Starting phenix.real_space_refine on Mon Mar 18 23:43:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8q_14560/03_2024/7z8q_14560.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8q_14560/03_2024/7z8q_14560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8q_14560/03_2024/7z8q_14560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8q_14560/03_2024/7z8q_14560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8q_14560/03_2024/7z8q_14560.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8q_14560/03_2024/7z8q_14560.pdb" } resolution = 4.08 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= -0.001 sd= 0.049 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 84 5.16 5 C 14091 2.51 5 N 3986 2.21 5 O 4321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22485 Number of models: 1 Model: "" Number of chains: 6 Chain: "a" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1700 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 208} Chain: "b" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1749 Classifications: {'peptide': 230} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 215} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 8453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8453 Classifications: {'peptide': 1089} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1027} Chain breaks: 1 Chain: "d" Number of atoms: 9939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 9939 Classifications: {'peptide': 1268} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1207} Chain breaks: 1 Chain: "e" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 74} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18958 SG CYS d 891 51.768 110.988 122.111 1.00 41.50 S ATOM 19532 SG CYS d 968 52.838 107.395 120.371 1.00 46.68 S ATOM 19574 SG CYS d 975 53.380 108.718 123.987 1.00 39.55 S ATOM 19592 SG CYS d 978 50.125 107.764 123.191 1.00 42.32 S ATOM 12378 SG CYS d 60 110.765 80.223 101.698 1.00112.36 S ATOM 12396 SG CYS d 62 112.453 80.038 98.849 1.00113.61 S ATOM 12505 SG CYS d 75 111.831 83.602 99.229 1.00114.67 S ATOM 12531 SG CYS d 78 109.306 81.717 98.326 1.00112.81 S Time building chain proxies: 11.30, per 1000 atoms: 0.50 Number of scatterers: 22485 At special positions: 0 Unit cell: (125.4, 133.1, 209, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 84 16.00 Mg 1 11.99 O 4321 8.00 N 3986 7.00 C 14091 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.91 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d1501 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 891 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 978 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 968 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 975 " pdb=" ZN d1502 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 78 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 60 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 75 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 62 " Number of angles added : 12 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5314 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 40 sheets defined 39.1% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'a' and resid 30 through 43 Processing helix chain 'a' and resid 72 through 82 removed outlier: 3.913A pdb=" N SER a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 110 No H-bonds generated for 'chain 'a' and resid 108 through 110' Processing helix chain 'a' and resid 148 through 153 Processing helix chain 'a' and resid 203 through 224 removed outlier: 3.533A pdb=" N ALA a 207 " --> pdb=" O SER a 203 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU a 221 " --> pdb=" O GLU a 217 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALA a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG a 223 " --> pdb=" O PHE a 219 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU a 224 " --> pdb=" O GLY a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 45 removed outlier: 4.022A pdb=" N THR b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER b 37 " --> pdb=" O THR b 33 " (cutoff:3.500A) Processing helix chain 'b' and resid 72 through 82 Processing helix chain 'b' and resid 108 through 110 No H-bonds generated for 'chain 'b' and resid 108 through 110' Processing helix chain 'b' and resid 148 through 153 Processing helix chain 'b' and resid 203 through 225 removed outlier: 4.024A pdb=" N LEU b 221 " --> pdb=" O GLU b 217 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA b 222 " --> pdb=" O LEU b 218 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU b 225 " --> pdb=" O LEU b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 66 removed outlier: 3.951A pdb=" N SER c 60 " --> pdb=" O VAL c 56 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE c 61 " --> pdb=" O GLN c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 78 Processing helix chain 'c' and resid 84 through 94 removed outlier: 3.568A pdb=" N LEU c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER c 94 " --> pdb=" O LEU c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 118 through 125 Processing helix chain 'c' and resid 234 through 241 Processing helix chain 'c' and resid 244 through 252 Processing helix chain 'c' and resid 256 through 265 Processing helix chain 'c' and resid 269 through 282 Processing helix chain 'c' and resid 288 through 301 removed outlier: 3.757A pdb=" N GLU c 297 " --> pdb=" O GLN c 293 " (cutoff:3.500A) Processing helix chain 'c' and resid 309 through 321 Processing helix chain 'c' and resid 334 through 351 Processing helix chain 'c' and resid 380 through 407 removed outlier: 3.510A pdb=" N LEU c 384 " --> pdb=" O THR c 380 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL c 399 " --> pdb=" O ARG c 395 " (cutoff:3.500A) Processing helix chain 'c' and resid 413 through 418 Processing helix chain 'c' and resid 420 through 434 Processing helix chain 'c' and resid 444 through 453 Processing helix chain 'c' and resid 470 through 474 Processing helix chain 'c' and resid 532 through 538 Processing helix chain 'c' and resid 590 through 594 removed outlier: 3.540A pdb=" N ILE c 594 " --> pdb=" O THR c 591 " (cutoff:3.500A) Processing helix chain 'c' and resid 601 through 613 removed outlier: 3.843A pdb=" N ARG c 613 " --> pdb=" O ALA c 609 " (cutoff:3.500A) Processing helix chain 'c' and resid 631 through 637 Processing helix chain 'c' and resid 739 through 744 Processing helix chain 'c' and resid 920 through 926 removed outlier: 4.108A pdb=" N ARG c 924 " --> pdb=" O HIS c 920 " (cutoff:3.500A) Processing helix chain 'c' and resid 928 through 943 removed outlier: 3.581A pdb=" N LEU c 932 " --> pdb=" O ILE c 928 " (cutoff:3.500A) Processing helix chain 'c' and resid 953 through 957 Processing helix chain 'c' and resid 981 through 990 removed outlier: 3.660A pdb=" N SER c 990 " --> pdb=" O GLN c 986 " (cutoff:3.500A) Processing helix chain 'c' and resid 1069 through 1080 removed outlier: 3.537A pdb=" N CYS c1073 " --> pdb=" O GLY c1069 " (cutoff:3.500A) Processing helix chain 'c' and resid 1082 through 1091 Processing helix chain 'c' and resid 1095 through 1108 Processing helix chain 'c' and resid 1118 through 1129 Processing helix chain 'd' and resid 16 through 24 Processing helix chain 'd' and resid 84 through 91 removed outlier: 4.084A pdb=" N ARG d 91 " --> pdb=" O ARG d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 108 removed outlier: 3.856A pdb=" N PHE d 107 " --> pdb=" O HIS d 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS d 108 " --> pdb=" O ILE d 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 103 through 108' Processing helix chain 'd' and resid 112 through 119 Processing helix chain 'd' and resid 121 through 131 Processing helix chain 'd' and resid 140 through 146 removed outlier: 3.729A pdb=" N ARG d 144 " --> pdb=" O ASP d 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 188 Processing helix chain 'd' and resid 190 through 228 Processing helix chain 'd' and resid 237 through 248 removed outlier: 3.551A pdb=" N TYR d 241 " --> pdb=" O ASP d 237 " (cutoff:3.500A) Processing helix chain 'd' and resid 258 through 268 Processing helix chain 'd' and resid 270 through 283 Processing helix chain 'd' and resid 285 through 306 removed outlier: 4.151A pdb=" N ARG d 291 " --> pdb=" O GLN d 287 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY d 306 " --> pdb=" O PHE d 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 308 through 311 removed outlier: 3.583A pdb=" N GLY d 311 " --> pdb=" O SER d 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 308 through 311' Processing helix chain 'd' and resid 339 through 361 Processing helix chain 'd' and resid 363 through 383 removed outlier: 3.711A pdb=" N VAL d 367 " --> pdb=" O PRO d 363 " (cutoff:3.500A) Processing helix chain 'd' and resid 401 through 406 Processing helix chain 'd' and resid 411 through 416 Processing helix chain 'd' and resid 445 through 452 removed outlier: 4.084A pdb=" N GLU d 450 " --> pdb=" O LEU d 446 " (cutoff:3.500A) Processing helix chain 'd' and resid 452 through 463 Processing helix chain 'd' and resid 468 through 479 Processing helix chain 'd' and resid 483 through 491 removed outlier: 3.650A pdb=" N ILE d 491 " --> pdb=" O LEU d 487 " (cutoff:3.500A) Processing helix chain 'd' and resid 505 through 507 No H-bonds generated for 'chain 'd' and resid 505 through 507' Processing helix chain 'd' and resid 525 through 527 No H-bonds generated for 'chain 'd' and resid 525 through 527' Processing helix chain 'd' and resid 528 through 533 Processing helix chain 'd' and resid 548 through 558 removed outlier: 3.863A pdb=" N ALA d 553 " --> pdb=" O ALA d 549 " (cutoff:3.500A) Processing helix chain 'd' and resid 580 through 590 Processing helix chain 'd' and resid 614 through 625 Processing helix chain 'd' and resid 643 through 651 removed outlier: 4.183A pdb=" N GLU d 649 " --> pdb=" O GLU d 645 " (cutoff:3.500A) Processing helix chain 'd' and resid 668 through 675 Processing helix chain 'd' and resid 689 through 704 Processing helix chain 'd' and resid 705 through 725 removed outlier: 4.022A pdb=" N THR d 725 " --> pdb=" O PHE d 721 " (cutoff:3.500A) Processing helix chain 'd' and resid 726 through 728 No H-bonds generated for 'chain 'd' and resid 726 through 728' Processing helix chain 'd' and resid 741 through 762 removed outlier: 3.621A pdb=" N ILE d 745 " --> pdb=" O ARG d 741 " (cutoff:3.500A) Processing helix chain 'd' and resid 766 through 793 Processing helix chain 'd' and resid 797 through 805 Processing helix chain 'd' and resid 810 through 819 removed outlier: 3.824A pdb=" N THR d 814 " --> pdb=" O ASN d 810 " (cutoff:3.500A) Processing helix chain 'd' and resid 845 through 881 removed outlier: 4.590A pdb=" N HIS d 854 " --> pdb=" O PHE d 850 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY d 855 " --> pdb=" O ILE d 851 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA d 856 " --> pdb=" O ASN d 852 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA d 868 " --> pdb=" O ALA d 864 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER d 881 " --> pdb=" O LEU d 877 " (cutoff:3.500A) Processing helix chain 'd' and resid 945 through 956 Processing helix chain 'd' and resid 975 through 980 Processing helix chain 'd' and resid 995 through 1005 Processing helix chain 'd' and resid 1006 through 1010 Processing helix chain 'd' and resid 1027 through 1037 removed outlier: 3.505A pdb=" N VAL d1031 " --> pdb=" O GLY d1027 " (cutoff:3.500A) Processing helix chain 'd' and resid 1117 through 1126 Processing helix chain 'd' and resid 1126 through 1145 removed outlier: 3.988A pdb=" N VAL d1130 " --> pdb=" O GLY d1126 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN d1145 " --> pdb=" O VAL d1141 " (cutoff:3.500A) Processing helix chain 'd' and resid 1151 through 1162 removed outlier: 4.139A pdb=" N ILE d1157 " --> pdb=" O HIS d1153 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN d1160 " --> pdb=" O VAL d1156 " (cutoff:3.500A) Processing helix chain 'd' and resid 1183 through 1196 Processing helix chain 'd' and resid 1209 through 1216 removed outlier: 3.757A pdb=" N ALA d1216 " --> pdb=" O LYS d1212 " (cutoff:3.500A) Processing helix chain 'd' and resid 1219 through 1227 Processing helix chain 'd' and resid 1228 through 1240 Processing helix chain 'd' and resid 1248 through 1255 Processing helix chain 'd' and resid 1260 through 1263 Processing helix chain 'd' and resid 1264 through 1269 removed outlier: 3.811A pdb=" N ASN d1269 " --> pdb=" O ASN d1265 " (cutoff:3.500A) Processing helix chain 'd' and resid 1275 through 1281 Processing helix chain 'e' and resid 39 through 47 removed outlier: 4.169A pdb=" N LEU e 43 " --> pdb=" O PRO e 39 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG e 46 " --> pdb=" O GLU e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 70 removed outlier: 3.607A pdb=" N VAL e 54 " --> pdb=" O LYS e 50 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE e 55 " --> pdb=" O TYR e 51 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG e 60 " --> pdb=" O TYR e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 90 through 100 Processing sheet with id=AA1, first strand: chain 'a' and resid 9 through 13 removed outlier: 3.689A pdb=" N LEU a 9 " --> pdb=" O GLU a 24 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU a 24 " --> pdb=" O LEU a 9 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP a 190 " --> pdb=" O PRO a 25 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE a 189 " --> pdb=" O THR a 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS a 173 " --> pdb=" O GLU a 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 93 through 100 removed outlier: 3.660A pdb=" N LEU a 138 " --> pdb=" O MET a 95 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER a 53 " --> pdb=" O VAL a 139 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU a 141 " --> pdb=" O VAL a 51 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL a 51 " --> pdb=" O GLU a 141 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY a 143 " --> pdb=" O ALA a 49 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA a 49 " --> pdb=" O GLY a 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 85 through 87 removed outlier: 3.577A pdb=" N SER a 86 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR a 117 " --> pdb=" O SER a 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'a' and resid 103 through 106 removed outlier: 3.556A pdb=" N GLY a 103 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU a 128 " --> pdb=" O GLY a 103 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA a 126 " --> pdb=" O VAL a 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 9 through 10 removed outlier: 6.681A pdb=" N ASP b 190 " --> pdb=" O PRO b 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 9 through 10 removed outlier: 6.681A pdb=" N ASP b 190 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE b 193 " --> pdb=" O LYS b 177 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS b 173 " --> pdb=" O GLU b 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 93 through 97 removed outlier: 6.264A pdb=" N GLU b 137 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE b 54 " --> pdb=" O GLU b 137 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL b 139 " --> pdb=" O THR b 52 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE b 54 " --> pdb=" O ILE b 162 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE b 162 " --> pdb=" O ILE b 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 93 through 97 removed outlier: 3.960A pdb=" N VAL b 147 " --> pdb=" O SER b 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 85 through 86 Processing sheet with id=AB1, first strand: chain 'b' and resid 103 through 106 removed outlier: 4.144A pdb=" N ALA b 126 " --> pdb=" O VAL b 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 96 through 97 removed outlier: 4.760A pdb=" N LEU c 105 " --> pdb=" O ILE c 140 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE c 140 " --> pdb=" O LEU c 105 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N PHE c 107 " --> pdb=" O GLU c 138 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU c 138 " --> pdb=" O PHE c 107 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASP c 109 " --> pdb=" O THR c 136 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR c 136 " --> pdb=" O ASP c 109 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA c 131 " --> pdb=" O ASP c 156 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP c 156 " --> pdb=" O ALA c 131 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU c 133 " --> pdb=" O MET c 154 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU c 146 " --> pdb=" O ASN c 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 166 through 168 removed outlier: 3.541A pdb=" N GLN c 438 " --> pdb=" O VAL c 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 376 through 379 removed outlier: 3.577A pdb=" N GLN c 178 " --> pdb=" O ARG c 379 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER c 177 " --> pdb=" O SER c 456 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU c 455 " --> pdb=" O GLY c 498 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 184 through 191 Processing sheet with id=AB6, first strand: chain 'c' and resid 223 through 224 Processing sheet with id=AB7, first strand: chain 'c' and resid 354 through 355 removed outlier: 3.612A pdb=" N VAL c 363 " --> pdb=" O MET c 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 529 through 531 Processing sheet with id=AB9, first strand: chain 'c' and resid 667 through 671 removed outlier: 6.944A pdb=" N TYR c 657 " --> pdb=" O VAL c 653 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL c 653 " --> pdb=" O TYR c 657 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR c 659 " --> pdb=" O GLU c 651 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 687 through 688 removed outlier: 3.668A pdb=" N ASP c 704 " --> pdb=" O CYS c 687 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'c' and resid 885 through 886 removed outlier: 4.128A pdb=" N ALA c 886 " --> pdb=" O MET c1031 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR c1024 " --> pdb=" O ILE c 723 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N ILE c 915 " --> pdb=" O ASN c 718 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU c 720 " --> pdb=" O ILE c 915 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU c 917 " --> pdb=" O LEU c 720 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA c 722 " --> pdb=" O LEU c 917 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE c 736 " --> pdb=" O ILE c 916 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE c 735 " --> pdb=" O GLY c 896 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE c 898 " --> pdb=" O ILE c 735 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU c 737 " --> pdb=" O ILE c 898 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'c' and resid 885 through 886 removed outlier: 4.128A pdb=" N ALA c 886 " --> pdb=" O MET c1031 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 748 through 752 removed outlier: 6.737A pdb=" N VAL c 865 " --> pdb=" O ASP c 761 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP c 761 " --> pdb=" O VAL c 865 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU c 867 " --> pdb=" O ALA c 759 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 748 through 752 removed outlier: 4.046A pdb=" N GLY c 849 " --> pdb=" O TYR c 872 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA c 874 " --> pdb=" O VAL c 847 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL c 847 " --> pdb=" O ALA c 874 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 768 through 769 removed outlier: 3.911A pdb=" N GLU c 768 " --> pdb=" O VAL c 806 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 801 through 803 removed outlier: 6.965A pdb=" N LEU c 837 " --> pdb=" O LEU c 802 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'c' and resid 1042 through 1044 removed outlier: 3.774A pdb=" N SER d 428 " --> pdb=" O MET d 541 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET d 541 " --> pdb=" O SER d 428 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU d 498 " --> pdb=" O GLN d 510 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN d 510 " --> pdb=" O LEU d 498 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 1042 through 1044 removed outlier: 7.546A pdb=" N ILE d 522 " --> pdb=" O ARG d 427 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL d 429 " --> pdb=" O ILE d 522 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU d 524 " --> pdb=" O VAL d 429 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL d 431 " --> pdb=" O LEU d 524 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'c' and resid 1133 through 1135 Processing sheet with id=AD2, first strand: chain 'd' and resid 9 through 10 Processing sheet with id=AD3, first strand: chain 'd' and resid 93 through 94 Processing sheet with id=AD4, first strand: chain 'd' and resid 101 through 102 Processing sheet with id=AD5, first strand: chain 'd' and resid 134 through 135 removed outlier: 3.645A pdb=" N TYR d 134 " --> pdb=" O ILE d 235 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE d 235 " --> pdb=" O TYR d 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'd' and resid 443 through 444 removed outlier: 5.453A pdb=" N LEU d 443 " --> pdb=" O VAL d 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'd' and resid 611 through 612 removed outlier: 3.580A pdb=" N TYR d 612 " --> pdb=" O LYS d 634 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU d 637 " --> pdb=" O TRP d 662 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP d 662 " --> pdb=" O LEU d 637 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'd' and resid 611 through 612 removed outlier: 3.580A pdb=" N TYR d 612 " --> pdb=" O LYS d 634 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 898 through 900 removed outlier: 3.791A pdb=" N VAL d 960 " --> pdb=" O VAL d 899 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 902 through 903 Processing sheet with id=AE2, first strand: chain 'd' and resid 1051 through 1056 removed outlier: 3.938A pdb=" N ILE d1066 " --> pdb=" O VAL d1075 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL d1075 " --> pdb=" O ILE d1066 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 1181 through 1182 removed outlier: 3.723A pdb=" N ARG d1164 " --> pdb=" O VAL d1206 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 1272 through 1274 917 hydrogen bonds defined for protein. 2577 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: 8.33 Time building geometry restraints manager: 8.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7755 1.34 - 1.46: 4452 1.46 - 1.58: 10515 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 22869 Sorted by residual: bond pdb=" N ILE e 75 " pdb=" CA ILE e 75 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.24e-02 6.50e+03 1.23e+01 bond pdb=" N GLY d 257 " pdb=" CA GLY d 257 " ideal model delta sigma weight residual 1.449 1.480 -0.032 1.00e-02 1.00e+04 1.00e+01 bond pdb=" N ARG d1060 " pdb=" CA ARG d1060 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.27e-02 6.20e+03 9.87e+00 bond pdb=" N GLU d 259 " pdb=" CA GLU d 259 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.23e-02 6.61e+03 9.29e+00 bond pdb=" N ILE d 129 " pdb=" CA ILE d 129 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.23e-02 6.61e+03 8.88e+00 ... (remaining 22864 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.46: 736 106.46 - 113.35: 12564 113.35 - 120.23: 8066 120.23 - 127.12: 9371 127.12 - 134.00: 247 Bond angle restraints: 30984 Sorted by residual: angle pdb=" N GLU e 77 " pdb=" CA GLU e 77 " pdb=" C GLU e 77 " ideal model delta sigma weight residual 114.04 106.26 7.78 1.24e+00 6.50e-01 3.94e+01 angle pdb=" CA GLY d 257 " pdb=" C GLY d 257 " pdb=" O GLY d 257 " ideal model delta sigma weight residual 122.33 118.18 4.15 8.10e-01 1.52e+00 2.63e+01 angle pdb=" CA THR d 893 " pdb=" C THR d 893 " pdb=" O THR d 893 " ideal model delta sigma weight residual 121.89 116.73 5.16 1.27e+00 6.20e-01 1.65e+01 angle pdb=" C ASN e 69 " pdb=" N GLN e 70 " pdb=" CA GLN e 70 " ideal model delta sigma weight residual 122.27 115.02 7.25 1.85e+00 2.92e-01 1.54e+01 angle pdb=" CA CYS d 968 " pdb=" C CYS d 968 " pdb=" O CYS d 968 " ideal model delta sigma weight residual 121.19 116.94 4.25 1.10e+00 8.26e-01 1.49e+01 ... (remaining 30979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13380 17.95 - 35.89: 558 35.89 - 53.84: 67 53.84 - 71.78: 17 71.78 - 89.73: 5 Dihedral angle restraints: 14027 sinusoidal: 5758 harmonic: 8269 Sorted by residual: dihedral pdb=" CA GLY d 257 " pdb=" C GLY d 257 " pdb=" N ALA d 258 " pdb=" CA ALA d 258 " ideal model delta harmonic sigma weight residual 180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PRO d 577 " pdb=" C PRO d 577 " pdb=" N ARG d 578 " pdb=" CA ARG d 578 " ideal model delta harmonic sigma weight residual -180.00 -161.30 -18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLN d 882 " pdb=" C GLN d 882 " pdb=" N ASP d 883 " pdb=" CA ASP d 883 " ideal model delta harmonic sigma weight residual -180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 14024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2973 0.053 - 0.105: 416 0.105 - 0.158: 124 0.158 - 0.211: 6 0.211 - 0.263: 4 Chirality restraints: 3523 Sorted by residual: chirality pdb=" CA ILE e 75 " pdb=" N ILE e 75 " pdb=" C ILE e 75 " pdb=" CB ILE e 75 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA THR e 107 " pdb=" N THR e 107 " pdb=" C THR e 107 " pdb=" CB THR e 107 " both_signs ideal model delta sigma weight residual False 2.53 2.76 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PHE d 131 " pdb=" N PHE d 131 " pdb=" C PHE d 131 " pdb=" CB PHE d 131 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3520 not shown) Planarity restraints: 4096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET d 256 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C MET d 256 " -0.065 2.00e-02 2.50e+03 pdb=" O MET d 256 " 0.025 2.00e-02 2.50e+03 pdb=" N GLY d 257 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE d 128 " -0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C ILE d 128 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE d 128 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE d 129 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN d 352 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.71e+00 pdb=" C ASN d 352 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN d 352 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG d 353 " -0.017 2.00e-02 2.50e+03 ... (remaining 4093 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 228 2.59 - 3.17: 20414 3.17 - 3.74: 32333 3.74 - 4.32: 43508 4.32 - 4.90: 73493 Nonbonded interactions: 169976 Sorted by model distance: nonbonded pdb=" OH TYR d 241 " pdb=" O GLY d 254 " model vdw 2.012 2.440 nonbonded pdb=" OG1 THR c 356 " pdb=" OE1 GLU c 362 " model vdw 2.034 2.440 nonbonded pdb=" OD1 ASP d 539 " pdb="MG MG d1503 " model vdw 2.067 2.170 nonbonded pdb=" OD1 ASP d 537 " pdb="MG MG d1503 " model vdw 2.071 2.170 nonbonded pdb=" OD1 ASP d 535 " pdb="MG MG d1503 " model vdw 2.072 2.170 ... (remaining 169971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and (resid 4 through 210 or (resid 211 through 212 and (name N or nam \ e CA or name C or name O )) or resid 213 through 226)) selection = (chain 'b' and resid 4 through 226) } 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.070 Check model and map are aligned: 0.320 Set scattering table: 0.220 Process input model: 59.830 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 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 : 0.003 0.044 22869 Z= 0.171 Angle : 0.516 7.782 30984 Z= 0.296 Chirality : 0.043 0.263 3523 Planarity : 0.003 0.048 4096 Dihedral : 9.984 89.730 8713 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.90 % Rotamer: Outliers : 0.37 % Allowed : 4.05 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % 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: -0.46 (0.16), residues: 2877 helix: 1.32 (0.17), residues: 1006 sheet: -1.43 (0.29), residues: 324 loop : -1.17 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 778 HIS 0.002 0.000 HIS d 439 PHE 0.009 0.001 PHE c 139 TYR 0.013 0.001 TYR e 56 ARG 0.010 0.000 ARG d1143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 612 time to evaluate : 2.577 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: a 168 TYR cc_start: 0.7617 (m-80) cc_final: 0.7282 (m-80) REVERT: b 61 HIS cc_start: 0.6337 (m-70) cc_final: 0.6136 (m90) REVERT: c 444 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8017 (p0) REVERT: c 591 THR cc_start: 0.8834 (p) cc_final: 0.8056 (t) REVERT: c 612 GLN cc_start: 0.7960 (mt0) cc_final: 0.7323 (tp40) REVERT: d 736 VAL cc_start: 0.8530 (t) cc_final: 0.8321 (m) REVERT: d 816 THR cc_start: 0.9092 (m) cc_final: 0.8881 (p) REVERT: d 966 LEU cc_start: 0.6139 (tp) cc_final: 0.5591 (tt) outliers start: 9 outliers final: 0 residues processed: 620 average time/residue: 0.4301 time to fit residues: 392.7734 Evaluate side-chains 303 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 302 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 120 optimal weight: 0.0060 chunk 74 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 136 optimal weight: 0.0870 chunk 167 optimal weight: 10.0000 chunk 260 optimal weight: 0.5980 overall best weight: 2.1378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 185 GLN c 889 HIS c1042 HIS d 341 ASN ** d 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 797 ASN d 882 GLN e 70 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22869 Z= 0.259 Angle : 0.638 9.473 30984 Z= 0.326 Chirality : 0.045 0.249 3523 Planarity : 0.005 0.053 4096 Dihedral : 4.102 20.949 3171 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.12 % Allowed : 3.36 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % 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: -0.50 (0.16), residues: 2877 helix: 1.00 (0.16), residues: 1036 sheet: -1.17 (0.29), residues: 332 loop : -1.08 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c1074 HIS 0.006 0.001 HIS e 106 PHE 0.017 0.002 PHE c 252 TYR 0.019 0.002 TYR b 32 ARG 0.004 0.001 ARG d 414 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 348 time to evaluate : 2.600 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: c 195 THR cc_start: 0.6797 (m) cc_final: 0.6569 (m) REVERT: c 417 LEU cc_start: 0.8728 (mt) cc_final: 0.8509 (mt) REVERT: c 724 MET cc_start: 0.8193 (ppp) cc_final: 0.7957 (ppp) REVERT: c 883 ASP cc_start: 0.7422 (m-30) cc_final: 0.7174 (m-30) REVERT: d 1012 MET cc_start: 0.0277 (ptp) cc_final: -0.0513 (tpp) REVERT: e 69 ASN cc_start: 0.8141 (t0) cc_final: 0.7789 (t0) REVERT: e 94 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8204 (tp) outliers start: 3 outliers final: 0 residues processed: 349 average time/residue: 0.3651 time to fit residues: 191.4723 Evaluate side-chains 226 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 144 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 232 optimal weight: 6.9990 chunk 258 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 209 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 185 GLN c 372 HIS c 386 GLN ** d 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 368 ASN ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 510 GLN d 564 ASN ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 882 GLN e 63 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22869 Z= 0.353 Angle : 0.676 13.778 30984 Z= 0.346 Chirality : 0.045 0.318 3523 Planarity : 0.005 0.056 4096 Dihedral : 4.420 22.660 3171 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.12 % Allowed : 5.77 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % 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: -0.60 (0.16), residues: 2877 helix: 0.81 (0.16), residues: 1028 sheet: -1.07 (0.28), residues: 320 loop : -1.09 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 723 HIS 0.006 0.001 HIS b 61 PHE 0.016 0.002 PHE d 268 TYR 0.032 0.002 TYR c 731 ARG 0.020 0.001 ARG e 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 293 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 304 LYS cc_start: 0.7918 (tttt) cc_final: 0.7713 (tttm) REVERT: c 612 GLN cc_start: 0.8319 (tp40) cc_final: 0.8112 (tp40) REVERT: c 724 MET cc_start: 0.8333 (ppp) cc_final: 0.8048 (ppp) REVERT: c 1031 MET cc_start: 0.8306 (mtm) cc_final: 0.7862 (mtm) REVERT: c 1076 MET cc_start: 0.7667 (mmm) cc_final: 0.7132 (mmm) REVERT: c 1119 GLU cc_start: 0.6375 (mp0) cc_final: 0.6081 (mp0) REVERT: d 148 LEU cc_start: 0.6664 (mt) cc_final: 0.6339 (mt) REVERT: d 457 MET cc_start: 0.7597 (mmm) cc_final: 0.7220 (mmt) REVERT: d 975 CYS cc_start: 0.6760 (OUTLIER) cc_final: 0.6205 (p) REVERT: d 1012 MET cc_start: 0.0548 (ptp) cc_final: -0.0385 (tpp) REVERT: e 69 ASN cc_start: 0.8217 (t0) cc_final: 0.7764 (t0) REVERT: e 94 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8483 (tp) outliers start: 3 outliers final: 0 residues processed: 295 average time/residue: 0.3945 time to fit residues: 177.6293 Evaluate side-chains 199 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 257 optimal weight: 0.5980 chunk 196 optimal weight: 0.6980 chunk 135 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 124 optimal weight: 0.0050 chunk 175 optimal weight: 2.9990 chunk 262 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.8754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 386 GLN d 349 ASN d 440 GLN ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22869 Z= 0.166 Angle : 0.578 10.405 30984 Z= 0.292 Chirality : 0.043 0.248 3523 Planarity : 0.004 0.057 4096 Dihedral : 4.122 23.099 3171 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % 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: -0.24 (0.16), residues: 2877 helix: 1.12 (0.17), residues: 1020 sheet: -0.71 (0.29), residues: 309 loop : -0.91 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP d 484 HIS 0.010 0.001 HIS c 479 PHE 0.018 0.001 PHE c 252 TYR 0.041 0.002 TYR d 134 ARG 0.008 0.000 ARG d 556 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 2.520 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: c 103 MET cc_start: 0.4417 (tpt) cc_final: 0.3759 (tpt) REVERT: c 307 ASP cc_start: 0.6654 (p0) cc_final: 0.6201 (t0) REVERT: c 396 MET cc_start: 0.7548 (tmm) cc_final: 0.7300 (tmm) REVERT: c 513 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7227 (mm-30) REVERT: c 593 MET cc_start: 0.7589 (ppp) cc_final: 0.6411 (ppp) REVERT: c 724 MET cc_start: 0.8296 (ppp) cc_final: 0.7932 (ppp) REVERT: c 1031 MET cc_start: 0.8260 (mtm) cc_final: 0.7942 (mtt) REVERT: c 1076 MET cc_start: 0.7482 (mmm) cc_final: 0.7062 (mmm) REVERT: d 148 LEU cc_start: 0.6589 (mt) cc_final: 0.6375 (mt) REVERT: d 1012 MET cc_start: 0.0659 (ptp) cc_final: -0.0258 (tpp) REVERT: e 69 ASN cc_start: 0.8236 (t0) cc_final: 0.7850 (t0) outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.3452 time to fit residues: 155.7669 Evaluate side-chains 206 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 231 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 206 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 0.0170 chunk 249 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 494 HIS ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 761 GLN d1119 HIS ** e 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22869 Z= 0.338 Angle : 0.667 13.573 30984 Z= 0.344 Chirality : 0.045 0.242 3523 Planarity : 0.005 0.065 4096 Dihedral : 4.471 22.109 3171 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % 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: -0.40 (0.16), residues: 2877 helix: 0.97 (0.16), residues: 1024 sheet: -0.82 (0.28), residues: 323 loop : -0.99 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 723 HIS 0.009 0.001 HIS d 689 PHE 0.015 0.002 PHE d 268 TYR 0.038 0.002 TYR d 134 ARG 0.007 0.001 ARG c1014 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.821 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: c 160 MET cc_start: 0.8491 (tpt) cc_final: 0.8040 (tpt) REVERT: c 307 ASP cc_start: 0.6814 (p0) cc_final: 0.6455 (p0) REVERT: c 593 MET cc_start: 0.7702 (ppp) cc_final: 0.7390 (ppp) REVERT: c 926 MET cc_start: 0.8423 (tpp) cc_final: 0.8203 (mmm) REVERT: c 1071 MET cc_start: 0.7851 (mmm) cc_final: 0.7642 (mpp) REVERT: c 1119 GLU cc_start: 0.6604 (mp0) cc_final: 0.6233 (mp0) REVERT: d 736 VAL cc_start: 0.8599 (t) cc_final: 0.8309 (t) REVERT: e 69 ASN cc_start: 0.8238 (t0) cc_final: 0.7828 (t0) REVERT: e 94 ILE cc_start: 0.8809 (mp) cc_final: 0.8168 (mm) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.3334 time to fit residues: 130.0452 Evaluate side-chains 182 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 93 optimal weight: 0.9980 chunk 249 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 162 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22869 Z= 0.251 Angle : 0.602 12.626 30984 Z= 0.308 Chirality : 0.044 0.199 3523 Planarity : 0.004 0.053 4096 Dihedral : 4.333 20.663 3171 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % 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: -0.28 (0.16), residues: 2877 helix: 1.04 (0.16), residues: 1020 sheet: -0.68 (0.29), residues: 324 loop : -0.90 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 243 HIS 0.009 0.001 HIS c 200 PHE 0.015 0.002 PHE d 268 TYR 0.022 0.002 TYR d 793 ARG 0.007 0.000 ARG e 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.479 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: c 160 MET cc_start: 0.8665 (tpt) cc_final: 0.8228 (tpt) REVERT: c 307 ASP cc_start: 0.6523 (p0) cc_final: 0.6244 (p0) REVERT: c 593 MET cc_start: 0.7902 (ppp) cc_final: 0.7683 (ppp) REVERT: c 926 MET cc_start: 0.8366 (tpp) cc_final: 0.8161 (tpt) REVERT: c 1071 MET cc_start: 0.7975 (mmm) cc_final: 0.7723 (mpp) REVERT: d 148 LEU cc_start: 0.6668 (mt) cc_final: 0.6400 (mt) REVERT: d 736 VAL cc_start: 0.8572 (t) cc_final: 0.8294 (t) REVERT: e 69 ASN cc_start: 0.8218 (t0) cc_final: 0.7958 (t0) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.3576 time to fit residues: 137.8276 Evaluate side-chains 181 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 267 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 233 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22869 Z= 0.264 Angle : 0.619 12.863 30984 Z= 0.318 Chirality : 0.044 0.325 3523 Planarity : 0.004 0.047 4096 Dihedral : 4.396 23.735 3171 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % 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: -0.33 (0.16), residues: 2877 helix: 1.00 (0.16), residues: 1024 sheet: -0.84 (0.26), residues: 353 loop : -0.90 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP d 484 HIS 0.008 0.001 HIS c 200 PHE 0.016 0.002 PHE d 268 TYR 0.020 0.002 TYR d 134 ARG 0.005 0.000 ARG d 556 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 160 MET cc_start: 0.8703 (tpt) cc_final: 0.8131 (tpt) REVERT: c 307 ASP cc_start: 0.6477 (p0) cc_final: 0.6249 (p0) REVERT: d 148 LEU cc_start: 0.6625 (mt) cc_final: 0.6415 (mt) REVERT: d 556 ARG cc_start: 0.8033 (ptm-80) cc_final: 0.7784 (ptm-80) REVERT: d 736 VAL cc_start: 0.8548 (t) cc_final: 0.8229 (t) REVERT: e 69 ASN cc_start: 0.8220 (t0) cc_final: 0.7966 (t0) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.3541 time to fit residues: 131.3137 Evaluate side-chains 180 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 54 optimal weight: 0.0470 chunk 53 optimal weight: 4.9990 chunk 175 optimal weight: 0.0980 chunk 188 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 217 optimal weight: 0.0370 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 505 HIS ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22869 Z= 0.165 Angle : 0.577 10.607 30984 Z= 0.295 Chirality : 0.044 0.261 3523 Planarity : 0.004 0.048 4096 Dihedral : 4.139 23.586 3171 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % 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: -0.15 (0.16), residues: 2877 helix: 1.10 (0.16), residues: 1021 sheet: -0.58 (0.28), residues: 317 loop : -0.79 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP c 243 HIS 0.006 0.001 HIS c 200 PHE 0.012 0.001 PHE d 268 TYR 0.027 0.001 TYR d 793 ARG 0.006 0.000 ARG c 421 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.458 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: c 160 MET cc_start: 0.8609 (tpt) cc_final: 0.8288 (tpt) REVERT: c 307 ASP cc_start: 0.6339 (p0) cc_final: 0.6094 (p0) REVERT: c 727 GLU cc_start: 0.7867 (mp0) cc_final: 0.7540 (mp0) REVERT: d 256 MET cc_start: 0.2928 (mmp) cc_final: 0.2722 (mmp) REVERT: d 576 MET cc_start: 0.8144 (ppp) cc_final: 0.7889 (ptt) REVERT: d 581 MET cc_start: 0.7713 (pmm) cc_final: 0.7486 (pmm) REVERT: d 736 VAL cc_start: 0.8447 (t) cc_final: 0.8158 (t) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3474 time to fit residues: 138.9787 Evaluate side-chains 189 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 251 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 257 optimal weight: 0.1980 chunk 264 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 232 optimal weight: 0.8980 chunk 243 optimal weight: 7.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 679 ASN ** d 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22869 Z= 0.245 Angle : 0.618 11.576 30984 Z= 0.315 Chirality : 0.044 0.267 3523 Planarity : 0.004 0.046 4096 Dihedral : 4.251 22.230 3171 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % 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: -0.18 (0.16), residues: 2877 helix: 1.11 (0.17), residues: 1026 sheet: -0.65 (0.27), residues: 349 loop : -0.83 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 243 HIS 0.007 0.001 HIS c 200 PHE 0.014 0.002 PHE d 536 TYR 0.027 0.002 TYR d 793 ARG 0.007 0.000 ARG d 556 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 2.877 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: b 90 ASP cc_start: 0.7909 (p0) cc_final: 0.7533 (p0) REVERT: c 99 PHE cc_start: 0.8159 (p90) cc_final: 0.7823 (p90) REVERT: c 160 MET cc_start: 0.8730 (tpt) cc_final: 0.8421 (tpt) REVERT: c 307 ASP cc_start: 0.6642 (p0) cc_final: 0.6382 (p0) REVERT: c 393 MET cc_start: 0.8485 (tpp) cc_final: 0.7838 (tpp) REVERT: d 138 SER cc_start: 0.6336 (p) cc_final: 0.6123 (p) REVERT: d 256 MET cc_start: 0.3289 (mmp) cc_final: 0.3033 (mmp) REVERT: d 581 MET cc_start: 0.7753 (pmm) cc_final: 0.7452 (pmm) REVERT: d 736 VAL cc_start: 0.8455 (t) cc_final: 0.8131 (t) REVERT: d 1012 MET cc_start: 0.1129 (ptp) cc_final: 0.0501 (ttt) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.3643 time to fit residues: 139.6525 Evaluate side-chains 180 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 256 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 272 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 285 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 175 optimal weight: 0.0870 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 94 HIS ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22869 Z= 0.211 Angle : 0.597 10.986 30984 Z= 0.304 Chirality : 0.044 0.262 3523 Planarity : 0.004 0.106 4096 Dihedral : 4.216 21.387 3171 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % 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: -0.15 (0.16), residues: 2877 helix: 1.12 (0.16), residues: 1027 sheet: -0.65 (0.28), residues: 328 loop : -0.81 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP c 243 HIS 0.007 0.001 HIS c 200 PHE 0.011 0.001 PHE a 189 TYR 0.022 0.002 TYR d 793 ARG 0.009 0.000 ARG d 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5754 Ramachandran restraints generated. 2877 Oldfield, 0 Emsley, 2877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.715 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: c 160 MET cc_start: 0.8632 (tpt) cc_final: 0.8342 (tpt) REVERT: c 393 MET cc_start: 0.8424 (tpp) cc_final: 0.7763 (tpp) REVERT: c 611 MET cc_start: 0.6313 (ttm) cc_final: 0.5240 (ttp) REVERT: c 661 MET cc_start: 0.6874 (mmm) cc_final: 0.6488 (mmm) REVERT: c 727 GLU cc_start: 0.7957 (mp0) cc_final: 0.7518 (mp0) REVERT: c 926 MET cc_start: 0.8306 (tpp) cc_final: 0.8044 (tpt) REVERT: d 148 LEU cc_start: 0.6473 (mt) cc_final: 0.6263 (mt) REVERT: d 256 MET cc_start: 0.3241 (mmp) cc_final: 0.3011 (mmp) REVERT: d 457 MET cc_start: 0.7490 (mmm) cc_final: 0.7104 (mmt) REVERT: d 576 MET cc_start: 0.8091 (ppp) cc_final: 0.7820 (ptt) REVERT: d 581 MET cc_start: 0.7802 (pmm) cc_final: 0.7536 (pmm) REVERT: d 736 VAL cc_start: 0.8457 (t) cc_final: 0.8090 (t) REVERT: d 1012 MET cc_start: 0.1208 (ptp) cc_final: 0.0572 (ttt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.3546 time to fit residues: 133.2139 Evaluate side-chains 180 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 139 optimal weight: 0.7980 chunk 180 optimal weight: 0.0050 chunk 242 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 209 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.085783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.063561 restraints weight = 95924.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065355 restraints weight = 54923.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066499 restraints weight = 37509.294| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.6448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22869 Z= 0.209 Angle : 0.594 10.863 30984 Z= 0.303 Chirality : 0.044 0.241 3523 Planarity : 0.004 0.092 4096 Dihedral : 4.210 20.517 3171 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % 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: -0.09 (0.16), residues: 2877 helix: 1.21 (0.17), residues: 1018 sheet: -0.66 (0.27), residues: 342 loop : -0.78 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 243 HIS 0.007 0.001 HIS c 200 PHE 0.014 0.001 PHE d 673 TYR 0.022 0.002 TYR d 793 ARG 0.009 0.000 ARG d 556 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4343.74 seconds wall clock time: 80 minutes 3.15 seconds (4803.15 seconds total)