Starting phenix.real_space_refine on Sun Dec 29 19:16:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7enj_31211/12_2024/7enj_31211.cif Found real_map, /net/cci-nas-00/data/ceres_data/7enj_31211/12_2024/7enj_31211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7enj_31211/12_2024/7enj_31211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7enj_31211/12_2024/7enj_31211.map" model { file = "/net/cci-nas-00/data/ceres_data/7enj_31211/12_2024/7enj_31211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7enj_31211/12_2024/7enj_31211.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 360 5.16 5 C 36893 2.51 5 N 10051 2.21 5 O 10666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 57971 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3578 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 30, 'TRANS': 436} Chain breaks: 5 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1268 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain breaks: 1 Chain: "F" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1374 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 9, 'TRANS': 157} Chain breaks: 1 Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1348 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 10, 'TRANS': 150} Chain: "H" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1422 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain breaks: 1 Chain: "I" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 605 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Chain: "J" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 840 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 100 Chain: "K" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 879 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "N" Number of atoms: 7772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7772 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 61, 'TRANS': 955} Chain breaks: 10 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "O" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1226 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 16, 'TRANS': 140} Chain breaks: 1 Chain: "P" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3226 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 16, 'TRANS': 403} Chain breaks: 2 Chain: "Q" Number of atoms: 4361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4361 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 27, 'TRANS': 523} Chain breaks: 5 Chain: "R" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1532 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 8, 'TRANS': 182} Chain: "S" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 476 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 7, 'TRANS': 67} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'HIS:plan': 2, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "T" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1499 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain breaks: 1 Chain: "U" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "V" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1063 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain: "W" Number of atoms: 10774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10774 Classifications: {'peptide': 1334} Link IDs: {'PTRANS': 70, 'TRANS': 1263} Chain: "X" Number of atoms: 7061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 7061 Classifications: {'peptide': 897} Link IDs: {'PTRANS': 35, 'TRANS': 861} Chain breaks: 9 Chain: "Z" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 765 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain breaks: 1 Chain: "0" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2159 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 9, 'TRANS': 257} Chain breaks: 2 Chain: "1" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain breaks: 1 Chain: "2" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 899 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain breaks: 1 Chain: "3" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1022 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 3 Chain: "4" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 986 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "0" 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 54001 SG CYS 0 281 116.245 198.626 115.919 1.00 78.68 S ATOM 54027 SG CYS 0 284 115.398 201.723 117.950 1.00 81.40 S ATOM 54235 SG CYS 0 309 112.126 199.629 116.320 1.00 79.33 S Time building chain proxies: 23.74, per 1000 atoms: 0.41 Number of scatterers: 57971 At special positions: 0 Unit cell: (198.152, 354.144, 255.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 360 16.00 O 10666 8.00 N 10051 7.00 C 36893 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: 10.79 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 401 " pdb="ZN ZN 0 401 " - pdb=" SG CYS 0 281 " pdb="ZN ZN 0 401 " - pdb=" SG CYS 0 284 " pdb="ZN ZN 0 401 " - pdb=" SG CYS 0 309 " 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14114 Finding SS restraints... Secondary structure from input PDB file: 277 helices and 38 sheets defined 59.0% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.05 Creating SS restraints... Processing helix chain 'A' and resid 13 through 27 removed outlier: 3.825A pdb=" N SER A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 46 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 73 through 89 Processing helix chain 'A' and resid 135 through 144 removed outlier: 3.679A pdb=" N GLU A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 161 removed outlier: 3.613A pdb=" N PHE A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 195 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.940A pdb=" N LEU A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 403 through 423 Processing helix chain 'A' and resid 490 through 502 Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.650A pdb=" N THR A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 518 " --> pdb=" O LYS A 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 18 Processing helix chain 'D' and resid 27 through 52 Processing helix chain 'D' and resid 63 through 141 removed outlier: 4.020A pdb=" N GLN D 113 " --> pdb=" O GLN D 109 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 157 Processing helix chain 'D' and resid 178 through 184 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'F' and resid 9 through 13 removed outlier: 3.653A pdb=" N ILE F 13 " --> pdb=" O LEU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 25 through 33 removed outlier: 4.096A pdb=" N LEU F 30 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 53 removed outlier: 4.003A pdb=" N VAL F 49 " --> pdb=" O CYS F 45 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN F 53 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 136 removed outlier: 3.827A pdb=" N VAL F 114 " --> pdb=" O ASP F 110 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER F 135 " --> pdb=" O ASP F 131 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 188 Processing helix chain 'G' and resid 18 through 26 removed outlier: 3.958A pdb=" N THR G 22 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE G 26 " --> pdb=" O THR G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 99 Processing helix chain 'G' and resid 103 through 125 removed outlier: 3.645A pdb=" N GLU G 107 " --> pdb=" O ILE G 103 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE G 123 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU G 125 " --> pdb=" O HIS G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 175 removed outlier: 4.559A pdb=" N HIS G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Proline residue: G 172 - end of helix Processing helix chain 'H' and resid 4 through 36 Processing helix chain 'H' and resid 41 through 66 removed outlier: 3.578A pdb=" N GLU H 66 " --> pdb=" O VAL H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 94 removed outlier: 3.633A pdb=" N GLU H 94 " --> pdb=" O MET H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 109 Processing helix chain 'H' and resid 114 through 129 Processing helix chain 'H' and resid 134 through 158 Processing helix chain 'H' and resid 174 through 187 removed outlier: 3.560A pdb=" N PHE H 187 " --> pdb=" O ALA H 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 79 Processing helix chain 'I' and resid 86 through 102 Processing helix chain 'I' and resid 110 through 138 Processing helix chain 'J' and resid 8 through 29 Processing helix chain 'J' and resid 35 through 60 removed outlier: 3.990A pdb=" N GLN J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 73 removed outlier: 4.042A pdb=" N PHE J 68 " --> pdb=" O PRO J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 117 Processing helix chain 'J' and resid 117 through 128 removed outlier: 3.553A pdb=" N MET J 121 " --> pdb=" O PHE J 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 35 Processing helix chain 'K' and resid 41 through 73 Processing helix chain 'K' and resid 83 through 116 removed outlier: 3.769A pdb=" N ARG K 87 " --> pdb=" O SER K 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 73 Processing helix chain 'N' and resid 77 through 106 removed outlier: 3.897A pdb=" N ILE N 83 " --> pdb=" O VAL N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 142 removed outlier: 3.601A pdb=" N VAL N 112 " --> pdb=" O ASN N 108 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP N 142 " --> pdb=" O SER N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 162 removed outlier: 3.788A pdb=" N ALA N 157 " --> pdb=" O ALA N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 178 Processing helix chain 'N' and resid 186 through 204 Processing helix chain 'N' and resid 217 through 221 Processing helix chain 'N' and resid 267 through 284 Processing helix chain 'N' and resid 287 through 318 removed outlier: 3.860A pdb=" N ASP N 291 " --> pdb=" O LYS N 287 " (cutoff:3.500A) Processing helix chain 'N' and resid 382 through 389 removed outlier: 3.707A pdb=" N GLU N 387 " --> pdb=" O SER N 383 " (cutoff:3.500A) Processing helix chain 'N' and resid 396 through 424 removed outlier: 3.529A pdb=" N LEU N 400 " --> pdb=" O SER N 396 " (cutoff:3.500A) Processing helix chain 'N' and resid 471 through 485 Processing helix chain 'N' and resid 488 through 507 removed outlier: 3.899A pdb=" N TRP N 492 " --> pdb=" O ARG N 488 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN N 494 " --> pdb=" O ILE N 490 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE N 498 " --> pdb=" O GLN N 494 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP N 499 " --> pdb=" O GLN N 495 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 652 removed outlier: 3.594A pdb=" N ALA N 642 " --> pdb=" O ASN N 638 " (cutoff:3.500A) Processing helix chain 'N' and resid 652 through 664 removed outlier: 4.038A pdb=" N GLY N 656 " --> pdb=" O MET N 652 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU N 657 " --> pdb=" O PRO N 653 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU N 664 " --> pdb=" O GLU N 660 " (cutoff:3.500A) Processing helix chain 'N' and resid 694 through 702 Processing helix chain 'N' and resid 714 through 718 removed outlier: 4.184A pdb=" N ARG N 718 " --> pdb=" O ARG N 715 " (cutoff:3.500A) Processing helix chain 'N' and resid 759 through 787 removed outlier: 3.840A pdb=" N VAL N 763 " --> pdb=" O GLY N 759 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS N 779 " --> pdb=" O ARG N 775 " (cutoff:3.500A) Processing helix chain 'N' and resid 793 through 797 Processing helix chain 'N' and resid 851 through 862 Processing helix chain 'N' and resid 864 through 883 removed outlier: 5.042A pdb=" N ALA N 877 " --> pdb=" O PHE N 873 " (cutoff:3.500A) Proline residue: N 878 - end of helix removed outlier: 3.647A pdb=" N ALA N 881 " --> pdb=" O ALA N 877 " (cutoff:3.500A) Processing helix chain 'N' and resid 958 through 967 removed outlier: 3.540A pdb=" N PHE N 962 " --> pdb=" O GLY N 958 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE N 966 " --> pdb=" O PHE N 962 " (cutoff:3.500A) Processing helix chain 'N' and resid 1179 through 1187 Processing helix chain 'N' and resid 1205 through 1226 Processing helix chain 'N' and resid 1276 through 1289 Processing helix chain 'N' and resid 1295 through 1306 removed outlier: 4.020A pdb=" N LEU N1299 " --> pdb=" O LYS N1295 " (cutoff:3.500A) Processing helix chain 'N' and resid 1311 through 1325 Processing helix chain 'O' and resid 618 through 628 removed outlier: 3.610A pdb=" N LEU O 622 " --> pdb=" O CYS O 618 " (cutoff:3.500A) Processing helix chain 'O' and resid 633 through 650 Proline residue: O 644 - end of helix Processing helix chain 'O' and resid 675 through 684 removed outlier: 3.536A pdb=" N GLN O 679 " --> pdb=" O PRO O 675 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG O 684 " --> pdb=" O GLY O 680 " (cutoff:3.500A) Processing helix chain 'O' and resid 746 through 762 Processing helix chain 'O' and resid 768 through 788 removed outlier: 4.018A pdb=" N LEU O 772 " --> pdb=" O SER O 768 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA O 787 " --> pdb=" O ALA O 783 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 59 Processing helix chain 'P' and resid 147 through 150 Processing helix chain 'P' and resid 154 through 158 Processing helix chain 'P' and resid 364 through 374 Processing helix chain 'P' and resid 466 through 472 Processing helix chain 'Q' and resid 36 through 47 removed outlier: 3.645A pdb=" N LEU Q 40 " --> pdb=" O MET Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 121 Processing helix chain 'Q' and resid 139 through 172 removed outlier: 3.590A pdb=" N THR Q 143 " --> pdb=" O GLN Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 194 Processing helix chain 'Q' and resid 290 through 318 removed outlier: 3.778A pdb=" N LYS Q 294 " --> pdb=" O HIS Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 387 removed outlier: 3.939A pdb=" N GLU Q 372 " --> pdb=" O LEU Q 368 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR Q 386 " --> pdb=" O PHE Q 382 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU Q 387 " --> pdb=" O HIS Q 383 " (cutoff:3.500A) Processing helix chain 'Q' and resid 388 through 392 removed outlier: 3.709A pdb=" N MET Q 391 " --> pdb=" O SER Q 388 " (cutoff:3.500A) Processing helix chain 'Q' and resid 402 through 408 Processing helix chain 'Q' and resid 414 through 422 removed outlier: 3.541A pdb=" N ILE Q 418 " --> pdb=" O ASP Q 414 " (cutoff:3.500A) Processing helix chain 'Q' and resid 426 through 455 removed outlier: 3.574A pdb=" N LYS Q 430 " --> pdb=" O GLY Q 426 " (cutoff:3.500A) Processing helix chain 'Q' and resid 519 through 544 removed outlier: 3.923A pdb=" N VAL Q 534 " --> pdb=" O SER Q 530 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL Q 537 " --> pdb=" O GLN Q 533 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL Q 543 " --> pdb=" O GLN Q 539 " (cutoff:3.500A) Processing helix chain 'Q' and resid 613 through 617 Processing helix chain 'Q' and resid 635 through 646 Processing helix chain 'R' and resid 28 through 43 removed outlier: 4.483A pdb=" N GLU R 33 " --> pdb=" O ASP R 29 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N SER R 34 " --> pdb=" O HIS R 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU R 35 " --> pdb=" O SER R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 122 removed outlier: 3.538A pdb=" N GLY R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 192 Processing helix chain 'S' and resid 82 through 87 Processing helix chain 'S' and resid 89 through 97 removed outlier: 3.501A pdb=" N TYR S 93 " --> pdb=" O LEU S 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 117 Processing helix chain 'S' and resid 128 through 139 Proline residue: S 134 - end of helix Processing helix chain 'S' and resid 147 through 153 Processing helix chain 'T' and resid 16 through 32 Processing helix chain 'T' and resid 90 through 99 Processing helix chain 'T' and resid 153 through 165 Processing helix chain 'T' and resid 173 through 178 removed outlier: 3.654A pdb=" N ASN T 178 " --> pdb=" O ALA T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 204 removed outlier: 4.106A pdb=" N THR T 189 " --> pdb=" O GLY T 185 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET T 190 " --> pdb=" O PRO T 186 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 29 Processing helix chain 'U' and resid 49 through 76 Processing helix chain 'U' and resid 82 through 133 Processing helix chain 'V' and resid 11 through 40 Processing helix chain 'V' and resid 49 through 90 Processing helix chain 'V' and resid 90 through 136 removed outlier: 3.689A pdb=" N VAL V 94 " --> pdb=" O ASP V 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 22 removed outlier: 3.647A pdb=" N PHE W 22 " --> pdb=" O ILE W 18 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 49 Processing helix chain 'W' and resid 57 through 69 Processing helix chain 'W' and resid 72 through 89 Processing helix chain 'W' and resid 95 through 103 Processing helix chain 'W' and resid 111 through 126 Processing helix chain 'W' and resid 127 through 129 No H-bonds generated for 'chain 'W' and resid 127 through 129' Processing helix chain 'W' and resid 130 through 146 Processing helix chain 'W' and resid 156 through 161 Processing helix chain 'W' and resid 161 through 171 removed outlier: 3.709A pdb=" N GLU W 165 " --> pdb=" O LEU W 161 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL W 166 " --> pdb=" O ALA W 162 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 191 removed outlier: 3.586A pdb=" N ALA W 183 " --> pdb=" O PRO W 179 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 211 removed outlier: 4.201A pdb=" N PHE W 208 " --> pdb=" O LEU W 204 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 219 removed outlier: 3.568A pdb=" N ALA W 216 " --> pdb=" O PHE W 212 " (cutoff:3.500A) Processing helix chain 'W' and resid 223 through 227 removed outlier: 3.717A pdb=" N LEU W 227 " --> pdb=" O ARG W 224 " (cutoff:3.500A) Processing helix chain 'W' and resid 259 through 264 Processing helix chain 'W' and resid 266 through 275 removed outlier: 3.842A pdb=" N LEU W 270 " --> pdb=" O GLN W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 280 through 288 Processing helix chain 'W' and resid 297 through 318 removed outlier: 4.517A pdb=" N GLU W 318 " --> pdb=" O ARG W 314 " (cutoff:3.500A) Processing helix chain 'W' and resid 326 through 344 Processing helix chain 'W' and resid 348 through 360 removed outlier: 3.667A pdb=" N MET W 352 " --> pdb=" O SER W 348 " (cutoff:3.500A) Processing helix chain 'W' and resid 368 through 384 removed outlier: 3.568A pdb=" N LEU W 372 " --> pdb=" O GLY W 368 " (cutoff:3.500A) Processing helix chain 'W' and resid 388 through 393 removed outlier: 4.132A pdb=" N PHE W 392 " --> pdb=" O ALA W 388 " (cutoff:3.500A) Processing helix chain 'W' and resid 394 through 403 removed outlier: 3.845A pdb=" N LEU W 398 " --> pdb=" O PRO W 394 " (cutoff:3.500A) Processing helix chain 'W' and resid 418 through 423 Processing helix chain 'W' and resid 423 through 437 Processing helix chain 'W' and resid 451 through 464 Processing helix chain 'W' and resid 472 through 481 Processing helix chain 'W' and resid 488 through 501 removed outlier: 3.900A pdb=" N ALA W 494 " --> pdb=" O LEU W 490 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR W 498 " --> pdb=" O ALA W 494 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE W 499 " --> pdb=" O LEU W 495 " (cutoff:3.500A) Processing helix chain 'W' and resid 524 through 530 Processing helix chain 'W' and resid 532 through 553 Processing helix chain 'W' and resid 560 through 571 Processing helix chain 'W' and resid 573 through 579 removed outlier: 3.640A pdb=" N ILE W 576 " --> pdb=" O TYR W 573 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU W 577 " --> pdb=" O MET W 574 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER W 578 " --> pdb=" O GLU W 575 " (cutoff:3.500A) Processing helix chain 'W' and resid 580 through 587 Processing helix chain 'W' and resid 587 through 595 Processing helix chain 'W' and resid 599 through 611 Processing helix chain 'W' and resid 616 through 633 Processing helix chain 'W' and resid 638 through 654 Processing helix chain 'W' and resid 660 through 666 Processing helix chain 'W' and resid 671 through 676 removed outlier: 3.575A pdb=" N THR W 674 " --> pdb=" O ASP W 671 " (cutoff:3.500A) Processing helix chain 'W' and resid 680 through 698 removed outlier: 4.153A pdb=" N ASN W 684 " --> pdb=" O SER W 680 " (cutoff:3.500A) Processing helix chain 'W' and resid 710 through 721 removed outlier: 4.376A pdb=" N ASP W 714 " --> pdb=" O THR W 710 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE W 715 " --> pdb=" O TRP W 711 " (cutoff:3.500A) Processing helix chain 'W' and resid 728 through 733 Processing helix chain 'W' and resid 736 through 745 removed outlier: 3.943A pdb=" N GLN W 745 " --> pdb=" O ALA W 741 " (cutoff:3.500A) Processing helix chain 'W' and resid 752 through 770 Processing helix chain 'W' and resid 772 through 781 removed outlier: 3.624A pdb=" N SER W 781 " --> pdb=" O ILE W 777 " (cutoff:3.500A) Processing helix chain 'W' and resid 788 through 800 removed outlier: 3.754A pdb=" N GLU W 799 " --> pdb=" O LYS W 795 " (cutoff:3.500A) Processing helix chain 'W' and resid 805 through 815 removed outlier: 3.862A pdb=" N ARG W 809 " --> pdb=" O GLN W 805 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY W 815 " --> pdb=" O LEU W 811 " (cutoff:3.500A) Processing helix chain 'W' and resid 815 through 837 removed outlier: 3.605A pdb=" N LEU W 819 " --> pdb=" O GLY W 815 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL W 820 " --> pdb=" O ALA W 816 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA W 821 " --> pdb=" O ARG W 817 " (cutoff:3.500A) Processing helix chain 'W' and resid 840 through 855 Processing helix chain 'W' and resid 861 through 871 Processing helix chain 'W' and resid 876 through 892 Processing helix chain 'W' and resid 896 through 906 removed outlier: 3.652A pdb=" N GLU W 906 " --> pdb=" O ASP W 902 " (cutoff:3.500A) Processing helix chain 'W' and resid 916 through 928 removed outlier: 3.751A pdb=" N LYS W 920 " --> pdb=" O ASP W 916 " (cutoff:3.500A) Processing helix chain 'W' and resid 934 through 941 Processing helix chain 'W' and resid 959 through 977 removed outlier: 3.872A pdb=" N LEU W 964 " --> pdb=" O CYS W 960 " (cutoff:3.500A) Proline residue: W 965 - end of helix Processing helix chain 'W' and resid 980 through 991 removed outlier: 3.670A pdb=" N LEU W 984 " --> pdb=" O VAL W 980 " (cutoff:3.500A) Processing helix chain 'W' and resid 992 through 998 Processing helix chain 'W' and resid 1000 through 1012 Processing helix chain 'W' and resid 1019 through 1033 removed outlier: 3.556A pdb=" N LYS W1023 " --> pdb=" O ARG W1019 " (cutoff:3.500A) Processing helix chain 'W' and resid 1045 through 1052 removed outlier: 3.543A pdb=" N CYS W1051 " --> pdb=" O THR W1047 " (cutoff:3.500A) Processing helix chain 'W' and resid 1064 through 1081 removed outlier: 3.697A pdb=" N TYR W1068 " --> pdb=" O ASP W1064 " (cutoff:3.500A) Processing helix chain 'W' and resid 1091 through 1095 removed outlier: 3.817A pdb=" N ASN W1095 " --> pdb=" O TRP W1092 " (cutoff:3.500A) Processing helix chain 'W' and resid 1099 through 1114 removed outlier: 3.632A pdb=" N HIS W1103 " --> pdb=" O ASN W1099 " (cutoff:3.500A) Processing helix chain 'W' and resid 1118 through 1131 removed outlier: 4.220A pdb=" N VAL W1130 " --> pdb=" O LEU W1126 " (cutoff:3.500A) Processing helix chain 'W' and resid 1141 through 1155 removed outlier: 3.751A pdb=" N TRP W1145 " --> pdb=" O ASN W1141 " (cutoff:3.500A) Processing helix chain 'W' and resid 1157 through 1162 removed outlier: 3.573A pdb=" N TRP W1161 " --> pdb=" O PRO W1157 " (cutoff:3.500A) Processing helix chain 'W' and resid 1162 through 1173 removed outlier: 4.052A pdb=" N ASP W1166 " --> pdb=" O ILE W1162 " (cutoff:3.500A) Processing helix chain 'W' and resid 1186 through 1191 Processing helix chain 'W' and resid 1192 through 1198 Processing helix chain 'W' and resid 1203 through 1219 removed outlier: 3.708A pdb=" N HIS W1218 " --> pdb=" O ALA W1214 " (cutoff:3.500A) Processing helix chain 'W' and resid 1220 through 1225 Processing helix chain 'W' and resid 1226 through 1234 Processing helix chain 'W' and resid 1241 through 1253 Processing helix chain 'W' and resid 1255 through 1263 Processing helix chain 'W' and resid 1263 through 1284 removed outlier: 4.115A pdb=" N MET W1267 " --> pdb=" O ARG W1263 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE W1268 " --> pdb=" O THR W1264 " (cutoff:3.500A) Processing helix chain 'W' and resid 1290 through 1305 removed outlier: 3.555A pdb=" N ILE W1294 " --> pdb=" O TYR W1290 " (cutoff:3.500A) Processing helix chain 'W' and resid 1311 through 1320 removed outlier: 3.645A pdb=" N GLU W1315 " --> pdb=" O LYS W1311 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS W1316 " --> pdb=" O GLU W1312 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE W1317 " --> pdb=" O GLN W1313 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN W1320 " --> pdb=" O LYS W1316 " (cutoff:3.500A) Processing helix chain 'W' and resid 1322 through 1330 Processing helix chain 'W' and resid 1331 through 1334 removed outlier: 3.623A pdb=" N HIS W1334 " --> pdb=" O PHE W1331 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 1331 through 1334' Processing helix chain 'X' and resid 5 through 16 Processing helix chain 'X' and resid 19 through 31 Processing helix chain 'X' and resid 34 through 38 removed outlier: 3.579A pdb=" N ASP X 38 " --> pdb=" O ALA X 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 49 Processing helix chain 'X' and resid 57 through 70 Processing helix chain 'X' and resid 74 through 84 removed outlier: 3.546A pdb=" N VAL X 78 " --> pdb=" O SER X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 105 removed outlier: 3.634A pdb=" N VAL X 94 " --> pdb=" O ARG X 90 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE X 104 " --> pdb=" O ILE X 100 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 146 Processing helix chain 'X' and resid 156 through 171 removed outlier: 4.112A pdb=" N SER X 171 " --> pdb=" O LYS X 167 " (cutoff:3.500A) Processing helix chain 'X' and resid 171 through 185 removed outlier: 4.248A pdb=" N LEU X 183 " --> pdb=" O HIS X 179 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU X 184 " --> pdb=" O ILE X 180 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU X 185 " --> pdb=" O ALA X 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 187 through 206 removed outlier: 3.743A pdb=" N ALA X 191 " --> pdb=" O SER X 187 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU X 206 " --> pdb=" O ILE X 202 " (cutoff:3.500A) Processing helix chain 'X' and resid 210 through 225 Processing helix chain 'X' and resid 241 through 254 removed outlier: 3.736A pdb=" N HIS X 245 " --> pdb=" O PHE X 241 " (cutoff:3.500A) Processing helix chain 'X' and resid 259 through 274 removed outlier: 3.735A pdb=" N LEU X 263 " --> pdb=" O GLU X 259 " (cutoff:3.500A) Processing helix chain 'X' and resid 277 through 295 Processing helix chain 'X' and resid 299 through 312 removed outlier: 3.659A pdb=" N LEU X 303 " --> pdb=" O GLY X 299 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 323 Processing helix chain 'X' and resid 330 through 343 Processing helix chain 'X' and resid 344 through 356 Processing helix chain 'X' and resid 358 through 370 Processing helix chain 'X' and resid 374 through 391 removed outlier: 4.086A pdb=" N HIS X 391 " --> pdb=" O ALA X 387 " (cutoff:3.500A) Processing helix chain 'X' and resid 405 through 424 Proline residue: X 415 - end of helix Processing helix chain 'X' and resid 426 through 431 Processing helix chain 'X' and resid 431 through 444 Processing helix chain 'X' and resid 446 through 458 Processing helix chain 'X' and resid 460 through 477 removed outlier: 4.559A pdb=" N TYR X 477 " --> pdb=" O GLU X 473 " (cutoff:3.500A) Processing helix chain 'X' and resid 482 through 507 removed outlier: 4.164A pdb=" N ALA X 486 " --> pdb=" O SER X 482 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU X 491 " --> pdb=" O SER X 487 " (cutoff:3.500A) Processing helix chain 'X' and resid 523 through 533 removed outlier: 3.516A pdb=" N THR X 527 " --> pdb=" O PRO X 523 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET X 533 " --> pdb=" O MET X 529 " (cutoff:3.500A) Processing helix chain 'X' and resid 544 through 548 Processing helix chain 'X' and resid 551 through 562 removed outlier: 3.732A pdb=" N GLU X 555 " --> pdb=" O SER X 551 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER X 556 " --> pdb=" O THR X 552 " (cutoff:3.500A) Processing helix chain 'X' and resid 573 through 595 removed outlier: 4.881A pdb=" N SER X 582 " --> pdb=" O CYS X 578 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ALA X 583 " --> pdb=" O LEU X 579 " (cutoff:3.500A) Processing helix chain 'X' and resid 598 through 611 Processing helix chain 'X' and resid 614 through 631 Processing helix chain 'X' and resid 636 through 647 removed outlier: 3.903A pdb=" N GLN X 641 " --> pdb=" O GLU X 637 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET X 642 " --> pdb=" O LYS X 638 " (cutoff:3.500A) Processing helix chain 'X' and resid 658 through 675 Processing helix chain 'X' and resid 676 through 681 removed outlier: 3.515A pdb=" N THR X 681 " --> pdb=" O VAL X 677 " (cutoff:3.500A) Processing helix chain 'X' and resid 706 through 722 removed outlier: 3.836A pdb=" N VAL X 710 " --> pdb=" O PRO X 706 " (cutoff:3.500A) Processing helix chain 'X' and resid 725 through 754 removed outlier: 3.525A pdb=" N ILE X 729 " --> pdb=" O ASP X 725 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL X 741 " --> pdb=" O HIS X 737 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N TYR X 742 " --> pdb=" O MET X 738 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TRP X 743 " --> pdb=" O GLY X 739 " (cutoff:3.500A) Processing helix chain 'X' and resid 757 through 773 removed outlier: 4.222A pdb=" N SER X 770 " --> pdb=" O GLU X 766 " (cutoff:3.500A) Processing helix chain 'X' and resid 775 through 786 Processing helix chain 'X' and resid 786 through 794 Processing helix chain 'X' and resid 796 through 801 removed outlier: 4.117A pdb=" N HIS X 799 " --> pdb=" O SER X 796 " (cutoff:3.500A) Processing helix chain 'X' and resid 802 through 823 removed outlier: 4.227A pdb=" N ALA X 808 " --> pdb=" O PRO X 804 " (cutoff:3.500A) Processing helix chain 'X' and resid 829 through 839 Processing helix chain 'X' and resid 842 through 847 Processing helix chain 'X' and resid 895 through 914 removed outlier: 3.539A pdb=" N ARG X 899 " --> pdb=" O ASP X 895 " (cutoff:3.500A) Processing helix chain 'X' and resid 918 through 935 removed outlier: 3.533A pdb=" N GLN X 922 " --> pdb=" O GLY X 918 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU X 935 " --> pdb=" O CYS X 931 " (cutoff:3.500A) Processing helix chain 'X' and resid 942 through 947 Processing helix chain 'X' and resid 949 through 958 removed outlier: 4.020A pdb=" N SER X 953 " --> pdb=" O PHE X 949 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL X 956 " --> pdb=" O VAL X 952 " (cutoff:3.500A) Processing helix chain 'X' and resid 966 through 970 Processing helix chain 'X' and resid 975 through 988 removed outlier: 4.074A pdb=" N GLN X 980 " --> pdb=" O PRO X 976 " (cutoff:3.500A) Processing helix chain 'Z' and resid 484 through 500 Processing helix chain 'Z' and resid 549 through 557 Processing helix chain '0' and resid 8 through 38 removed outlier: 3.614A pdb=" N GLY 0 38 " --> pdb=" O CYS 0 34 " (cutoff:3.500A) Processing helix chain '0' and resid 44 through 77 Processing helix chain '0' and resid 104 through 131 removed outlier: 3.695A pdb=" N GLN 0 131 " --> pdb=" O LEU 0 127 " (cutoff:3.500A) Processing helix chain '0' and resid 158 through 172 removed outlier: 3.569A pdb=" N VAL 0 162 " --> pdb=" O PRO 0 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET 0 172 " --> pdb=" O ARG 0 168 " (cutoff:3.500A) Processing helix chain '0' and resid 236 through 253 removed outlier: 3.646A pdb=" N GLN 0 240 " --> pdb=" O TYR 0 236 " (cutoff:3.500A) Processing helix chain '0' and resid 259 through 272 removed outlier: 3.740A pdb=" N SER 0 272 " --> pdb=" O THR 0 268 " (cutoff:3.500A) Processing helix chain '0' and resid 273 through 276 Processing helix chain '0' and resid 306 through 310 Processing helix chain '1' and resid 43 through 56 removed outlier: 3.710A pdb=" N GLU 1 47 " --> pdb=" O THR 1 43 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE 1 56 " --> pdb=" O PHE 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 70 through 106 Processing helix chain '1' and resid 107 through 144 Processing helix chain '2' and resid 56 through 90 Proline residue: 2 65 - end of helix Processing helix chain '2' and resid 101 through 136 removed outlier: 4.239A pdb=" N CYS 2 105 " --> pdb=" O ARG 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 156 through 186 removed outlier: 4.326A pdb=" N THR 2 186 " --> pdb=" O ALA 2 182 " (cutoff:3.500A) Processing helix chain '3' and resid 30 through 58 removed outlier: 4.529A pdb=" N ARG 3 35 " --> pdb=" O ALA 3 31 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR 3 46 " --> pdb=" O GLN 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 70 through 102 Processing helix chain '3' and resid 137 through 176 Processing helix chain '4' and resid 11 through 29 Processing helix chain '4' and resid 30 through 40 Processing helix chain '4' and resid 45 through 55 removed outlier: 3.675A pdb=" N VAL 4 49 " --> pdb=" O ASP 4 45 " (cutoff:3.500A) Processing helix chain '4' and resid 56 through 59 Processing helix chain '4' and resid 60 through 65 Processing helix chain '4' and resid 71 through 80 Processing helix chain '4' and resid 82 through 87 removed outlier: 3.597A pdb=" N LYS 4 86 " --> pdb=" O GLU 4 82 " (cutoff:3.500A) Processing helix chain '4' and resid 90 through 106 removed outlier: 3.618A pdb=" N ALA 4 94 " --> pdb=" O ASN 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 106 through 122 removed outlier: 3.822A pdb=" N GLN 4 122 " --> pdb=" O ALA 4 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 212 removed outlier: 3.665A pdb=" N TYR A 210 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ASN A 221 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A 257 " --> pdb=" O ASN A 221 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LYS A 223 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA A 255 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 225 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N ASN A 254 " --> pdb=" O PRO A 308 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER A 394 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N GLN A 309 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N LEU A 392 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N ILE A 311 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N GLY A 390 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 269 removed outlier: 3.502A pdb=" N VAL A 297 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 362 through 366 removed outlier: 7.177A pdb=" N GLN A 371 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE A 440 " --> pdb=" O GLN A 371 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N CYS A 373 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL A 442 " --> pdb=" O CYS A 373 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE A 375 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLN A 439 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN A 455 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 445 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 143 through 144 Processing sheet with id=AA6, first strand: chain 'F' and resid 66 through 73 removed outlier: 6.327A pdb=" N ILE F 80 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE F 79 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLN F 85 " --> pdb=" O PRO F 94 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLN F 87 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL F 92 " --> pdb=" O GLN F 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 137 through 140 Processing sheet with id=AA8, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AA9, first strand: chain 'N' and resid 224 through 226 removed outlier: 3.623A pdb=" N PHE N 230 " --> pdb=" O VAL N 226 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS N 249 " --> pdb=" O THR N 233 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N THR N 235 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU N 247 " --> pdb=" O THR N 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 324 through 330 removed outlier: 6.645A pdb=" N SER N 336 " --> pdb=" O GLU N 327 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR N 329 " --> pdb=" O CYS N 334 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS N 334 " --> pdb=" O TYR N 329 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 430 through 432 Processing sheet with id=AB3, first strand: chain 'N' and resid 514 through 517 removed outlier: 5.270A pdb=" N TYR N 548 " --> pdb=" O LEU N 542 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER N 572 " --> pdb=" O LEU N 586 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 682 through 683 removed outlier: 5.297A pdb=" N LEU N 705 " --> pdb=" O ALA N 727 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA N 727 " --> pdb=" O LEU N 705 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP N 707 " --> pdb=" O VAL N 725 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR N 709 " --> pdb=" O GLU N 723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 798 through 803 removed outlier: 5.328A pdb=" N VAL N 800 " --> pdb=" O CYS N 811 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N CYS N 811 " --> pdb=" O VAL N 800 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 904 through 908 removed outlier: 4.240A pdb=" N VAL N 933 " --> pdb=" O ARG N 929 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 1240 through 1242 Processing sheet with id=AB8, first strand: chain 'N' and resid 1338 through 1339 Processing sheet with id=AB9, first strand: chain 'O' and resid 692 through 693 removed outlier: 4.440A pdb=" N GLU O 722 " --> pdb=" O ILE O 737 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 14 through 19 removed outlier: 5.486A pdb=" N LEU P 15 " --> pdb=" O ARG P 456 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG P 456 " --> pdb=" O LEU P 15 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR P 17 " --> pdb=" O VAL P 454 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA P 442 " --> pdb=" O LEU P 436 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU P 436 " --> pdb=" O ALA P 442 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL P 444 " --> pdb=" O MET P 434 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N MET P 434 " --> pdb=" O VAL P 444 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE P 446 " --> pdb=" O LYS P 432 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 37 through 39 Processing sheet with id=AC3, first strand: chain 'P' and resid 84 through 89 removed outlier: 6.442A pdb=" N ILE P 105 " --> pdb=" O GLY P 123 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY P 123 " --> pdb=" O ILE P 105 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N CYS P 107 " --> pdb=" O SER P 121 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER P 121 " --> pdb=" O CYS P 107 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER P 117 " --> pdb=" O ALA P 111 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 131 through 136 removed outlier: 6.454A pdb=" N VAL P 182 " --> pdb=" O VAL P 132 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU P 134 " --> pdb=" O ILE P 180 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE P 180 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TRP P 136 " --> pdb=" O GLY P 178 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY P 178 " --> pdb=" O TRP P 136 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU P 177 " --> pdb=" O LEU P 193 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LEU P 187 " --> pdb=" O THR P 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 143 through 145 Processing sheet with id=AC6, first strand: chain 'P' and resid 215 through 220 Processing sheet with id=AC7, first strand: chain 'P' and resid 279 through 287 removed outlier: 5.182A pdb=" N ILE P 280 " --> pdb=" O SER P 299 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N SER P 299 " --> pdb=" O ILE P 280 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS P 282 " --> pdb=" O CYS P 297 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLN P 293 " --> pdb=" O LEU P 286 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL P 306 " --> pdb=" O ALA P 344 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA P 344 " --> pdb=" O VAL P 306 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS P 308 " --> pdb=" O LEU P 342 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 351 through 355 removed outlier: 4.112A pdb=" N ALA P 353 " --> pdb=" O ALA P 385 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL P 391 " --> pdb=" O VAL P 404 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL P 404 " --> pdb=" O VAL P 391 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE P 393 " --> pdb=" O MET P 402 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 195 through 199 removed outlier: 4.556A pdb=" N LYS Q 195 " --> pdb=" O ASP Q 206 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILE Q 203 " --> pdb=" O VAL Q 224 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 255 through 262 Processing sheet with id=AD2, first strand: chain 'Q' and resid 461 through 462 Processing sheet with id=AD3, first strand: chain 'Q' and resid 461 through 462 removed outlier: 3.767A pdb=" N ILE Q 502 " --> pdb=" O LEU Q 514 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 547 through 555 removed outlier: 6.824A pdb=" N LEU Q 549 " --> pdb=" O ALA Q 572 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ALA Q 572 " --> pdb=" O LEU Q 549 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N PHE Q 551 " --> pdb=" O THR Q 570 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR Q 570 " --> pdb=" O PHE Q 551 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASN Q 553 " --> pdb=" O ALA Q 568 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ALA Q 568 " --> pdb=" O ASN Q 553 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA Q 566 " --> pdb=" O VAL Q 555 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N TYR Q 578 " --> pdb=" O SER Q 573 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 160 through 162 removed outlier: 4.323A pdb=" N MET R 18 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU R 88 " --> pdb=" O VAL R 69 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL R 69 " --> pdb=" O LEU R 88 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS R 127 " --> pdb=" O VAL R 57 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU R 59 " --> pdb=" O MET R 125 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N MET R 125 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLU R 128 " --> pdb=" O ILE R 151 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE R 151 " --> pdb=" O GLU R 128 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 3 through 9 removed outlier: 3.897A pdb=" N ILE T 138 " --> pdb=" O MET T 9 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER T 134 " --> pdb=" O MET T 131 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL T 129 " --> pdb=" O ARG T 136 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE T 138 " --> pdb=" O GLY T 127 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLY T 127 " --> pdb=" O ILE T 138 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL T 140 " --> pdb=" O LYS T 125 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS T 125 " --> pdb=" O VAL T 140 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL T 142 " --> pdb=" O LEU T 123 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU T 123 " --> pdb=" O VAL T 142 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL T 126 " --> pdb=" O THR T 115 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR T 115 " --> pdb=" O VAL T 126 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG T 113 " --> pdb=" O THR T 128 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU T 111 " --> pdb=" O THR T 130 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY T 37 " --> pdb=" O ARG T 116 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLN T 118 " --> pdb=" O LYS T 35 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LYS T 35 " --> pdb=" O GLN T 118 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'W' and resid 506 through 507 removed outlier: 7.013A pdb=" N MET W 515 " --> pdb=" O ALA W 558 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Z' and resid 565 through 566 Processing sheet with id=AD9, first strand: chain 'Z' and resid 580 through 582 Processing sheet with id=AE1, first strand: chain '0' and resid 176 through 181 Processing sheet with id=AE2, first strand: chain '0' and resid 296 through 297 3485 hydrogen bonds defined for protein. 10164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.59 Time building geometry restraints manager: 12.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11790 1.32 - 1.45: 13779 1.45 - 1.58: 32983 1.58 - 1.70: 0 1.70 - 1.83: 555 Bond restraints: 59107 Sorted by residual: bond pdb=" C VAL O 643 " pdb=" N PRO O 644 " ideal model delta sigma weight residual 1.336 1.396 -0.061 1.23e-02 6.61e+03 2.44e+01 bond pdb=" C VAL W 13 " pdb=" O VAL W 13 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.13e-02 7.83e+03 1.98e+01 bond pdb=" C VAL W 12 " pdb=" O VAL W 12 " ideal model delta sigma weight residual 1.237 1.286 -0.049 1.13e-02 7.83e+03 1.91e+01 bond pdb=" N ILE A 270 " pdb=" CA ILE A 270 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.09e-02 8.42e+03 1.66e+01 bond pdb=" N LEU U 76 " pdb=" CA LEU U 76 " ideal model delta sigma weight residual 1.457 1.512 -0.055 1.41e-02 5.03e+03 1.55e+01 ... (remaining 59102 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 76786 2.65 - 5.31: 2799 5.31 - 7.96: 349 7.96 - 10.61: 85 10.61 - 13.27: 12 Bond angle restraints: 80031 Sorted by residual: angle pdb=" N PRO N1351 " pdb=" CA PRO N1351 " pdb=" CB PRO N1351 " ideal model delta sigma weight residual 103.08 112.24 -9.16 9.70e-01 1.06e+00 8.92e+01 angle pdb=" N PRO N1343 " pdb=" CA PRO N1343 " pdb=" CB PRO N1343 " ideal model delta sigma weight residual 103.08 112.02 -8.94 9.70e-01 1.06e+00 8.50e+01 angle pdb=" N HIS 4 83 " pdb=" CA HIS 4 83 " pdb=" C HIS 4 83 " ideal model delta sigma weight residual 112.90 100.94 11.96 1.31e+00 5.83e-01 8.34e+01 angle pdb=" N GLN F 173 " pdb=" CA GLN F 173 " pdb=" C GLN F 173 " ideal model delta sigma weight residual 112.94 100.83 12.11 1.41e+00 5.03e-01 7.37e+01 angle pdb=" N PRO N1355 " pdb=" CA PRO N1355 " pdb=" CB PRO N1355 " ideal model delta sigma weight residual 103.25 111.60 -8.35 1.05e+00 9.07e-01 6.32e+01 ... (remaining 80026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 31836 18.00 - 35.99: 3454 35.99 - 53.99: 643 53.99 - 71.98: 89 71.98 - 89.98: 40 Dihedral angle restraints: 36062 sinusoidal: 14472 harmonic: 21590 Sorted by residual: dihedral pdb=" C TYR 4 81 " pdb=" N TYR 4 81 " pdb=" CA TYR 4 81 " pdb=" CB TYR 4 81 " ideal model delta harmonic sigma weight residual -122.60 -139.06 16.46 0 2.50e+00 1.60e-01 4.33e+01 dihedral pdb=" CA ASP W 942 " pdb=" C ASP W 942 " pdb=" N PRO W 943 " pdb=" CA PRO W 943 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA LEU A 242 " pdb=" C LEU A 242 " pdb=" N HIS A 243 " pdb=" CA HIS A 243 " ideal model delta harmonic sigma weight residual -180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 36059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 8338 0.113 - 0.227: 731 0.227 - 0.340: 93 0.340 - 0.453: 9 0.453 - 0.566: 4 Chirality restraints: 9175 Sorted by residual: chirality pdb=" CA TYR 4 81 " pdb=" N TYR 4 81 " pdb=" C TYR 4 81 " pdb=" CB TYR 4 81 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.02e+00 chirality pdb=" CA GLN T 204 " pdb=" N GLN T 204 " pdb=" C GLN T 204 " pdb=" CB GLN T 204 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" CA PRO O 720 " pdb=" N PRO O 720 " pdb=" C PRO O 720 " pdb=" CB PRO O 720 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 6.08e+00 ... (remaining 9172 not shown) Planarity restraints: 10229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO W 30 " -0.021 2.00e-02 2.50e+03 4.40e-02 1.94e+01 pdb=" C PRO W 30 " 0.076 2.00e-02 2.50e+03 pdb=" O PRO W 30 " -0.029 2.00e-02 2.50e+03 pdb=" N GLU W 31 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 167 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.74e+01 pdb=" C ASN A 167 " 0.072 2.00e-02 2.50e+03 pdb=" O ASN A 167 " -0.026 2.00e-02 2.50e+03 pdb=" N LYS A 168 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU X 975 " -0.061 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO X 976 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO X 976 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO X 976 " -0.050 5.00e-02 4.00e+02 ... (remaining 10226 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 9022 2.75 - 3.29: 56157 3.29 - 3.82: 96748 3.82 - 4.36: 111550 4.36 - 4.90: 191444 Nonbonded interactions: 464921 Sorted by model distance: nonbonded pdb=" O ASN W 726 " pdb=" OG SER W 873 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR W 764 " pdb=" OE2 GLU W 799 " model vdw 2.216 3.040 nonbonded pdb=" O GLY H 54 " pdb=" OG1 THR H 58 " model vdw 2.217 3.040 nonbonded pdb=" CD1 ILE G 18 " pdb=" OH TYR 4 51 " model vdw 2.224 3.460 nonbonded pdb=" OG SER P 40 " pdb=" O ARG P 42 " model vdw 2.236 3.040 ... (remaining 464916 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.760 Check model and map are aligned: 0.330 Set scattering table: 0.430 Process input model: 106.420 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4910 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 : 0.011 0.107 59107 Z= 0.745 Angle : 1.178 13.268 80031 Z= 0.705 Chirality : 0.070 0.566 9175 Planarity : 0.009 0.092 10229 Dihedral : 15.292 89.975 21948 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.73 % Favored : 93.70 % Rotamer: Outliers : 1.23 % Allowed : 8.62 % Favored : 90.16 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.67 (0.08), residues: 7192 helix: -1.13 (0.07), residues: 3963 sheet: -1.36 (0.17), residues: 767 loop : -2.81 (0.11), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP X 798 HIS 0.017 0.002 HIS Q 383 PHE 0.037 0.003 PHE N 152 TYR 0.026 0.003 TYR Q 369 ARG 0.011 0.001 ARG W1189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 437 time to evaluate : 5.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 TYR cc_start: 0.6699 (OUTLIER) cc_final: 0.5847 (p90) REVERT: K 92 MET cc_start: 0.9575 (mmm) cc_final: 0.9231 (mmm) REVERT: N 117 MET cc_start: 0.1434 (tmm) cc_final: 0.0866 (ptt) REVERT: N 237 MET cc_start: 0.8869 (mmm) cc_final: 0.7994 (mmm) REVERT: N 462 MET cc_start: 0.8177 (mmt) cc_final: 0.7964 (mmm) REVERT: N 538 LEU cc_start: 0.9462 (tp) cc_final: 0.8981 (mp) REVERT: N 554 MET cc_start: 0.8715 (mtm) cc_final: 0.8256 (ptp) REVERT: N 571 MET cc_start: 0.8678 (ttm) cc_final: 0.8377 (ttm) REVERT: N 725 VAL cc_start: 0.9464 (OUTLIER) cc_final: 0.9199 (p) REVERT: O 714 ASP cc_start: 0.8453 (m-30) cc_final: 0.8243 (t0) REVERT: Q 92 LEU cc_start: 0.0604 (OUTLIER) cc_final: 0.0081 (tp) REVERT: Q 405 MET cc_start: 0.8391 (mmm) cc_final: 0.7366 (ptp) REVERT: Q 569 ILE cc_start: 0.9708 (pt) cc_final: 0.8849 (mt) REVERT: Q 639 MET cc_start: 0.9240 (mmm) cc_final: 0.8965 (tpp) REVERT: Q 642 LEU cc_start: 0.9536 (tp) cc_final: 0.9231 (mm) REVERT: Q 643 MET cc_start: 0.9191 (mtt) cc_final: 0.8799 (mtm) REVERT: R 76 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8861 (mtm) REVERT: R 119 MET cc_start: 0.9275 (mmm) cc_final: 0.8970 (mmm) REVERT: T 95 MET cc_start: 0.9047 (mmm) cc_final: 0.8803 (tpp) REVERT: T 190 MET cc_start: 0.9052 (mmm) cc_final: 0.8816 (mmm) REVERT: V 30 MET cc_start: 0.8382 (mmm) cc_final: 0.7867 (mmm) REVERT: V 61 MET cc_start: 0.8026 (mtt) cc_final: 0.7798 (ttm) REVERT: V 76 MET cc_start: 0.8952 (mmm) cc_final: 0.8473 (mmm) REVERT: V 88 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.8996 (tt) REVERT: W 2 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8343 (mm-30) REVERT: W 32 ASP cc_start: 0.3067 (OUTLIER) cc_final: 0.2366 (m-30) REVERT: W 45 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6720 (tmm160) REVERT: W 312 MET cc_start: -0.1859 (tpt) cc_final: -0.2718 (tpt) REVERT: W 574 MET cc_start: -0.2526 (ptt) cc_final: -0.3066 (ppp) REVERT: W 796 MET cc_start: -0.1540 (mtt) cc_final: -0.1893 (mtt) REVERT: X 484 LYS cc_start: 0.5576 (OUTLIER) cc_final: 0.3441 (tptt) REVERT: X 695 MET cc_start: 0.3276 (mtm) cc_final: 0.1688 (tpt) REVERT: 0 19 SER cc_start: 0.9333 (t) cc_final: 0.9111 (p) REVERT: 0 189 MET cc_start: 0.8614 (mtt) cc_final: 0.8050 (mpp) REVERT: 0 204 MET cc_start: 0.9101 (mmm) cc_final: 0.7694 (tpp) REVERT: 0 225 ASP cc_start: 0.8514 (m-30) cc_final: 0.7796 (t70) REVERT: 0 288 LEU cc_start: 0.9404 (mt) cc_final: 0.8915 (tp) REVERT: 1 143 LEU cc_start: 0.9266 (mt) cc_final: 0.8950 (tp) REVERT: 2 124 HIS cc_start: 0.9315 (t-90) cc_final: 0.8966 (t70) REVERT: 3 49 MET cc_start: 0.8893 (tmm) cc_final: 0.8459 (tmm) REVERT: 3 173 MET cc_start: 0.9298 (mtm) cc_final: 0.8817 (mtm) REVERT: 3 176 MET cc_start: 0.8981 (mmm) cc_final: 0.8595 (tpp) outliers start: 78 outliers final: 20 residues processed: 505 average time/residue: 0.5664 time to fit residues: 479.1929 Evaluate side-chains 320 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 291 time to evaluate : 5.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 613 optimal weight: 10.0000 chunk 550 optimal weight: 7.9990 chunk 305 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 371 optimal weight: 1.9990 chunk 293 optimal weight: 20.0000 chunk 569 optimal weight: 6.9990 chunk 220 optimal weight: 0.4980 chunk 346 optimal weight: 5.9990 chunk 423 optimal weight: 1.9990 chunk 659 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 218 HIS A 221 ASN ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN A 359 HIS A 400 HIS A 414 GLN D 77 GLN D 86 GLN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 GLN H 18 GLN I 119 GLN K 27 ASN ** K 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 GLN K 113 GLN N 309 HIS N 330 HIS ** N 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 532 ASN ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 590 GLN N 638 ASN ** N 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 832 HIS N 856 GLN N 964 ASN N1179 HIS O 619 GLN ** O 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 679 GLN O 740 GLN O 742 GLN O 746 ASN O 753 HIS P 63 HIS P 69 HIS P 80 HIS P 225 ASN P 272 ASN P 282 HIS ** P 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 387 HIS P 435 GLN ** Q 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 GLN Q 193 HIS Q 219 HIS Q 321 GLN ** Q 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 402 HIS Q 411 GLN Q 437 HIS Q 468 ASN Q 492 GLN Q 494 GLN Q 506 HIS Q 517 GLN Q 528 GLN Q 532 HIS Q 565 ASN ** Q 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 611 GLN R 54 HIS R 97 ASN ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 56 GLN U 119 GLN W 46 GLN ** W 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 378 GLN ** W 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 433 ASN W 513 ASN ** W 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 844 ASN W 851 ASN W 923 ASN W 948 GLN W 972 HIS W1059 ASN W1134 GLN W1300 HIS W1320 ASN X 8 GLN X 49 GLN X 179 HIS X 217 GLN X 361 ASN ** X 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 402 ASN X 472 ASN X 502 HIS X 544 HIS X 627 HIS X 760 HIS X 832 GLN ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 160 GLN 0 306 HIS ** 1 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 84 GLN 2 129 GLN 3 42 GLN ** 4 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 90 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4991 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 59107 Z= 0.223 Angle : 0.686 13.339 80031 Z= 0.353 Chirality : 0.043 0.239 9175 Planarity : 0.005 0.100 10229 Dihedral : 5.577 27.487 7828 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.74 % Favored : 95.12 % Rotamer: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.65 (0.10), residues: 7192 helix: 0.79 (0.08), residues: 3996 sheet: -0.95 (0.17), residues: 780 loop : -2.33 (0.11), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP X 798 HIS 0.010 0.001 HIS Q 324 PHE 0.023 0.002 PHE W 9 TYR 0.030 0.002 TYR V 59 ARG 0.015 0.001 ARG K 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 319 time to evaluate : 5.451 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: D 93 MET cc_start: 0.8077 (mmt) cc_final: 0.7377 (mmm) REVERT: D 190 MET cc_start: 0.4640 (ptt) cc_final: 0.3236 (ptt) REVERT: K 92 MET cc_start: 0.9559 (mmm) cc_final: 0.9278 (mmm) REVERT: N 117 MET cc_start: 0.1264 (tmm) cc_final: 0.0112 (ptt) REVERT: N 237 MET cc_start: 0.8809 (mmm) cc_final: 0.7821 (mmm) REVERT: N 400 LEU cc_start: 0.8421 (tp) cc_final: 0.8219 (tt) REVERT: N 554 MET cc_start: 0.9017 (mtm) cc_final: 0.8059 (ptp) REVERT: O 723 LEU cc_start: 0.9014 (mt) cc_final: 0.8624 (mt) REVERT: Q 375 LEU cc_start: 0.9555 (mt) cc_final: 0.8863 (mt) REVERT: Q 639 MET cc_start: 0.9229 (mmm) cc_final: 0.8969 (tpp) REVERT: T 95 MET cc_start: 0.8866 (mmm) cc_final: 0.8519 (tpt) REVERT: T 181 ASP cc_start: 0.9080 (p0) cc_final: 0.8450 (p0) REVERT: V 30 MET cc_start: 0.8477 (mmm) cc_final: 0.7811 (mmm) REVERT: V 61 MET cc_start: 0.7849 (mtt) cc_final: 0.7545 (ttm) REVERT: V 76 MET cc_start: 0.8977 (mmm) cc_final: 0.8706 (mmt) REVERT: W 312 MET cc_start: -0.1561 (tpt) cc_final: -0.2613 (tpt) REVERT: W 396 MET cc_start: 0.4674 (mmt) cc_final: 0.3909 (mmp) REVERT: W 469 MET cc_start: -0.0334 (tpt) cc_final: -0.2001 (tpt) REVERT: W 525 MET cc_start: 0.6670 (tpt) cc_final: 0.6402 (tpp) REVERT: W 574 MET cc_start: -0.2502 (ptt) cc_final: -0.3265 (ppp) REVERT: W 796 MET cc_start: -0.0663 (mtt) cc_final: -0.1328 (mtt) REVERT: W 1079 MET cc_start: 0.1531 (mtp) cc_final: 0.1253 (mtt) REVERT: X 254 MET cc_start: 0.1483 (mtm) cc_final: 0.0435 (ptp) REVERT: X 382 MET cc_start: -0.0891 (mmt) cc_final: -0.1287 (mmm) REVERT: X 442 MET cc_start: -0.7059 (ttt) cc_final: -0.8029 (tpt) REVERT: X 695 MET cc_start: 0.2366 (mtm) cc_final: 0.0962 (mmm) REVERT: 0 39 MET cc_start: 0.2361 (tpt) cc_final: 0.2088 (tpt) REVERT: 0 140 MET cc_start: 0.5545 (mtm) cc_final: 0.5296 (mpp) REVERT: 0 204 MET cc_start: 0.8708 (mmm) cc_final: 0.7601 (tpp) REVERT: 0 225 ASP cc_start: 0.8835 (m-30) cc_final: 0.8250 (t70) REVERT: 0 288 LEU cc_start: 0.9446 (mt) cc_final: 0.9063 (tp) REVERT: 2 124 HIS cc_start: 0.9415 (t-90) cc_final: 0.8966 (t70) REVERT: 3 49 MET cc_start: 0.9051 (tmm) cc_final: 0.8402 (tmm) REVERT: 3 159 ILE cc_start: 0.9709 (mt) cc_final: 0.9443 (mm) REVERT: 3 173 MET cc_start: 0.9260 (mtm) cc_final: 0.8887 (mtm) outliers start: 5 outliers final: 1 residues processed: 324 average time/residue: 0.5623 time to fit residues: 311.1476 Evaluate side-chains 268 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 5.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 366 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 chunk 548 optimal weight: 7.9990 chunk 448 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 660 optimal weight: 7.9990 chunk 713 optimal weight: 0.7980 chunk 588 optimal weight: 50.0000 chunk 654 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 529 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN N 197 GLN N 267 HIS ** N 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 411 GLN ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 732 ASN ** O 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 705 HIS ** P 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 463 HIS ** Q 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 184 ASN ** Q 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 626 GLN R 30 HIS T 67 HIS ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 26 ASN X 49 GLN X 502 HIS Z 556 GLN ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 90 GLN 1 109 GLN 1 132 HIS 2 72 GLN ** 4 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 101 GLN 4 107 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5076 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 59107 Z= 0.245 Angle : 0.654 10.942 80031 Z= 0.335 Chirality : 0.041 0.222 9175 Planarity : 0.005 0.071 10229 Dihedral : 5.050 30.452 7828 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.80 % Favored : 95.06 % Rotamer: Outliers : 0.02 % Allowed : 3.74 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.15 (0.10), residues: 7192 helix: 1.49 (0.08), residues: 4034 sheet: -0.66 (0.18), residues: 757 loop : -2.11 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP P 71 HIS 0.006 0.001 HIS X 836 PHE 0.042 0.002 PHE W 488 TYR 0.018 0.001 TYR 2 60 ARG 0.008 0.001 ARG W 753 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 5.488 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: D 93 MET cc_start: 0.8065 (mmt) cc_final: 0.7519 (mmm) REVERT: D 190 MET cc_start: 0.4748 (ptt) cc_final: 0.3540 (ptt) REVERT: I 76 MET cc_start: 0.4591 (mtp) cc_final: 0.4184 (ttm) REVERT: I 140 MET cc_start: 0.7535 (mmm) cc_final: 0.6563 (mmt) REVERT: N 117 MET cc_start: 0.1388 (tmm) cc_final: 0.0250 (ptt) REVERT: N 237 MET cc_start: 0.8804 (mmm) cc_final: 0.7875 (mmm) REVERT: N 314 MET cc_start: 0.7735 (tpp) cc_final: 0.7068 (tpp) REVERT: N 462 MET cc_start: 0.8473 (mmp) cc_final: 0.7826 (mmp) REVERT: N 554 MET cc_start: 0.8974 (mtm) cc_final: 0.8157 (ptp) REVERT: N 707 ASP cc_start: 0.6161 (t0) cc_final: 0.5917 (t70) REVERT: O 723 LEU cc_start: 0.9057 (mt) cc_final: 0.8814 (mt) REVERT: O 756 MET cc_start: 0.9456 (tpp) cc_final: 0.8254 (tpt) REVERT: P 49 MET cc_start: 0.4450 (tpp) cc_final: 0.4138 (mmm) REVERT: Q 125 MET cc_start: 0.8164 (mmp) cc_final: 0.7854 (mmm) REVERT: Q 375 LEU cc_start: 0.9628 (mt) cc_final: 0.8876 (mt) REVERT: Q 392 MET cc_start: 0.8872 (mmp) cc_final: 0.8253 (mmp) REVERT: Q 639 MET cc_start: 0.9193 (mmm) cc_final: 0.8920 (tpp) REVERT: R 19 MET cc_start: 0.8727 (mmp) cc_final: 0.8441 (mmp) REVERT: T 63 MET cc_start: 0.8018 (mmm) cc_final: 0.7762 (mmm) REVERT: T 181 ASP cc_start: 0.9187 (p0) cc_final: 0.8533 (p0) REVERT: V 30 MET cc_start: 0.8384 (mmm) cc_final: 0.7906 (mmm) REVERT: V 61 MET cc_start: 0.8268 (mtt) cc_final: 0.7717 (ttm) REVERT: W 286 MET cc_start: 0.0732 (mmp) cc_final: -0.0685 (mtt) REVERT: W 312 MET cc_start: -0.1769 (tpt) cc_final: -0.2769 (tpt) REVERT: W 396 MET cc_start: 0.4364 (mmt) cc_final: 0.4061 (mmp) REVERT: W 469 MET cc_start: -0.0125 (tpt) cc_final: -0.2069 (tpt) REVERT: W 525 MET cc_start: 0.6665 (tpt) cc_final: 0.6421 (tpp) REVERT: W 574 MET cc_start: -0.2232 (ptt) cc_final: -0.3169 (ppp) REVERT: W 720 MET cc_start: 0.4911 (mmp) cc_final: 0.4369 (mmp) REVERT: W 796 MET cc_start: -0.0627 (mtt) cc_final: -0.1115 (mtt) REVERT: W 871 MET cc_start: -0.1633 (tpp) cc_final: -0.2084 (tpp) REVERT: X 103 MET cc_start: 0.8256 (mtp) cc_final: 0.7856 (mtp) REVERT: X 160 MET cc_start: 0.8670 (ptt) cc_final: 0.8395 (ptm) REVERT: X 572 MET cc_start: 0.0904 (ptm) cc_final: -0.0072 (ppp) REVERT: X 695 MET cc_start: 0.3044 (mtm) cc_final: 0.1465 (mmt) REVERT: 0 198 LEU cc_start: 0.9552 (mt) cc_final: 0.9154 (mt) REVERT: 0 204 MET cc_start: 0.8577 (mmm) cc_final: 0.8052 (tpp) REVERT: 0 225 ASP cc_start: 0.8964 (m-30) cc_final: 0.8180 (t70) REVERT: 0 244 ASP cc_start: 0.9341 (m-30) cc_final: 0.9121 (m-30) REVERT: 0 288 LEU cc_start: 0.9425 (mt) cc_final: 0.9136 (tp) REVERT: 2 124 HIS cc_start: 0.9082 (t-90) cc_final: 0.8713 (t70) REVERT: 3 49 MET cc_start: 0.9134 (tmm) cc_final: 0.8470 (tmm) REVERT: 3 159 ILE cc_start: 0.9404 (mt) cc_final: 0.9166 (tp) REVERT: 3 173 MET cc_start: 0.9339 (mtm) cc_final: 0.9088 (mtm) outliers start: 1 outliers final: 1 residues processed: 292 average time/residue: 0.5471 time to fit residues: 279.4081 Evaluate side-chains 251 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 5.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 652 optimal weight: 0.5980 chunk 496 optimal weight: 50.0000 chunk 342 optimal weight: 0.9980 chunk 73 optimal weight: 0.0010 chunk 315 optimal weight: 0.9990 chunk 443 optimal weight: 6.9990 chunk 662 optimal weight: 1.9990 chunk 701 optimal weight: 7.9990 chunk 346 optimal weight: 2.9990 chunk 628 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 HIS ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN G 25 ASN G 129 HIS ** K 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 267 HIS N 294 ASN ** N 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 411 GLN ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 832 HIS ** O 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 ASN ** Q 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 402 HIS Q 599 ASN T 67 HIS ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 97 ASN ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 628 HIS ** W 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 914 GLN W1217 HIS X 266 GLN 2 136 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5032 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 59107 Z= 0.168 Angle : 0.597 10.155 80031 Z= 0.302 Chirality : 0.041 0.310 9175 Planarity : 0.004 0.069 10229 Dihedral : 4.756 29.497 7828 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.33 % Rotamer: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.61 (0.10), residues: 7192 helix: 1.88 (0.08), residues: 4029 sheet: -0.46 (0.18), residues: 733 loop : -1.93 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP X 798 HIS 0.015 0.001 HIS K 58 PHE 0.031 0.001 PHE H 49 TYR 0.016 0.001 TYR 2 60 ARG 0.007 0.000 ARG Z 554 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 278 time to evaluate : 5.552 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: D 93 MET cc_start: 0.7983 (mmt) cc_final: 0.7458 (mmm) REVERT: D 190 MET cc_start: 0.4785 (ptt) cc_final: 0.3406 (ptt) REVERT: I 76 MET cc_start: 0.4574 (mtp) cc_final: 0.4128 (ttm) REVERT: I 140 MET cc_start: 0.7545 (mmm) cc_final: 0.7294 (mtm) REVERT: N 117 MET cc_start: 0.1821 (tmm) cc_final: 0.0954 (ptt) REVERT: N 237 MET cc_start: 0.8803 (mmm) cc_final: 0.7807 (mmm) REVERT: N 314 MET cc_start: 0.8035 (tpp) cc_final: 0.7360 (tpp) REVERT: N 375 ASP cc_start: 0.6784 (OUTLIER) cc_final: 0.5916 (p0) REVERT: N 554 MET cc_start: 0.8600 (mtm) cc_final: 0.7389 (ptp) REVERT: O 723 LEU cc_start: 0.9327 (mt) cc_final: 0.8912 (mp) REVERT: O 756 MET cc_start: 0.9482 (tpp) cc_final: 0.8549 (tpt) REVERT: P 434 MET cc_start: -0.1856 (ptt) cc_final: -0.2246 (ptt) REVERT: Q 125 MET cc_start: 0.8058 (mmp) cc_final: 0.7836 (mmm) REVERT: Q 369 TYR cc_start: 0.9205 (t80) cc_final: 0.8921 (t80) REVERT: Q 392 MET cc_start: 0.8807 (mmp) cc_final: 0.8228 (mmp) REVERT: Q 405 MET cc_start: 0.8293 (mmm) cc_final: 0.7068 (mtm) REVERT: T 63 MET cc_start: 0.7790 (mmm) cc_final: 0.7580 (mmm) REVERT: T 181 ASP cc_start: 0.9210 (p0) cc_final: 0.8499 (p0) REVERT: V 30 MET cc_start: 0.8600 (mmm) cc_final: 0.7884 (mmm) REVERT: V 61 MET cc_start: 0.7984 (mtt) cc_final: 0.7498 (ttm) REVERT: W 41 LEU cc_start: 0.3921 (tt) cc_final: 0.3189 (tp) REVERT: W 85 MET cc_start: 0.9151 (mmp) cc_final: 0.8581 (mmp) REVERT: W 286 MET cc_start: -0.0328 (mmp) cc_final: -0.1112 (mtt) REVERT: W 312 MET cc_start: -0.1696 (tpt) cc_final: -0.2769 (tpt) REVERT: W 373 MET cc_start: -0.0707 (ptt) cc_final: -0.1134 (ptt) REVERT: W 396 MET cc_start: 0.4217 (mmt) cc_final: 0.3896 (mmp) REVERT: W 469 MET cc_start: -0.1742 (tpt) cc_final: -0.3296 (tpt) REVERT: W 525 MET cc_start: 0.6599 (tpt) cc_final: 0.6360 (tpp) REVERT: W 574 MET cc_start: -0.2044 (ptt) cc_final: -0.3049 (ppp) REVERT: W 720 MET cc_start: 0.5036 (mmp) cc_final: 0.4598 (mmp) REVERT: W 796 MET cc_start: -0.0410 (mtt) cc_final: -0.1058 (mtt) REVERT: W 871 MET cc_start: -0.1757 (tpp) cc_final: -0.2037 (tpp) REVERT: X 103 MET cc_start: 0.8214 (mtp) cc_final: 0.7634 (mtp) REVERT: X 160 MET cc_start: 0.8478 (ptt) cc_final: 0.8127 (ptm) REVERT: X 572 MET cc_start: 0.0881 (ptm) cc_final: -0.0113 (ppp) REVERT: X 695 MET cc_start: 0.2787 (mtm) cc_final: 0.1389 (mmt) REVERT: 0 198 LEU cc_start: 0.9596 (mt) cc_final: 0.8935 (mt) REVERT: 0 204 MET cc_start: 0.8687 (mmm) cc_final: 0.7847 (tpp) REVERT: 0 244 ASP cc_start: 0.8999 (m-30) cc_final: 0.8772 (m-30) REVERT: 0 288 LEU cc_start: 0.9375 (mt) cc_final: 0.9050 (tp) REVERT: 2 124 HIS cc_start: 0.9025 (t-90) cc_final: 0.8645 (t70) REVERT: 3 49 MET cc_start: 0.8670 (tmm) cc_final: 0.8104 (tmm) REVERT: 3 161 ASP cc_start: 0.8746 (t0) cc_final: 0.8506 (t0) outliers start: 4 outliers final: 1 residues processed: 281 average time/residue: 0.5428 time to fit residues: 264.7107 Evaluate side-chains 252 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 250 time to evaluate : 5.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 584 optimal weight: 40.0000 chunk 398 optimal weight: 0.0870 chunk 10 optimal weight: 8.9990 chunk 522 optimal weight: 5.9990 chunk 289 optimal weight: 50.0000 chunk 598 optimal weight: 50.0000 chunk 485 optimal weight: 10.0000 chunk 0 optimal weight: 70.0000 chunk 358 optimal weight: 3.9990 chunk 629 optimal weight: 50.0000 chunk 177 optimal weight: 0.7980 overall best weight: 3.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 128 HIS A 282 ASN A 295 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN ** N 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 325 GLN N 464 GLN ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 744 HIS N 793 HIS N 832 HIS O 628 ASN ** O 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 321 GLN ** Q 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 367 HIS ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 HIS ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 805 GLN W 822 HIS X 157 GLN Z 549 GLN 1 79 GLN ** 3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 151 GLN 4 50 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5183 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 59107 Z= 0.355 Angle : 0.716 12.714 80031 Z= 0.362 Chirality : 0.042 0.270 9175 Planarity : 0.005 0.196 10229 Dihedral : 4.794 30.996 7828 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.05 % Favored : 94.81 % Rotamer: Outliers : 0.03 % Allowed : 2.37 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: 0.65 (0.10), residues: 7192 helix: 1.89 (0.08), residues: 4044 sheet: -0.53 (0.18), residues: 739 loop : -1.87 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP X 798 HIS 0.013 0.001 HIS Q 554 PHE 0.027 0.002 PHE T 91 TYR 0.026 0.002 TYR T 144 ARG 0.022 0.001 ARG N 718 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 261 time to evaluate : 5.491 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: D 93 MET cc_start: 0.8188 (mmt) cc_final: 0.7705 (mmm) REVERT: D 190 MET cc_start: 0.4158 (ptt) cc_final: 0.2839 (ptt) REVERT: H 146 MET cc_start: 0.7187 (ttt) cc_final: 0.5961 (ppp) REVERT: I 76 MET cc_start: 0.4436 (mtp) cc_final: 0.3990 (ttm) REVERT: I 140 MET cc_start: 0.7635 (mmm) cc_final: 0.6843 (mmt) REVERT: N 117 MET cc_start: 0.2044 (tmm) cc_final: 0.1103 (ptt) REVERT: N 237 MET cc_start: 0.8653 (mmm) cc_final: 0.7658 (mmm) REVERT: N 314 MET cc_start: 0.8058 (tpp) cc_final: 0.7636 (tpp) REVERT: N 554 MET cc_start: 0.8783 (mtm) cc_final: 0.7742 (ptp) REVERT: Q 125 MET cc_start: 0.8215 (mmp) cc_final: 0.7976 (mmm) REVERT: Q 392 MET cc_start: 0.8849 (mmp) cc_final: 0.8638 (mmp) REVERT: R 125 MET cc_start: 0.8427 (tpt) cc_final: 0.8200 (tpt) REVERT: T 9 MET cc_start: 0.7866 (tpt) cc_final: 0.7538 (tpt) REVERT: T 63 MET cc_start: 0.7923 (mmm) cc_final: 0.7398 (mmm) REVERT: T 95 MET cc_start: 0.7907 (tpt) cc_final: 0.7603 (tpp) REVERT: T 181 ASP cc_start: 0.9315 (p0) cc_final: 0.8753 (p0) REVERT: V 30 MET cc_start: 0.8855 (mmm) cc_final: 0.8001 (mmm) REVERT: V 76 MET cc_start: 0.8450 (mmp) cc_final: 0.8212 (mmm) REVERT: W 41 LEU cc_start: 0.4885 (tt) cc_final: 0.4277 (tp) REVERT: W 286 MET cc_start: -0.0126 (mmp) cc_final: -0.0972 (mtt) REVERT: W 312 MET cc_start: -0.1720 (tpt) cc_final: -0.2832 (tpt) REVERT: W 469 MET cc_start: -0.1621 (tpt) cc_final: -0.3410 (tpt) REVERT: W 525 MET cc_start: 0.6548 (tpt) cc_final: 0.6336 (tpp) REVERT: W 574 MET cc_start: -0.1287 (ptt) cc_final: -0.2535 (ppp) REVERT: W 720 MET cc_start: 0.4785 (mmp) cc_final: 0.4341 (mmp) REVERT: W 796 MET cc_start: -0.0534 (mtt) cc_final: -0.1025 (mtt) REVERT: X 101 MET cc_start: 0.8819 (ppp) cc_final: 0.8583 (ppp) REVERT: X 103 MET cc_start: 0.8316 (mtp) cc_final: 0.7692 (mtp) REVERT: X 160 MET cc_start: 0.8756 (ptt) cc_final: 0.8494 (ptm) REVERT: X 442 MET cc_start: -0.6632 (tpt) cc_final: -0.6998 (tpt) REVERT: X 572 MET cc_start: -0.1794 (ptm) cc_final: -0.2313 (ppp) REVERT: X 695 MET cc_start: 0.2602 (mtm) cc_final: 0.1348 (mmt) REVERT: 0 140 MET cc_start: 0.4254 (mtm) cc_final: 0.3555 (mtm) REVERT: 0 198 LEU cc_start: 0.9620 (mt) cc_final: 0.9339 (mt) REVERT: 0 204 MET cc_start: 0.8616 (mmm) cc_final: 0.8065 (tpp) REVERT: 3 49 MET cc_start: 0.8656 (tmm) cc_final: 0.8212 (tmm) REVERT: 3 161 ASP cc_start: 0.8873 (t0) cc_final: 0.8539 (t0) REVERT: 3 173 MET cc_start: 0.9351 (mtm) cc_final: 0.9087 (mtm) REVERT: 3 176 MET cc_start: 0.8798 (tpp) cc_final: 0.8524 (tpp) outliers start: 2 outliers final: 0 residues processed: 263 average time/residue: 0.5724 time to fit residues: 261.8278 Evaluate side-chains 235 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 5.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 236 optimal weight: 20.0000 chunk 631 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 412 optimal weight: 0.9990 chunk 173 optimal weight: 0.7980 chunk 702 optimal weight: 0.9980 chunk 583 optimal weight: 30.0000 chunk 325 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 232 optimal weight: 0.9980 chunk 368 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 HIS ** N 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 464 GLN ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 832 HIS O 650 HIS P 240 GLN ** P 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 367 HIS ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 599 ASN T 67 HIS ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 805 GLN X 157 GLN X 274 GLN ** 3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5081 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 59107 Z= 0.166 Angle : 0.585 9.401 80031 Z= 0.295 Chirality : 0.041 0.234 9175 Planarity : 0.004 0.130 10229 Dihedral : 4.559 28.991 7828 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.34 % Favored : 95.54 % Rotamer: Outliers : 0.02 % Allowed : 1.40 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.99 (0.10), residues: 7192 helix: 2.21 (0.08), residues: 4036 sheet: -0.49 (0.18), residues: 737 loop : -1.76 (0.12), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP X 798 HIS 0.010 0.001 HIS K 58 PHE 0.039 0.001 PHE X 732 TYR 0.014 0.001 TYR F 32 ARG 0.013 0.000 ARG K 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 5.408 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: D 80 MET cc_start: 0.7895 (ptt) cc_final: 0.7473 (ptt) REVERT: D 93 MET cc_start: 0.8093 (mmt) cc_final: 0.7533 (mmm) REVERT: D 190 MET cc_start: 0.5025 (ptt) cc_final: 0.3561 (ptt) REVERT: F 25 ASN cc_start: 0.8377 (t0) cc_final: 0.8154 (t0) REVERT: F 63 MET cc_start: 0.3042 (ptt) cc_final: 0.2763 (ptt) REVERT: G 138 MET cc_start: 0.7434 (ptp) cc_final: 0.6834 (tmm) REVERT: H 146 MET cc_start: 0.7273 (ttt) cc_final: 0.6047 (ppp) REVERT: I 76 MET cc_start: 0.4324 (mtp) cc_final: 0.4057 (ttm) REVERT: I 140 MET cc_start: 0.7673 (mmm) cc_final: 0.6871 (mmt) REVERT: N 117 MET cc_start: 0.2056 (tmm) cc_final: 0.1125 (ptt) REVERT: N 237 MET cc_start: 0.8032 (mmm) cc_final: 0.6855 (mmm) REVERT: N 269 MET cc_start: 0.9222 (ptm) cc_final: 0.8292 (ptp) REVERT: N 314 MET cc_start: 0.7918 (tpp) cc_final: 0.7568 (tmm) REVERT: N 554 MET cc_start: 0.8561 (mtm) cc_final: 0.7345 (ptp) REVERT: O 723 LEU cc_start: 0.9589 (mt) cc_final: 0.9335 (mt) REVERT: O 756 MET cc_start: 0.9574 (tpp) cc_final: 0.9288 (tpp) REVERT: Q 125 MET cc_start: 0.8240 (mmp) cc_final: 0.7998 (mmm) REVERT: Q 391 MET cc_start: 0.8230 (mpp) cc_final: 0.7840 (mpp) REVERT: Q 405 MET cc_start: 0.8388 (mmm) cc_final: 0.7162 (ptp) REVERT: Q 521 LEU cc_start: 0.9017 (tp) cc_final: 0.8786 (tp) REVERT: R 18 MET cc_start: 0.8307 (mmp) cc_final: 0.7828 (mmp) REVERT: R 19 MET cc_start: 0.8799 (mmm) cc_final: 0.8349 (mmp) REVERT: T 9 MET cc_start: 0.8011 (tpt) cc_final: 0.7734 (tpt) REVERT: T 63 MET cc_start: 0.7805 (mmm) cc_final: 0.7516 (mmm) REVERT: T 95 MET cc_start: 0.7640 (tpt) cc_final: 0.6862 (tpp) REVERT: T 181 ASP cc_start: 0.9021 (p0) cc_final: 0.8451 (p0) REVERT: V 30 MET cc_start: 0.9124 (mmm) cc_final: 0.8414 (mmm) REVERT: V 61 MET cc_start: 0.8281 (mtt) cc_final: 0.7756 (ttm) REVERT: W 41 LEU cc_start: 0.4444 (tt) cc_final: 0.3817 (tp) REVERT: W 286 MET cc_start: -0.0221 (mmp) cc_final: -0.1017 (mtt) REVERT: W 312 MET cc_start: -0.1810 (tpt) cc_final: -0.2882 (tpt) REVERT: W 373 MET cc_start: 0.0688 (ptt) cc_final: 0.0198 (ptt) REVERT: W 469 MET cc_start: -0.1650 (tpt) cc_final: -0.3529 (tpt) REVERT: W 525 MET cc_start: 0.6486 (tpt) cc_final: 0.6272 (tpp) REVERT: W 574 MET cc_start: -0.1090 (ptt) cc_final: -0.2442 (ppp) REVERT: W 720 MET cc_start: 0.5039 (mmp) cc_final: 0.4612 (mmp) REVERT: W 796 MET cc_start: 0.0415 (mtt) cc_final: -0.0098 (mtt) REVERT: W 871 MET cc_start: -0.0866 (tpp) cc_final: -0.1092 (tpp) REVERT: X 103 MET cc_start: 0.8093 (mtp) cc_final: 0.7474 (mtp) REVERT: X 160 MET cc_start: 0.8515 (ptt) cc_final: 0.8176 (ptm) REVERT: X 442 MET cc_start: -0.5659 (tpt) cc_final: -0.5995 (tpt) REVERT: X 572 MET cc_start: -0.2043 (ptm) cc_final: -0.2501 (ppp) REVERT: X 695 MET cc_start: 0.2537 (mtm) cc_final: 0.1380 (mmt) REVERT: 0 140 MET cc_start: 0.4253 (mtm) cc_final: 0.3513 (mtm) REVERT: 0 198 LEU cc_start: 0.9597 (mt) cc_final: 0.8960 (mt) REVERT: 0 204 MET cc_start: 0.8737 (mmm) cc_final: 0.7852 (tpp) REVERT: 0 288 LEU cc_start: 0.9344 (mt) cc_final: 0.9066 (tp) REVERT: 2 124 HIS cc_start: 0.8791 (t-90) cc_final: 0.8495 (t70) REVERT: 3 49 MET cc_start: 0.8698 (tmm) cc_final: 0.8121 (tmm) REVERT: 3 161 ASP cc_start: 0.8665 (t0) cc_final: 0.8325 (t0) REVERT: 3 176 MET cc_start: 0.8774 (tpp) cc_final: 0.8545 (tpp) outliers start: 1 outliers final: 0 residues processed: 278 average time/residue: 0.5458 time to fit residues: 264.4581 Evaluate side-chains 239 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 5.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 677 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 400 optimal weight: 0.7980 chunk 512 optimal weight: 50.0000 chunk 397 optimal weight: 4.9990 chunk 591 optimal weight: 6.9990 chunk 392 optimal weight: 1.9990 chunk 699 optimal weight: 2.9990 chunk 437 optimal weight: 6.9990 chunk 426 optimal weight: 0.6980 chunk 323 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 832 HIS ** P 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN Q 367 HIS ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 599 ASN ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 357 HIS W 358 GLN X 157 GLN X 274 GLN ** 3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5106 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 59107 Z= 0.189 Angle : 0.593 10.569 80031 Z= 0.300 Chirality : 0.040 0.280 9175 Planarity : 0.004 0.124 10229 Dihedral : 4.459 30.221 7828 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.62 % Favored : 95.26 % Rotamer: Outliers : 0.02 % Allowed : 1.34 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.11 (0.10), residues: 7192 helix: 2.30 (0.08), residues: 4041 sheet: -0.50 (0.18), residues: 753 loop : -1.69 (0.13), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 4 105 HIS 0.010 0.001 HIS X 836 PHE 0.023 0.001 PHE X 732 TYR 0.014 0.001 TYR W 181 ARG 0.013 0.000 ARG W 809 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 5.523 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: D 80 MET cc_start: 0.7893 (ptt) cc_final: 0.7467 (ptt) REVERT: D 93 MET cc_start: 0.8199 (mmt) cc_final: 0.7652 (mmm) REVERT: D 190 MET cc_start: 0.5093 (ptt) cc_final: 0.3605 (ptt) REVERT: G 138 MET cc_start: 0.7453 (ptp) cc_final: 0.6844 (tmm) REVERT: H 146 MET cc_start: 0.7359 (ttt) cc_final: 0.6189 (ppp) REVERT: I 76 MET cc_start: 0.4313 (mtp) cc_final: 0.4098 (ttm) REVERT: I 140 MET cc_start: 0.7709 (mmm) cc_final: 0.6899 (mmt) REVERT: N 117 MET cc_start: 0.2109 (tmm) cc_final: 0.1165 (ptt) REVERT: N 237 MET cc_start: 0.8049 (mmm) cc_final: 0.6855 (mmm) REVERT: N 269 MET cc_start: 0.9192 (ptm) cc_final: 0.8289 (ptp) REVERT: N 314 MET cc_start: 0.7926 (tpp) cc_final: 0.7571 (tmm) REVERT: N 554 MET cc_start: 0.8580 (mtm) cc_final: 0.7411 (ptp) REVERT: N 1220 LEU cc_start: 0.8809 (tp) cc_final: 0.8547 (pp) REVERT: O 723 LEU cc_start: 0.9594 (mt) cc_final: 0.9338 (mt) REVERT: P 434 MET cc_start: -0.2659 (ptt) cc_final: -0.3019 (ptt) REVERT: Q 392 MET cc_start: 0.9116 (mmp) cc_final: 0.8633 (mmp) REVERT: Q 405 MET cc_start: 0.8524 (mmm) cc_final: 0.7256 (mtm) REVERT: Q 521 LEU cc_start: 0.9001 (tp) cc_final: 0.8776 (tp) REVERT: R 19 MET cc_start: 0.7971 (mmm) cc_final: 0.7518 (mmm) REVERT: R 186 MET cc_start: 0.8802 (ptm) cc_final: 0.8510 (ptm) REVERT: T 9 MET cc_start: 0.8020 (tpt) cc_final: 0.7745 (tpt) REVERT: T 63 MET cc_start: 0.7892 (mmm) cc_final: 0.7686 (mmm) REVERT: T 95 MET cc_start: 0.7711 (tpt) cc_final: 0.6985 (tpp) REVERT: T 181 ASP cc_start: 0.9036 (p0) cc_final: 0.8461 (p0) REVERT: V 30 MET cc_start: 0.9076 (mmm) cc_final: 0.8405 (mmm) REVERT: V 61 MET cc_start: 0.8287 (mtt) cc_final: 0.7763 (ttm) REVERT: V 76 MET cc_start: 0.8476 (mmp) cc_final: 0.7741 (mmm) REVERT: W 41 LEU cc_start: 0.4403 (tt) cc_final: 0.3846 (tp) REVERT: W 286 MET cc_start: -0.0251 (mmp) cc_final: -0.1028 (mtt) REVERT: W 312 MET cc_start: -0.2226 (tpt) cc_final: -0.2913 (tpt) REVERT: W 373 MET cc_start: 0.0827 (ptt) cc_final: 0.0321 (ptt) REVERT: W 469 MET cc_start: -0.1654 (tpt) cc_final: -0.2256 (tpt) REVERT: W 574 MET cc_start: -0.0841 (ptt) cc_final: -0.2358 (ppp) REVERT: W 720 MET cc_start: 0.5293 (mmp) cc_final: 0.4862 (mmp) REVERT: W 796 MET cc_start: 0.0058 (mtt) cc_final: -0.0148 (mtt) REVERT: W 871 MET cc_start: -0.0993 (tpp) cc_final: -0.1230 (tpp) REVERT: X 103 MET cc_start: 0.8096 (mtp) cc_final: 0.7477 (mtp) REVERT: X 160 MET cc_start: 0.8536 (ptt) cc_final: 0.8209 (ptm) REVERT: X 442 MET cc_start: -0.5682 (tpt) cc_final: -0.6022 (tpt) REVERT: X 572 MET cc_start: -0.2103 (ptm) cc_final: -0.2539 (ppp) REVERT: X 695 MET cc_start: 0.2338 (mtm) cc_final: 0.1329 (mmt) REVERT: 0 140 MET cc_start: 0.4374 (mtm) cc_final: 0.3601 (mtm) REVERT: 0 204 MET cc_start: 0.8728 (mmm) cc_final: 0.7906 (mmp) REVERT: 0 244 ASP cc_start: 0.9171 (m-30) cc_final: 0.8930 (m-30) REVERT: 0 288 LEU cc_start: 0.9371 (mt) cc_final: 0.8898 (tp) REVERT: 2 124 HIS cc_start: 0.9378 (t-90) cc_final: 0.8623 (t70) REVERT: 3 49 MET cc_start: 0.8695 (tmm) cc_final: 0.8080 (tmm) REVERT: 3 173 MET cc_start: 0.9487 (mtm) cc_final: 0.9203 (mtm) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.5474 time to fit residues: 259.2015 Evaluate side-chains 238 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 5.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 432 optimal weight: 5.9990 chunk 279 optimal weight: 20.0000 chunk 417 optimal weight: 3.9990 chunk 210 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 444 optimal weight: 6.9990 chunk 476 optimal weight: 50.0000 chunk 345 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 550 optimal weight: 20.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 HIS ** P 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 HIS Q 367 HIS ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 599 ASN ** Q 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 157 GLN X 274 GLN ** 3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5174 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 59107 Z= 0.265 Angle : 0.647 10.873 80031 Z= 0.327 Chirality : 0.041 0.305 9175 Planarity : 0.004 0.107 10229 Dihedral : 4.534 32.783 7828 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.92 % Favored : 94.94 % Rotamer: Outliers : 0.02 % Allowed : 0.82 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.10), residues: 7192 helix: 2.25 (0.08), residues: 4053 sheet: -0.53 (0.18), residues: 749 loop : -1.70 (0.13), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP X 798 HIS 0.013 0.001 HIS F 59 PHE 0.026 0.002 PHE T 91 TYR 0.026 0.001 TYR 4 54 ARG 0.010 0.000 ARG N 718 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 5.490 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: D 80 MET cc_start: 0.7951 (ptt) cc_final: 0.7519 (ptt) REVERT: D 93 MET cc_start: 0.8329 (mmt) cc_final: 0.7871 (mmm) REVERT: D 190 MET cc_start: 0.4437 (ptt) cc_final: 0.3014 (ptt) REVERT: G 138 MET cc_start: 0.7921 (ptp) cc_final: 0.7258 (tmm) REVERT: H 146 MET cc_start: 0.7518 (ttt) cc_final: 0.6414 (ppp) REVERT: I 140 MET cc_start: 0.7759 (mmm) cc_final: 0.6727 (mmt) REVERT: N 117 MET cc_start: 0.2272 (tmm) cc_final: 0.1274 (ptt) REVERT: N 237 MET cc_start: 0.8062 (mmm) cc_final: 0.6869 (mmm) REVERT: N 269 MET cc_start: 0.9236 (ptm) cc_final: 0.8299 (ptp) REVERT: N 314 MET cc_start: 0.7977 (tpp) cc_final: 0.7481 (tpp) REVERT: N 466 MET cc_start: 0.8689 (tpp) cc_final: 0.7982 (tpp) REVERT: N 554 MET cc_start: 0.8643 (mtm) cc_final: 0.7578 (ptp) REVERT: N 868 LEU cc_start: 0.9315 (tp) cc_final: 0.9087 (tt) REVERT: N 1216 MET cc_start: 0.6905 (mpp) cc_final: 0.6024 (mpp) REVERT: N 1220 LEU cc_start: 0.9042 (tp) cc_final: 0.8759 (pp) REVERT: O 723 LEU cc_start: 0.9395 (mt) cc_final: 0.9179 (mt) REVERT: P 434 MET cc_start: -0.2795 (ptt) cc_final: -0.3271 (ptt) REVERT: Q 392 MET cc_start: 0.9171 (mmp) cc_final: 0.8360 (mpp) REVERT: Q 521 LEU cc_start: 0.9173 (tp) cc_final: 0.8882 (tp) REVERT: R 19 MET cc_start: 0.8238 (mmm) cc_final: 0.7665 (mmm) REVERT: T 9 MET cc_start: 0.8051 (tpt) cc_final: 0.7761 (tpt) REVERT: T 63 MET cc_start: 0.7824 (mmm) cc_final: 0.7359 (mmm) REVERT: T 95 MET cc_start: 0.7709 (tpt) cc_final: 0.6932 (tpp) REVERT: T 181 ASP cc_start: 0.8719 (p0) cc_final: 0.8159 (p0) REVERT: V 30 MET cc_start: 0.9020 (mmm) cc_final: 0.8708 (mmm) REVERT: V 61 MET cc_start: 0.8389 (mtt) cc_final: 0.7943 (ttm) REVERT: V 76 MET cc_start: 0.8611 (mmp) cc_final: 0.8351 (mmm) REVERT: W 41 LEU cc_start: 0.4420 (tt) cc_final: 0.3924 (tp) REVERT: W 286 MET cc_start: -0.0312 (mmp) cc_final: -0.1046 (mtt) REVERT: W 312 MET cc_start: -0.1998 (tpt) cc_final: -0.2725 (tpt) REVERT: W 373 MET cc_start: 0.0862 (ptt) cc_final: 0.0535 (ptt) REVERT: W 469 MET cc_start: -0.1896 (tpt) cc_final: -0.2353 (tpt) REVERT: W 574 MET cc_start: -0.1114 (ptt) cc_final: -0.1734 (ppp) REVERT: W 796 MET cc_start: 0.0674 (mtt) cc_final: 0.0269 (mtt) REVERT: W 871 MET cc_start: -0.1003 (tpp) cc_final: -0.1241 (tpp) REVERT: X 103 MET cc_start: 0.8362 (mtp) cc_final: 0.7505 (mtp) REVERT: X 160 MET cc_start: 0.8754 (ptt) cc_final: 0.8493 (ptm) REVERT: X 442 MET cc_start: -0.6918 (tpt) cc_final: -0.7165 (tpt) REVERT: X 572 MET cc_start: -0.2379 (ptm) cc_final: -0.2689 (ppp) REVERT: X 695 MET cc_start: 0.3815 (mtm) cc_final: 0.2719 (mmt) REVERT: 0 140 MET cc_start: 0.4609 (mtm) cc_final: 0.3916 (mtm) REVERT: 0 204 MET cc_start: 0.8474 (mmm) cc_final: 0.7950 (tpp) REVERT: 3 49 MET cc_start: 0.8671 (tmm) cc_final: 0.8151 (tmm) REVERT: 3 161 ASP cc_start: 0.8764 (t70) cc_final: 0.8522 (t0) outliers start: 1 outliers final: 1 residues processed: 258 average time/residue: 0.5670 time to fit residues: 256.6548 Evaluate side-chains 234 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 5.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 636 optimal weight: 6.9990 chunk 670 optimal weight: 6.9990 chunk 611 optimal weight: 40.0000 chunk 652 optimal weight: 0.0170 chunk 392 optimal weight: 0.6980 chunk 284 optimal weight: 8.9990 chunk 512 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 589 optimal weight: 30.0000 chunk 616 optimal weight: 20.0000 chunk 649 optimal weight: 5.9990 overall best weight: 3.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 464 GLN ** N 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 HIS ** P 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 367 HIS ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 599 ASN ** Q 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 168 HIS ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN W 552 HIS ** W 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 GLN X 26 ASN X 274 GLN ** X 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 116 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5232 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 59107 Z= 0.342 Angle : 0.715 12.540 80031 Z= 0.361 Chirality : 0.042 0.283 9175 Planarity : 0.005 0.106 10229 Dihedral : 4.713 32.357 7828 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.34 % Favored : 94.49 % Rotamer: Outliers : 0.02 % Allowed : 0.58 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: 0.87 (0.10), residues: 7192 helix: 2.07 (0.08), residues: 4063 sheet: -0.64 (0.18), residues: 771 loop : -1.74 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP X 798 HIS 0.011 0.001 HIS Q 554 PHE 0.045 0.002 PHE X 905 TYR 0.022 0.002 TYR T 144 ARG 0.012 0.001 ARG 1 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 5.503 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: D 80 MET cc_start: 0.7313 (ptt) cc_final: 0.6679 (ptt) REVERT: D 93 MET cc_start: 0.8380 (mmt) cc_final: 0.7771 (mmm) REVERT: F 63 MET cc_start: 0.6187 (ptt) cc_final: 0.5854 (ptt) REVERT: G 43 MET cc_start: 0.8744 (mmp) cc_final: 0.7800 (tpp) REVERT: G 138 MET cc_start: 0.8021 (ptp) cc_final: 0.7330 (tmm) REVERT: H 119 GLU cc_start: 0.9275 (mp0) cc_final: 0.9045 (tp30) REVERT: H 146 MET cc_start: 0.7729 (ttt) cc_final: 0.6718 (ppp) REVERT: I 140 MET cc_start: 0.7961 (mmm) cc_final: 0.6751 (mmt) REVERT: N 117 MET cc_start: 0.2524 (tmm) cc_final: 0.1455 (ptt) REVERT: N 237 MET cc_start: 0.7993 (mmm) cc_final: 0.6808 (mmm) REVERT: N 269 MET cc_start: 0.9099 (ptm) cc_final: 0.8215 (ptp) REVERT: N 314 MET cc_start: 0.8086 (tpp) cc_final: 0.7674 (tpp) REVERT: N 466 MET cc_start: 0.8773 (tpp) cc_final: 0.8135 (tpp) REVERT: N 478 MET cc_start: 0.8770 (ttm) cc_final: 0.8327 (ttp) REVERT: N 554 MET cc_start: 0.8701 (mtm) cc_final: 0.7737 (ptp) REVERT: N 868 LEU cc_start: 0.9279 (tp) cc_final: 0.9015 (tt) REVERT: N 1216 MET cc_start: 0.6410 (mpp) cc_final: 0.5996 (mpp) REVERT: Q 125 MET cc_start: 0.8355 (mmp) cc_final: 0.7822 (mmm) REVERT: Q 392 MET cc_start: 0.9226 (mmp) cc_final: 0.8532 (mpp) REVERT: Q 405 MET cc_start: 0.8400 (mmm) cc_final: 0.7222 (mtm) REVERT: Q 521 LEU cc_start: 0.9165 (tp) cc_final: 0.8841 (tp) REVERT: R 19 MET cc_start: 0.8326 (mmm) cc_final: 0.7754 (mmm) REVERT: R 181 MET cc_start: 0.7801 (tpt) cc_final: 0.7476 (tmm) REVERT: T 9 MET cc_start: 0.8243 (tpt) cc_final: 0.7985 (tpp) REVERT: T 63 MET cc_start: 0.7812 (mmm) cc_final: 0.7318 (mmm) REVERT: T 95 MET cc_start: 0.7762 (tpt) cc_final: 0.6953 (tpp) REVERT: T 181 ASP cc_start: 0.8835 (p0) cc_final: 0.8302 (p0) REVERT: U 1 MET cc_start: 0.2897 (pmm) cc_final: 0.2338 (pmm) REVERT: V 61 MET cc_start: 0.8400 (mtt) cc_final: 0.7998 (ttm) REVERT: W 286 MET cc_start: -0.0380 (mmp) cc_final: -0.1214 (mtp) REVERT: W 312 MET cc_start: -0.1880 (tpt) cc_final: -0.2718 (tpt) REVERT: W 352 MET cc_start: -0.5365 (tpt) cc_final: -0.5788 (tpt) REVERT: W 373 MET cc_start: 0.1153 (ptt) cc_final: 0.0756 (ptt) REVERT: W 469 MET cc_start: -0.1708 (tpt) cc_final: -0.3374 (tpt) REVERT: W 525 MET cc_start: 0.6591 (tpt) cc_final: 0.6378 (tpp) REVERT: W 871 MET cc_start: -0.1231 (tpp) cc_final: -0.1465 (tpp) REVERT: X 103 MET cc_start: 0.8389 (mtp) cc_final: 0.7508 (mtp) REVERT: X 442 MET cc_start: -0.6925 (tpt) cc_final: -0.7169 (tpt) REVERT: X 533 MET cc_start: 0.1951 (mmp) cc_final: 0.1607 (mmp) REVERT: X 572 MET cc_start: -0.2248 (ptm) cc_final: -0.2620 (ppp) REVERT: X 695 MET cc_start: 0.3600 (mtm) cc_final: 0.2704 (mmt) REVERT: 0 140 MET cc_start: 0.4633 (mtm) cc_final: 0.4109 (mtm) REVERT: 0 204 MET cc_start: 0.8540 (mmm) cc_final: 0.7997 (tpp) REVERT: 3 49 MET cc_start: 0.8733 (tmm) cc_final: 0.8192 (tmm) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.5473 time to fit residues: 242.7923 Evaluate side-chains 225 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 5.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 428 optimal weight: 4.9990 chunk 689 optimal weight: 3.9990 chunk 420 optimal weight: 0.8980 chunk 327 optimal weight: 0.5980 chunk 479 optimal weight: 9.9990 chunk 723 optimal weight: 0.0270 chunk 665 optimal weight: 2.9990 chunk 575 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 444 optimal weight: 5.9990 chunk 353 optimal weight: 0.6980 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 464 GLN ** N 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 274 GLN ** X 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5132 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 59107 Z= 0.173 Angle : 0.606 11.597 80031 Z= 0.305 Chirality : 0.041 0.300 9175 Planarity : 0.004 0.100 10229 Dihedral : 4.493 30.409 7828 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.14 (0.10), residues: 7192 helix: 2.31 (0.08), residues: 4056 sheet: -0.56 (0.18), residues: 757 loop : -1.63 (0.13), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP X 798 HIS 0.010 0.001 HIS K 58 PHE 0.024 0.001 PHE Q 400 TYR 0.014 0.001 TYR A 374 ARG 0.014 0.000 ARG 1 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14384 Ramachandran restraints generated. 7192 Oldfield, 0 Emsley, 7192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 5.383 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: symmetry clash REVERT: A 361 MET cc_start: 0.8204 (tmm) cc_final: 0.7932 (tmm) REVERT: D 80 MET cc_start: 0.7255 (ptt) cc_final: 0.6647 (ptt) REVERT: D 93 MET cc_start: 0.8208 (mmt) cc_final: 0.7550 (mmm) REVERT: D 190 MET cc_start: 0.4797 (ptt) cc_final: 0.3411 (ptt) REVERT: G 43 MET cc_start: 0.8618 (mmp) cc_final: 0.7868 (tpp) REVERT: G 138 MET cc_start: 0.7939 (ptp) cc_final: 0.7310 (tmm) REVERT: H 146 MET cc_start: 0.7154 (ttt) cc_final: 0.6459 (ppp) REVERT: I 140 MET cc_start: 0.7815 (mmm) cc_final: 0.6985 (mmt) REVERT: N 117 MET cc_start: 0.2501 (tmm) cc_final: 0.1466 (ptt) REVERT: N 237 MET cc_start: 0.7951 (mmm) cc_final: 0.6635 (mmm) REVERT: N 269 MET cc_start: 0.8996 (ptm) cc_final: 0.8161 (ptp) REVERT: N 314 MET cc_start: 0.8008 (tpp) cc_final: 0.7765 (tmm) REVERT: N 466 MET cc_start: 0.8685 (tpp) cc_final: 0.7902 (tpp) REVERT: N 554 MET cc_start: 0.8495 (mtm) cc_final: 0.7421 (ptp) REVERT: O 723 LEU cc_start: 0.9487 (mt) cc_final: 0.9262 (mt) REVERT: O 756 MET cc_start: 0.9505 (tpt) cc_final: 0.8615 (tpt) REVERT: P 49 MET cc_start: 0.4609 (mmm) cc_final: 0.3544 (mmm) REVERT: P 434 MET cc_start: -0.3139 (ptt) cc_final: -0.3596 (ptt) REVERT: Q 125 MET cc_start: 0.8156 (mmp) cc_final: 0.7728 (mmm) REVERT: Q 392 MET cc_start: 0.9143 (mmp) cc_final: 0.8439 (mpp) REVERT: Q 405 MET cc_start: 0.8473 (mmm) cc_final: 0.7260 (mtm) REVERT: Q 521 LEU cc_start: 0.9131 (tp) cc_final: 0.8912 (tp) REVERT: R 19 MET cc_start: 0.8223 (mmm) cc_final: 0.7795 (mmm) REVERT: T 63 MET cc_start: 0.7805 (mmm) cc_final: 0.7463 (mmm) REVERT: T 66 MET cc_start: 0.7438 (mpp) cc_final: 0.6664 (mpp) REVERT: T 95 MET cc_start: 0.7535 (tpt) cc_final: 0.6713 (tpp) REVERT: T 181 ASP cc_start: 0.8798 (p0) cc_final: 0.8232 (p0) REVERT: U 1 MET cc_start: 0.2331 (pmm) cc_final: 0.1994 (pmm) REVERT: V 61 MET cc_start: 0.8413 (mtt) cc_final: 0.7824 (ttm) REVERT: W 1 MET cc_start: 0.8821 (pmm) cc_final: 0.8586 (pmm) REVERT: W 286 MET cc_start: -0.0437 (mmp) cc_final: -0.1241 (mtp) REVERT: W 312 MET cc_start: -0.1945 (tpt) cc_final: -0.2734 (tpt) REVERT: W 373 MET cc_start: 0.1346 (ptt) cc_final: 0.1005 (ptt) REVERT: W 469 MET cc_start: -0.1718 (tpt) cc_final: -0.3353 (tpt) REVERT: W 871 MET cc_start: -0.1209 (tpp) cc_final: -0.1443 (tpp) REVERT: X 103 MET cc_start: 0.8291 (mtp) cc_final: 0.7586 (mtp) REVERT: X 160 MET cc_start: 0.8762 (ptt) cc_final: 0.8503 (ptm) REVERT: X 382 MET cc_start: -0.0797 (mmt) cc_final: -0.1009 (mmm) REVERT: X 442 MET cc_start: -0.6929 (tpt) cc_final: -0.7173 (tpt) REVERT: X 572 MET cc_start: -0.2496 (ptm) cc_final: -0.2778 (ppp) REVERT: X 695 MET cc_start: 0.3635 (mtm) cc_final: 0.2762 (mmt) REVERT: 0 140 MET cc_start: 0.4548 (mtm) cc_final: 0.3974 (mtm) REVERT: 0 204 MET cc_start: 0.8705 (mmm) cc_final: 0.7903 (tpp) REVERT: 0 288 LEU cc_start: 0.9354 (mt) cc_final: 0.9090 (tp) REVERT: 3 49 MET cc_start: 0.8714 (tmm) cc_final: 0.8116 (tmm) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.5449 time to fit residues: 248.7396 Evaluate side-chains 235 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 5.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 457 optimal weight: 50.0000 chunk 613 optimal weight: 40.0000 chunk 176 optimal weight: 0.8980 chunk 531 optimal weight: 6.9990 chunk 85 optimal weight: 30.0000 chunk 160 optimal weight: 0.0970 chunk 576 optimal weight: 0.5980 chunk 241 optimal weight: 5.9990 chunk 592 optimal weight: 30.0000 chunk 73 optimal weight: 0.2980 chunk 106 optimal weight: 0.0970 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 GLN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 28 GLN ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 628 HIS X 274 GLN ** X 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 493 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.106059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.080297 restraints weight = 319720.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.071829 restraints weight = 418550.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.070879 restraints weight = 465222.706| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 59107 Z= 0.157 Angle : 0.596 13.004 80031 Z= 0.299 Chirality : 0.040 0.272 9175 Planarity : 0.004 0.098 10229 Dihedral : 4.340 30.451 7828 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.25 (0.10), residues: 7192 helix: 2.39 (0.08), residues: 4050 sheet: -0.43 (0.19), residues: 743 loop : -1.59 (0.13), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP X 798 HIS 0.010 0.001 HIS N 853 PHE 0.042 0.001 PHE W 9 TYR 0.012 0.001 TYR F 32 ARG 0.013 0.000 ARG 1 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7806.60 seconds wall clock time: 141 minutes 35.18 seconds (8495.18 seconds total)