1381 VAL Chi-restraints excluded: chain O residue 648 SER Chi-restraints excluded: chain O residue 652 LEU Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain Q residue 479 ASP Chi-restraints excluded: chain Q residue 510 MET Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain Q residue 857 LEU Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 73 ASP Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 205 MET Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 196 LEU Chi-restraints excluded: chain X residue 241 THR Chi-restraints excluded: chain Z residue 182 VAL Chi-restraints excluded: chain Z residue 296 VAL Chi-restraints excluded: chain Z residue 396 PHE Chi-restraints excluded: chain Z residue 509 HIS Chi-restraints excluded: chain Z residue 602 VAL Chi-restraints excluded: chain a residue 50 GLU Chi-restraints excluded: chain b residue 87 VAL Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain c residue 74 LYS Chi-restraints excluded: chain d residue 57 LYS Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 57 LYS Chi-restraints excluded: chain h residue 93 GLU Chi-restraints excluded: chain l residue 1516 CYS Chi-restraints excluded: chain l residue 1602 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 80 optimal weight: 5.9990 chunk 378 optimal weight: 4.9990 chunk 568 optimal weight: 9.9990 chunk 711 optimal weight: 8.9990 chunk 480 optimal weight: 40.0000 chunk 41 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 629 optimal weight: 5.9990 chunk 384 optimal weight: 9.9990 chunk 554 optimal weight: 5.9990 chunk 278 optimal weight: 0.7980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1366 HIS O 667 HIS ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 305 GLN ** Q 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.087612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.064911 restraints weight = 469363.870| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 7.52 r_work: 0.3521 rms_B_bonded: 7.43 restraints_weight: 2.0000 r_work: 0.3609 rms_B_bonded: 5.65 restraints_weight: 4.0000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 74280 Z= 0.259 Angle : 0.608 26.753 101534 Z= 0.316 Chirality : 0.046 2.024 10802 Planarity : 0.004 0.050 12198 Dihedral : 19.326 179.849 13329 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.03 % Favored : 94.95 % Rotamer: Outliers : 1.83 % Allowed : 12.70 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.07 % Twisted Proline : 0.29 % 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: -0.60 (0.09), residues: 8501 helix: 1.19 (0.09), residues: 3477 sheet: -1.53 (0.17), residues: 898 loop : -1.56 (0.09), residues: 4126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 27 HIS 0.008 0.001 HIS A 839 PHE 0.017 0.001 PHE Q 174 TYR 0.021 0.001 TYR H 115 ARG 0.005 0.000 ARG A1213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 357 time to evaluate : 6.418 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: A 104 MET cc_start: 0.7600 (ttm) cc_final: 0.7141 (tpp) REVERT: A 266 MET cc_start: 0.0627 (tmm) cc_final: -0.0360 (tpp) REVERT: A 343 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8024 (pp) REVERT: A 469 MET cc_start: 0.8714 (mtp) cc_final: 0.8075 (mtp) REVERT: A 470 MET cc_start: 0.7967 (mpp) cc_final: 0.7499 (mtt) REVERT: A 496 PHE cc_start: 0.7786 (m-80) cc_final: 0.7534 (m-80) REVERT: A 565 MET cc_start: 0.8523 (tpt) cc_final: 0.8134 (tpt) REVERT: A 868 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7010 (ptp) REVERT: A 943 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8371 (mm) REVERT: A 1102 MET cc_start: 0.7332 (mmm) cc_final: 0.6653 (mmm) REVERT: A 1262 MET cc_start: 0.4634 (tpp) cc_final: 0.4079 (tpp) REVERT: A 1451 MET cc_start: 0.8499 (tpp) cc_final: 0.8091 (tpp) REVERT: B 297 MET cc_start: 0.8863 (ttt) cc_final: 0.7787 (tpt) REVERT: B 368 MET cc_start: 0.8661 (mmm) cc_final: 0.8446 (mmm) REVERT: B 422 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7197 (t80) REVERT: B 508 MET cc_start: 0.8035 (mmt) cc_final: 0.7606 (mmt) REVERT: B 790 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6575 (mt0) REVERT: B 840 MET cc_start: 0.5059 (ttp) cc_final: 0.4398 (ttm) REVERT: B 1165 MET cc_start: 0.7470 (mtp) cc_final: 0.7237 (mtp) REVERT: D 84 ARG cc_start: 0.9504 (mtp85) cc_final: 0.9120 (mtp180) REVERT: E 18 MET cc_start: 0.9135 (mmp) cc_final: 0.8913 (mmp) REVERT: E 59 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8198 (t) REVERT: E 94 MET cc_start: 0.8883 (tmm) cc_final: 0.8573 (tmm) REVERT: E 121 MET cc_start: 0.7579 (tmm) cc_final: 0.7252 (tmm) REVERT: F 80 MET cc_start: 0.7834 (mmm) cc_final: 0.7625 (mmm) REVERT: H 145 MET cc_start: 0.7819 (ptm) cc_final: 0.7487 (ptm) REVERT: J 26 GLN cc_start: 0.9140 (tt0) cc_final: 0.8532 (tp-100) REVERT: M 1346 MET cc_start: 0.5364 (ptt) cc_final: 0.5041 (ppp) REVERT: Q 145 MET cc_start: 0.1428 (tpp) cc_final: 0.1122 (tpp) REVERT: Q 244 ASN cc_start: 0.6547 (p0) cc_final: 0.6229 (p0) REVERT: Q 510 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7958 (tmm) REVERT: Q 703 MET cc_start: 0.8293 (mtp) cc_final: 0.7844 (ttt) REVERT: R 465 GLN cc_start: 0.7435 (pm20) cc_final: 0.6817 (tm-30) REVERT: Y 63 MET cc_start: 0.0916 (ppp) cc_final: 0.0409 (ptm) REVERT: Z 460 MET cc_start: 0.2627 (mtp) cc_final: 0.1417 (ptt) REVERT: a 36 MET cc_start: 0.1787 (OUTLIER) cc_final: -0.1644 (tpt) REVERT: a 41 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.6536 (m-80) REVERT: b 84 MET cc_start: 0.8782 (ppp) cc_final: 0.8479 (tmm) REVERT: d 111 VAL cc_start: 0.9342 (m) cc_final: 0.9096 (p) REVERT: e 90 MET cc_start: 0.8501 (mmm) cc_final: 0.8165 (mmm) REVERT: e 106 ASP cc_start: 0.9266 (m-30) cc_final: 0.9022 (t0) REVERT: e 125 GLN cc_start: 0.8844 (mt0) cc_final: 0.8533 (mm-40) REVERT: f 79 LYS cc_start: 0.7849 (tptt) cc_final: 0.7406 (tptt) REVERT: h 57 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8489 (pttm) REVERT: h 62 MET cc_start: 0.8892 (mmm) cc_final: 0.8547 (mmt) REVERT: h 105 GLU cc_start: 0.8868 (mp0) cc_final: 0.8495 (mp0) REVERT: l 1497 MET cc_start: 0.8029 (mmm) cc_final: 0.7454 (mmm) REVERT: l 1526 MET cc_start: 0.8782 (mmm) cc_final: 0.8401 (mmm) REVERT: l 1607 MET cc_start: 0.7898 (tmm) cc_final: 0.7235 (mmp) outliers start: 120 outliers final: 70 residues processed: 456 average time/residue: 0.6524 time to fit residues: 527.2050 Evaluate side-chains 421 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 341 time to evaluate : 6.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 115 TYR Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 23 HIS Chi-restraints excluded: chain O residue 648 SER Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain Q residue 479 ASP Chi-restraints excluded: chain Q residue 510 MET Chi-restraints excluded: chain Q residue 725 ARG Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 73 ASP Chi-restraints excluded: chain V residue 108 LEU Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 205 MET Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 196 LEU Chi-restraints excluded: chain X residue 241 THR Chi-restraints excluded: chain Z residue 182 VAL Chi-restraints excluded: chain Z residue 296 VAL Chi-restraints excluded: chain Z residue 509 HIS Chi-restraints excluded: chain Z residue 602 VAL Chi-restraints excluded: chain a residue 36 MET Chi-restraints excluded: chain a residue 41 TYR Chi-restraints excluded: chain a residue 50 GLU Chi-restraints excluded: chain b residue 87 VAL Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain c residue 74 LYS Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 57 LYS Chi-restraints excluded: chain l residue 1516 CYS Chi-restraints excluded: chain l residue 1602 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 474 optimal weight: 9.9990 chunk 549 optimal weight: 0.8980 chunk 628 optimal weight: 40.0000 chunk 34 optimal weight: 2.9990 chunk 818 optimal weight: 10.0000 chunk 687 optimal weight: 0.6980 chunk 246 optimal weight: 2.9990 chunk 418 optimal weight: 0.9980 chunk 597 optimal weight: 5.9990 chunk 322 optimal weight: 10.0000 chunk 241 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 HIS ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS M1366 HIS ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS Q 256 GLN ** Q 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 69 GLN ** Z 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 625 HIS ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1498 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 = 0.4357 r_free = 0.4357 target = 0.088107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.064424 restraints weight = 469430.375| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 8.08 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.6212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 74280 Z= 0.190 Angle : 0.582 26.761 101534 Z= 0.301 Chirality : 0.045 2.024 10802 Planarity : 0.004 0.050 12198 Dihedral : 19.183 179.905 13329 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.09 % Favored : 94.89 % Rotamer: Outliers : 1.37 % Allowed : 13.45 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.07 % Twisted Proline : 0.29 % 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: -0.40 (0.09), residues: 8501 helix: 1.33 (0.09), residues: 3481 sheet: -1.34 (0.17), residues: 859 loop : -1.45 (0.09), residues: 4161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 49 HIS 0.006 0.001 HIS J 52 PHE 0.013 0.001 PHE W 133 TYR 0.018 0.001 TYR Q 185 ARG 0.006 0.000 ARG Q 839 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 351 time to evaluate : 6.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7462 (ttm) cc_final: 0.7076 (tpp) REVERT: A 266 MET cc_start: 0.0309 (tmm) cc_final: -0.0730 (tpp) REVERT: A 343 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7833 (pp) REVERT: A 467 MET cc_start: 0.7984 (mmp) cc_final: 0.7769 (mmm) REVERT: A 469 MET cc_start: 0.8245 (mtp) cc_final: 0.7881 (mtp) REVERT: A 561 MET cc_start: 0.8470 (mtt) cc_final: 0.8223 (ttm) REVERT: A 565 MET cc_start: 0.8480 (tpt) cc_final: 0.8094 (tpt) REVERT: A 868 MET cc_start: 0.7792 (mtp) cc_final: 0.6897 (ptp) REVERT: A 943 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8349 (mm) REVERT: A 1102 MET cc_start: 0.7210 (mmm) cc_final: 0.6604 (mmm) REVERT: B 297 MET cc_start: 0.8822 (ttt) cc_final: 0.7673 (tpt) REVERT: B 452 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8607 (p0) REVERT: B 508 MET cc_start: 0.7654 (mmt) cc_final: 0.7190 (mmt) REVERT: B 840 MET cc_start: 0.4812 (ttp) cc_final: 0.4317 (ttm) REVERT: B 1165 MET cc_start: 0.7669 (mtp) cc_final: 0.7429 (mtp) REVERT: D 84 ARG cc_start: 0.9303 (mtp85) cc_final: 0.8803 (mtp180) REVERT: E 18 MET cc_start: 0.8993 (mmp) cc_final: 0.8762 (mmp) REVERT: E 94 MET cc_start: 0.8795 (tmm) cc_final: 0.8478 (tmm) REVERT: E 121 MET cc_start: 0.7441 (tmm) cc_final: 0.7188 (tmm) REVERT: H 37 MET cc_start: 0.7603 (mtp) cc_final: 0.7378 (mtm) REVERT: H 145 MET cc_start: 0.7821 (ptm) cc_final: 0.7528 (ptm) REVERT: J 48 MET cc_start: 0.8278 (mmm) cc_final: 0.7980 (mmt) REVERT: M 1346 MET cc_start: 0.5164 (ptt) cc_final: 0.4883 (ppp) REVERT: Q 145 MET cc_start: 0.1422 (tpp) cc_final: 0.1187 (tpp) REVERT: Q 244 ASN cc_start: 0.6722 (p0) cc_final: 0.6370 (p0) REVERT: Q 428 GLN cc_start: 0.9483 (tp40) cc_final: 0.9232 (pm20) REVERT: Q 510 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8020 (tmm) REVERT: Q 703 MET cc_start: 0.8522 (mtp) cc_final: 0.7943 (ttt) REVERT: R 465 GLN cc_start: 0.7619 (pm20) cc_final: 0.7051 (tm-30) REVERT: V 33 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.7989 (t) REVERT: Y 63 MET cc_start: 0.1221 (ppp) cc_final: 0.0784 (ptm) REVERT: Z 460 MET cc_start: 0.2843 (mtp) cc_final: 0.1667 (ptt) REVERT: Z 508 MET cc_start: 0.2031 (mmt) cc_final: 0.0414 (tmm) REVERT: Z 602 VAL cc_start: 0.1090 (OUTLIER) cc_final: 0.0767 (t) REVERT: a 36 MET cc_start: 0.1994 (OUTLIER) cc_final: -0.0875 (tpt) REVERT: b 84 MET cc_start: 0.8590 (ppp) cc_final: 0.8273 (ppp) REVERT: d 111 VAL cc_start: 0.9112 (m) cc_final: 0.8848 (p) REVERT: e 90 MET cc_start: 0.8290 (mmm) cc_final: 0.7938 (mmm) REVERT: e 106 ASP cc_start: 0.9170 (m-30) cc_final: 0.8755 (t0) REVERT: e 110 CYS cc_start: 0.9306 (m) cc_final: 0.8927 (m) REVERT: e 125 GLN cc_start: 0.8628 (mt0) cc_final: 0.8329 (mm-40) REVERT: h 42 TYR cc_start: 0.6724 (OUTLIER) cc_final: 0.6434 (m-80) REVERT: h 57 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8347 (pttm) REVERT: h 62 MET cc_start: 0.8840 (mmm) cc_final: 0.8479 (mmt) REVERT: h 105 GLU cc_start: 0.8279 (mp0) cc_final: 0.7996 (mp0) REVERT: l 1497 MET cc_start: 0.8193 (mmm) cc_final: 0.7470 (mmm) REVERT: l 1526 MET cc_start: 0.8893 (mmm) cc_final: 0.8297 (mmm) REVERT: l 1607 MET cc_start: 0.8245 (tmm) cc_final: 0.7192 (mmp) outliers start: 90 outliers final: 56 residues processed: 427 average time/residue: 0.6359 time to fit residues: 483.4530 Evaluate side-chains 405 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 340 time to evaluate : 6.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 23 HIS Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain Q residue 479 ASP Chi-restraints excluded: chain Q residue 510 MET Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain U residue 414 LEU Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 73 ASP Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 205 MET Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 196 LEU Chi-restraints excluded: chain X residue 241 THR Chi-restraints excluded: chain Z residue 296 VAL Chi-restraints excluded: chain Z residue 509 HIS Chi-restraints excluded: chain Z residue 602 VAL Chi-restraints excluded: chain a residue 36 MET Chi-restraints excluded: chain a residue 50 GLU Chi-restraints excluded: chain c residue 74 LYS Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 42 TYR Chi-restraints excluded: chain h residue 57 LYS Chi-restraints excluded: chain l residue 1516 CYS Chi-restraints excluded: chain l residue 1602 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 787 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 394 optimal weight: 20.0000 chunk 465 optimal weight: 10.0000 chunk 853 optimal weight: 2.9990 chunk 623 optimal weight: 10.0000 chunk 635 optimal weight: 20.0000 chunk 459 optimal weight: 20.0000 chunk 146 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 622 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1366 HIS O 667 HIS ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 GLN Q 245 ASN Q 289 GLN Q 319 GLN ** Q 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 359 ASN ** Q 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 220 HIS ** Z 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1498 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 = 0.4310 r_free = 0.4310 target = 0.085862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.062667 restraints weight = 481579.020| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 8.00 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.6819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 74280 Z= 0.490 Angle : 0.769 26.551 101534 Z= 0.401 Chirality : 0.050 2.011 10802 Planarity : 0.005 0.144 12198 Dihedral : 19.512 176.369 13329 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.14 % Favored : 92.84 % Rotamer: Outliers : 1.34 % Allowed : 13.74 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.07 % Twisted Proline : 0.29 % 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: -0.89 (0.09), residues: 8501 helix: 0.85 (0.09), residues: 3472 sheet: -1.60 (0.17), residues: 918 loop : -1.63 (0.09), residues: 4111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 453 HIS 0.012 0.002 HIS Z 737 PHE 0.031 0.002 PHE G 119 TYR 0.034 0.002 TYR Q 697 ARG 0.013 0.001 ARG Q 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17002 Ramachandran restraints generated. 8501 Oldfield, 0 Emsley, 8501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 339 time to evaluate : 6.465 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: A 104 MET cc_start: 0.7632 (ttm) cc_final: 0.7135 (tpp) REVERT: A 266 MET cc_start: 0.0573 (tmm) cc_final: -0.0438 (tpp) REVERT: A 343 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8012 (pp) REVERT: A 467 MET cc_start: 0.8498 (mmp) cc_final: 0.8174 (mmm) REVERT: A 469 MET cc_start: 0.8418 (mtp) cc_final: 0.7744 (mtp) REVERT: A 470 MET cc_start: 0.7939 (mpp) cc_final: 0.7587 (mtt) REVERT: A 561 MET cc_start: 0.8553 (mtt) cc_final: 0.8302 (ttm) REVERT: A 565 MET cc_start: 0.8686 (tpt) cc_final: 0.8199 (tpt) REVERT: A 943 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8279 (mm) REVERT: A 1102 MET cc_start: 0.7376 (mmm) cc_final: 0.6441 (mmm) REVERT: A 1296 MET cc_start: 0.7981 (tpt) cc_final: 0.7772 (tpp) REVERT: B 297 MET cc_start: 0.8880 (ttt) cc_final: 0.8372 (tpp) REVERT: B 422 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7061 (t80) REVERT: B 508 MET cc_start: 0.7606 (mmt) cc_final: 0.7260 (mmt) REVERT: B 840 MET cc_start: 0.4775 (ttp) cc_final: 0.4292 (ttm) REVERT: D 84 ARG cc_start: 0.9335 (mtp85) cc_final: 0.8821 (mtp180) REVERT: E 18 MET cc_start: 0.9073 (mmp) cc_final: 0.8850 (mmp) REVERT: E 121 MET cc_start: 0.7906 (tmm) cc_final: 0.7550 (tmm) REVERT: H 37 MET cc_start: 0.8128 (mtp) cc_final: 0.7801 (mtm) REVERT: H 145 MET cc_start: 0.7931 (ptm) cc_final: 0.7533 (ptm) REVERT: J 26 GLN cc_start: 0.8717 (tt0) cc_final: 0.8130 (tp40) REVERT: M 1346 MET cc_start: 0.5190 (ptt) cc_final: 0.4938 (ppp) REVERT: Q 510 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8213 (tmm) REVERT: Q 703 MET cc_start: 0.8750 (mtp) cc_final: 0.8247 (ttt) REVERT: R 465 GLN cc_start: 0.7002 (pm20) cc_final: 0.6437 (tm-30) REVERT: U 448 MET cc_start: 0.1850 (ppp) cc_final: 0.1111 (tpp) REVERT: V 132 ARG cc_start: 0.7292 (mtp180) cc_final: 0.6845 (mtm180) REVERT: Y 63 MET cc_start: 0.0815 (ppp) cc_final: 0.0301 (ptm) REVERT: Z 460 MET cc_start: 0.3323 (mtp) cc_final: 0.2261 (ptt) REVERT: Z 508 MET cc_start: 0.2389 (mmt) cc_final: 0.0840 (tmm) REVERT: Z 635 MET cc_start: -0.0866 (ttt) cc_final: -0.1066 (ttt) REVERT: a 36 MET cc_start: 0.2691 (OUTLIER) cc_final: 0.1382 (tpt) REVERT: a 41 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: b 84 MET cc_start: 0.8601 (ppp) cc_final: 0.8197 (ppp) REVERT: e 90 MET cc_start: 0.8474 (mmm) cc_final: 0.8100 (mmm) REVERT: e 125 GLN cc_start: 0.8834 (mt0) cc_final: 0.8530 (mm-40) REVERT: f 79 LYS cc_start: 0.7929 (tptt) cc_final: 0.7477 (tptt) REVERT: h 57 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8358 (pttm) REVERT: h 62 MET cc_start: 0.8984 (mmm) cc_final: 0.8636 (mmt) REVERT: l 1497 MET cc_start: 0.8393 (mmm) cc_final: 0.7582 (mmm) REVERT: l 1526 MET cc_start: 0.8922 (mmm) cc_final: 0.8523 (mmm) REVERT: l 1607 MET cc_start: 0.8156 (tmm) cc_final: 0.7863 (tmm) outliers start: 88 outliers final: 68 residues processed: 407 average time/residue: 0.6398 time to fit residues: 465.6566 Evaluate side-chains 406 residues out of total 7594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 331 time to evaluate : 6.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 115 TYR Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 23 HIS Chi-restraints excluded: chain Q residue 245 ASN Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain Q residue 479 ASP Chi-restraints excluded: chain Q residue 510 MET Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain U residue 414 LEU Chi-restraints excluded: chain U residue 440 ILE Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 73 ASP Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 205 MET Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 196 LEU Chi-restraints excluded: chain W residue 298 ILE Chi-restraints excluded: chain X residue 241 THR Chi-restraints excluded: chain Z residue 182 VAL Chi-restraints excluded: chain Z residue 296 VAL Chi-restraints excluded: chain Z residue 396 PHE Chi-restraints excluded: chain Z residue 509 HIS Chi-restraints excluded: chain Z residue 602 VAL Chi-restraints excluded: chain a residue 36 MET Chi-restraints excluded: chain a residue 41 TYR Chi-restraints excluded: chain a residue 50 GLU Chi-restraints excluded: chain b residue 87 VAL Chi-restraints excluded: chain c residue 74 LYS Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 57 LYS Chi-restraints excluded: chain l residue 1516 CYS Chi-restraints excluded: chain l residue 1602 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 887 random chunks: chunk 583 optimal weight: 0.8980 chunk 414 optimal weight: 40.0000 chunk 693 optimal weight: 40.0000 chunk 50 optimal weight: 1.9990 chunk 347 optimal weight: 0.0980 chunk 458 optimal weight: 8.9990 chunk 794 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 815 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 856 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1366 HIS ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 245 ASN ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1498 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 = 0.4314 r_free = 0.4314 target = 0.086017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.063762 restraints weight = 482543.251| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 7.40 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.6831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.179 74280 Z= 0.421 Angle : 0.799 59.174 101534 Z= 0.424 Chirality : 0.048 2.010 10802 Planarity : 0.005 0.135 12198 Dihedral : 19.518 176.340 13329 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.14 % Favored : 92.84 % Rotamer: Outliers : 1.37 % Allowed : 13.86 % Favored : 84.77 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.07 % Twisted Proline : 0.29 % 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: -0.90 (0.09), residues: 8501 helix: 0.84 (0.09), residues: 3467 sheet: -1.61 (0.17), residues: 918 loop : -1.63 (0.09), residues: 4116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 453 HIS 0.010 0.001 HIS Z 737 PHE 0.026 0.002 PHE G 119 TYR 0.032 0.002 TYR R 485 ARG 0.008 0.001 ARG Q 664 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51140.85 seconds wall clock time: 874 minutes 48.75 seconds (52488.75 seconds total)