Starting phenix.real_space_refine on Fri Aug 9 23:16:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7j_9047/08_2024/6m7j_9047_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7j_9047/08_2024/6m7j_9047.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7j_9047/08_2024/6m7j_9047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7j_9047/08_2024/6m7j_9047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7j_9047/08_2024/6m7j_9047_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7j_9047/08_2024/6m7j_9047_neut_trim.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= 0.006 sd= 0.082 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 55 5.49 5 Mg 1 5.21 5 S 98 5.16 5 C 16871 2.51 5 N 4836 2.21 5 O 5320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 467": "NH1" <-> "NH2" Residue "C ARG 482": "NH1" <-> "NH2" Residue "C ARG 791": "NH1" <-> "NH2" Residue "C ARG 855": "NH1" <-> "NH2" Residue "C ARG 925": "NH1" <-> "NH2" Residue "C TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1067": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 572": "NH1" <-> "NH2" Residue "D ARG 841": "NH1" <-> "NH2" Residue "D ARG 876": "NH1" <-> "NH2" Residue "D ARG 940": "NH1" <-> "NH2" Residue "D PHE 1061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "F ARG 229": "NH1" <-> "NH2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "F ARG 524": "NH1" <-> "NH2" Residue "J ARG 109": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27183 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 8586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8586 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 9873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 9873 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 57, 'TRANS': 1204} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2518 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 881 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 526 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, ' ZN': 2, 'C0L': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19125 SG CYS D 891 110.355 57.512 85.944 1.00199.50 S ATOM 19692 SG CYS D 968 106.381 58.194 87.216 1.00203.67 S ATOM 19734 SG CYS D 975 107.880 59.453 84.373 1.00192.01 S ATOM 19752 SG CYS D 978 108.130 56.056 83.748 1.00186.92 S ATOM 12567 SG CYS D 60 75.458 104.029 122.731 1.00238.85 S ATOM 12585 SG CYS D 62 73.867 104.451 125.750 1.00228.37 S Time building chain proxies: 13.92, per 1000 atoms: 0.51 Number of scatterers: 27183 At special positions: 0 Unit cell: (132.6, 159.9, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 98 16.00 P 55 15.00 Mg 1 11.99 O 5320 8.00 N 4836 7.00 C 16871 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.52 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1401 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 968 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 978 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 975 " pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " Number of angles added : 6 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6168 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 45 sheets defined 43.2% alpha, 11.5% beta 26 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 9.06 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.938A pdb=" N SER A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 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 203 through 224 removed outlier: 3.630A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.978A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.767A 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 203 through 224 removed outlier: 3.992A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.141A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 233 through 241 removed outlier: 3.614A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.508A pdb=" N ALA C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 301 removed outlier: 3.819A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 349 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.572A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 532 through 539 removed outlier: 3.699A pdb=" N GLU C 536 " --> pdb=" O THR C 532 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 3.758A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 613 removed outlier: 3.662A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 639 removed outlier: 4.385A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 745 Processing helix chain 'C' and resid 778 through 782 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 920 through 926 removed outlier: 4.654A pdb=" N ARG C 924 " --> pdb=" O HIS C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 943 removed outlier: 4.292A pdb=" N ILE C 931 " --> pdb=" O ASN C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1071 through 1080 removed outlier: 3.657A pdb=" N GLN C1077 " --> pdb=" O CYS C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1092 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.007A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.823A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.650A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 185 Processing helix chain 'D' and resid 190 through 228 Processing helix chain 'D' and resid 238 through 246 removed outlier: 4.401A pdb=" N ASP D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.534A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 4.136A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 305 removed outlier: 3.794A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 340 through 361 Processing helix chain 'D' and resid 363 through 384 removed outlier: 3.570A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.646A pdb=" N LEU D 406 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 492 removed outlier: 3.557A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 509 removed outlier: 4.339A pdb=" N ILE D 509 " --> pdb=" O ARG D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 533 removed outlier: 4.257A pdb=" N ALA D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 677 removed outlier: 3.830A pdb=" N LEU D 677 " --> pdb=" O PHE D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 728 removed outlier: 3.692A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY D 728 " --> pdb=" O ALA D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 736 Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.933A 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 806 removed outlier: 4.762A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 818 Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.705A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 865 " --> pdb=" O ALA D 861 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR D 867 " --> pdb=" O THR D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 921 removed outlier: 3.550A pdb=" N TYR D 921 " --> pdb=" O GLU D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.758A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1010 Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1145 removed outlier: 3.537A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix Processing helix chain 'D' and resid 1151 through 1162 Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 3.815A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1224 Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.594A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1255 removed outlier: 4.283A pdb=" N ASN D1251 " --> pdb=" O GLY D1247 " (cutoff:3.500A) Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 72 removed outlier: 4.079A pdb=" N GLY E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 212 through 224 removed outlier: 3.736A pdb=" N ARG F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS F 217 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER F 224 " --> pdb=" O GLU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 237 Processing helix chain 'F' and resid 242 through 266 Processing helix chain 'F' and resid 274 through 308 removed outlier: 4.386A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 334 Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.761A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 406 through 417 Processing helix chain 'F' and resid 434 through 437 Processing helix chain 'F' and resid 447 through 466 Processing helix chain 'F' and resid 468 through 480 removed outlier: 3.525A pdb=" N ALA F 472 " --> pdb=" O SER F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 521 Processing helix chain 'F' and resid 522 through 527 removed outlier: 3.750A pdb=" N ASP F 525 " --> pdb=" O VAL F 522 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 89 removed outlier: 3.819A pdb=" N ARG J 88 " --> pdb=" O MET J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 108 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.607A pdb=" N THR A 175 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.537A pdb=" N ILE A 54 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 100 Processing sheet with id=AA6, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.299A pdb=" N GLY A 103 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR A 127 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 12 Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA9, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AB1, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB2, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.464A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AB6, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB7, first strand: chain 'C' and resid 166 through 168 removed outlier: 3.862A pdb=" N PHE C 166 " --> pdb=" O ARG C 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.322A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 456 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 187 through 189 Processing sheet with id=AC1, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC2, first strand: chain 'C' and resid 517 through 520 removed outlier: 5.596A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 561 through 562 removed outlier: 4.123A pdb=" N VAL C 541 " --> pdb=" O ARG C 562 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AC5, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.458A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 667 through 668 removed outlier: 4.771A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC8, first strand: chain 'C' and resid 717 through 722 removed outlier: 3.843A pdb=" N ILE C 915 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 722 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE C 916 " --> pdb=" O ILE C 736 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 886 " --> pdb=" O MET C1031 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 717 " --> pdb=" O ILE C1030 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 748 through 749 Processing sheet with id=AD1, first strand: chain 'C' and resid 765 through 766 removed outlier: 3.688A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP C 761 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C 865 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD3, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.325A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 905 through 906 Processing sheet with id=AD5, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.656A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD7, first strand: chain 'C' and resid 1133 through 1138 Processing sheet with id=AD8, first strand: chain 'D' and resid 74 through 75 removed outlier: 3.674A pdb=" N CYS D 75 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL D 80 " --> pdb=" O CYS D 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 93 through 102 removed outlier: 9.801A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 234 through 236 removed outlier: 5.812A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 611 through 612 removed outlier: 7.251A pdb=" N TYR D 612 " --> pdb=" O ARG D 636 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE4, first strand: chain 'D' and resid 929 through 930 Processing sheet with id=AE5, first strand: chain 'D' and resid 1053 through 1054 removed outlier: 5.372A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1180 through 1182 Processing sheet with id=AE7, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE8, first strand: chain 'F' and resid 439 through 441 Processing sheet with id=AE9, first strand: chain 'J' and resid 39 through 45 1141 hydrogen bonds defined for protein. 3213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 11.75 Time building geometry restraints manager: 13.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4621 1.30 - 1.43: 6811 1.43 - 1.56: 16034 1.56 - 1.68: 115 1.68 - 1.81: 173 Bond restraints: 27754 Sorted by residual: bond pdb=" C23 C0L D1404 " pdb=" O24 C0L D1404 " ideal model delta sigma weight residual 1.204 1.389 -0.185 2.00e-02 2.50e+03 8.60e+01 bond pdb=" C18 C0L D1404 " pdb=" O19 C0L D1404 " ideal model delta sigma weight residual 1.224 1.392 -0.168 2.00e-02 2.50e+03 7.02e+01 bond pdb=" C PHE C1068 " pdb=" N GLY C1069 " ideal model delta sigma weight residual 1.331 1.450 -0.119 1.46e-02 4.69e+03 6.66e+01 bond pdb=" CA PHE C1068 " pdb=" C PHE C1068 " ideal model delta sigma weight residual 1.523 1.618 -0.095 1.34e-02 5.57e+03 5.04e+01 bond pdb=" CA TRP C1074 " pdb=" CB TRP C1074 " ideal model delta sigma weight residual 1.530 1.642 -0.111 1.69e-02 3.50e+03 4.34e+01 ... (remaining 27749 not shown) Histogram of bond angle deviations from ideal: 94.65 - 103.79: 613 103.79 - 112.92: 16080 112.92 - 122.06: 15639 122.06 - 131.19: 5425 131.19 - 140.33: 77 Bond angle restraints: 37834 Sorted by residual: angle pdb=" C ALA F 447 " pdb=" N VAL F 448 " pdb=" CA VAL F 448 " ideal model delta sigma weight residual 120.47 103.02 17.45 1.58e+00 4.01e-01 1.22e+02 angle pdb=" CA TRP C1074 " pdb=" CB TRP C1074 " pdb=" CG TRP C1074 " ideal model delta sigma weight residual 113.60 133.87 -20.27 1.90e+00 2.77e-01 1.14e+02 angle pdb=" C ARG C 282 " pdb=" N PRO C 283 " pdb=" CA PRO C 283 " ideal model delta sigma weight residual 119.83 108.80 11.03 1.08e+00 8.57e-01 1.04e+02 angle pdb=" N TRP C1074 " pdb=" CA TRP C1074 " pdb=" CB TRP C1074 " ideal model delta sigma weight residual 110.49 127.45 -16.96 1.69e+00 3.50e-01 1.01e+02 angle pdb=" N CYS C1073 " pdb=" CA CYS C1073 " pdb=" C CYS C1073 " ideal model delta sigma weight residual 110.80 94.65 16.15 2.13e+00 2.20e-01 5.75e+01 ... (remaining 37829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 16522 35.54 - 71.07: 331 71.07 - 106.61: 24 106.61 - 142.14: 1 142.14 - 177.68: 5 Dihedral angle restraints: 16883 sinusoidal: 7293 harmonic: 9590 Sorted by residual: dihedral pdb=" N TRP C1074 " pdb=" C TRP C1074 " pdb=" CA TRP C1074 " pdb=" CB TRP C1074 " ideal model delta harmonic sigma weight residual 122.80 137.25 -14.45 0 2.50e+00 1.60e-01 3.34e+01 dihedral pdb=" CA ARG D 480 " pdb=" C ARG D 480 " pdb=" N PRO D 481 " pdb=" CA PRO D 481 " ideal model delta harmonic sigma weight residual 180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ARG D 578 " pdb=" C ARG D 578 " pdb=" N LEU D 579 " pdb=" CA LEU D 579 " ideal model delta harmonic sigma weight residual -180.00 -152.67 -27.33 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 16880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4136 0.100 - 0.200: 161 0.200 - 0.299: 4 0.299 - 0.399: 1 0.399 - 0.499: 3 Chirality restraints: 4305 Sorted by residual: chirality pdb=" CA ALA F 225 " pdb=" N ALA F 225 " pdb=" C ALA F 225 " pdb=" CB ALA F 225 " both_signs ideal model delta sigma weight residual False 2.48 1.99 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CA GLN D 657 " pdb=" N GLN D 657 " pdb=" C GLN D 657 " pdb=" CB GLN D 657 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA VAL F 446 " pdb=" N VAL F 446 " pdb=" C VAL F 446 " pdb=" CB VAL F 446 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 4302 not shown) Planarity restraints: 4789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 223 " -0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ALA F 223 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA F 223 " -0.023 2.00e-02 2.50e+03 pdb=" N SER F 224 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C1056 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C PRO C1056 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO C1056 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU C1057 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1074 " 0.024 2.00e-02 2.50e+03 2.20e-02 1.21e+01 pdb=" CG TRP C1074 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP C1074 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C1074 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C1074 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C1074 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C1074 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1074 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1074 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C1074 " -0.000 2.00e-02 2.50e+03 ... (remaining 4786 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 128 2.21 - 2.89: 11392 2.89 - 3.56: 47263 3.56 - 4.23: 69140 4.23 - 4.90: 107087 Nonbonded interactions: 235010 Sorted by model distance: nonbonded pdb=" O ARG C 230 " pdb=" CG ARG C 231 " model vdw 1.543 3.440 nonbonded pdb=" CE MET C1051 " pdb=" CA ASP F 441 " model vdw 1.553 3.890 nonbonded pdb=" O CYS C1073 " pdb=" N ALA C1075 " model vdw 1.622 3.120 nonbonded pdb=" CE MET C1051 " pdb=" CB ASP F 441 " model vdw 1.827 3.860 nonbonded pdb=" CA GLN F 415 " pdb=" CD ARG F 418 " model vdw 1.972 3.870 ... (remaining 235005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 or (resid 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 2 \ 23 or (resid 224 and (name N or name CA or name C or name O or name CB )) or res \ id 225 through 226)) selection = (chain 'B' and resid 2 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: 1.110 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: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 84.200 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.090 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.185 27754 Z= 0.519 Angle : 1.073 22.001 37834 Z= 0.604 Chirality : 0.049 0.499 4305 Planarity : 0.005 0.072 4789 Dihedral : 13.779 177.678 10715 Min Nonbonded Distance : 1.543 Molprobity Statistics. All-atom Clashscore : 73.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.31 % Favored : 87.45 % Rotamer: Outliers : 0.22 % Allowed : 3.44 % Favored : 96.34 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.12), residues: 3331 helix: -2.26 (0.12), residues: 1231 sheet: -3.63 (0.22), residues: 329 loop : -3.04 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP C1074 HIS 0.018 0.004 HIS C 751 PHE 0.021 0.003 PHE D 7 TYR 0.033 0.003 TYR D 134 ARG 0.021 0.001 ARG D 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 215 time to evaluate : 3.247 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: A 75 GLU cc_start: 0.9239 (tp30) cc_final: 0.8983 (tm-30) REVERT: B 194 LEU cc_start: 0.9488 (mt) cc_final: 0.9078 (mp) REVERT: C 159 MET cc_start: 0.8831 (mmm) cc_final: 0.8479 (mmm) REVERT: C 611 MET cc_start: 0.9454 (mtm) cc_final: 0.8788 (mtp) REVERT: C 630 MET cc_start: 0.9284 (mmm) cc_final: 0.8869 (mmm) REVERT: C 661 MET cc_start: 0.8758 (tpt) cc_final: 0.8510 (tpt) REVERT: C 713 MET cc_start: 0.8873 (mmm) cc_final: 0.8461 (mmm) REVERT: C 724 MET cc_start: 0.9285 (ptm) cc_final: 0.8913 (ptm) REVERT: C 741 LEU cc_start: 0.9555 (mt) cc_final: 0.9342 (tt) REVERT: C 783 ASP cc_start: 0.9339 (m-30) cc_final: 0.9063 (t0) REVERT: C 904 MET cc_start: 0.9385 (tpp) cc_final: 0.8381 (mmm) REVERT: C 1028 MET cc_start: 0.9322 (ttt) cc_final: 0.8945 (tpp) REVERT: C 1031 MET cc_start: 0.7752 (mtm) cc_final: 0.7533 (mpp) REVERT: C 1127 GLU cc_start: 0.9583 (mt-10) cc_final: 0.9263 (mt-10) REVERT: D 120 LEU cc_start: 0.9059 (mp) cc_final: 0.8805 (tp) REVERT: D 373 MET cc_start: 0.9161 (mtp) cc_final: 0.8731 (mtp) REVERT: D 379 ASP cc_start: 0.9382 (m-30) cc_final: 0.9089 (m-30) REVERT: D 657 GLN cc_start: 0.6542 (OUTLIER) cc_final: 0.5935 (mp10) REVERT: D 733 MET cc_start: 0.9103 (pp-130) cc_final: 0.8878 (ppp) REVERT: D 983 MET cc_start: 0.8937 (mmm) cc_final: 0.8581 (mmt) REVERT: E 99 ILE cc_start: 0.9365 (mt) cc_final: 0.9118 (mt) REVERT: F 282 MET cc_start: 0.9765 (mmt) cc_final: 0.9554 (mmt) REVERT: F 343 PHE cc_start: 0.9252 (t80) cc_final: 0.8996 (t80) REVERT: J 69 LEU cc_start: 0.8849 (mt) cc_final: 0.8468 (tp) outliers start: 6 outliers final: 2 residues processed: 220 average time/residue: 0.4206 time to fit residues: 145.1885 Evaluate side-chains 130 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 263 optimal weight: 20.0000 chunk 101 optimal weight: 0.0020 chunk 160 optimal weight: 0.0570 chunk 196 optimal weight: 6.9990 chunk 305 optimal weight: 0.4980 overall best weight: 1.9110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN B 124 HIS C 298 ASN ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS C 875 GLN C 920 HIS C 969 ASN C1034 HIS D 307 ASN D 465 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS D 771 ASN ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1145 GLN F 294 HIS F 322 GLN F 325 ASN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27754 Z= 0.238 Angle : 0.723 13.591 37834 Z= 0.377 Chirality : 0.046 0.307 4305 Planarity : 0.005 0.071 4789 Dihedral : 16.259 176.771 4348 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.45 % Favored : 93.46 % Rotamer: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.48 (0.14), residues: 3331 helix: -0.41 (0.14), residues: 1278 sheet: -2.88 (0.24), residues: 338 loop : -2.40 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 70 HIS 0.016 0.002 HIS C1042 PHE 0.019 0.002 PHE A 63 TYR 0.032 0.002 TYR E 56 ARG 0.014 0.001 ARG C 584 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 2.939 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: A 123 MET cc_start: 0.8807 (ttm) cc_final: 0.8564 (ttp) REVERT: B 1 MET cc_start: 0.8192 (tpp) cc_final: 0.7658 (mtm) REVERT: B 192 LEU cc_start: 0.9756 (tp) cc_final: 0.9176 (pp) REVERT: C 355 MET cc_start: 0.8509 (tmm) cc_final: 0.8186 (tmm) REVERT: C 440 MET cc_start: 0.8857 (tmm) cc_final: 0.7964 (tmm) REVERT: C 607 MET cc_start: 0.9607 (mmp) cc_final: 0.9114 (mmm) REVERT: C 611 MET cc_start: 0.9665 (mtm) cc_final: 0.9019 (mtp) REVERT: C 661 MET cc_start: 0.8844 (tpt) cc_final: 0.8503 (tpt) REVERT: C 713 MET cc_start: 0.8657 (mmm) cc_final: 0.8279 (mmm) REVERT: C 724 MET cc_start: 0.9515 (ptm) cc_final: 0.9162 (ttp) REVERT: C 741 LEU cc_start: 0.9696 (mt) cc_final: 0.9424 (tt) REVERT: C 783 ASP cc_start: 0.9334 (m-30) cc_final: 0.9038 (p0) REVERT: C 926 MET cc_start: 0.9176 (mpp) cc_final: 0.8972 (mpp) REVERT: C 1031 MET cc_start: 0.8480 (mtm) cc_final: 0.7908 (mpp) REVERT: C 1076 MET cc_start: 0.9219 (ttt) cc_final: 0.8539 (tpp) REVERT: C 1127 GLU cc_start: 0.9678 (mt-10) cc_final: 0.9392 (mt-10) REVERT: D 106 TYR cc_start: 0.9361 (m-80) cc_final: 0.9106 (m-80) REVERT: D 114 LEU cc_start: 0.9643 (mt) cc_final: 0.9428 (mt) REVERT: D 120 LEU cc_start: 0.9018 (mp) cc_final: 0.8752 (tp) REVERT: D 143 MET cc_start: 0.8859 (mtp) cc_final: 0.8626 (ttm) REVERT: D 373 MET cc_start: 0.9176 (mtp) cc_final: 0.8884 (mtp) REVERT: D 379 ASP cc_start: 0.9366 (m-30) cc_final: 0.9012 (m-30) REVERT: D 422 VAL cc_start: 0.8901 (m) cc_final: 0.8680 (p) REVERT: D 457 MET cc_start: 0.9655 (mtp) cc_final: 0.9449 (mtt) REVERT: D 515 MET cc_start: 0.8149 (ptp) cc_final: 0.7879 (ptp) REVERT: D 559 MET cc_start: 0.9511 (mpp) cc_final: 0.8904 (mpp) REVERT: D 706 MET cc_start: 0.9402 (ttt) cc_final: 0.9168 (ttt) REVERT: D 983 MET cc_start: 0.8857 (mmm) cc_final: 0.8592 (mmt) REVERT: D 1208 MET cc_start: 0.9238 (pmm) cc_final: 0.8199 (pmm) REVERT: F 269 ARG cc_start: 0.9113 (pmt-80) cc_final: 0.8817 (mmm160) REVERT: F 281 MET cc_start: 0.9497 (ptp) cc_final: 0.9178 (ptm) REVERT: F 282 MET cc_start: 0.9756 (mmt) cc_final: 0.9464 (mmt) REVERT: F 343 PHE cc_start: 0.9249 (t80) cc_final: 0.8986 (t80) REVERT: J 68 ASP cc_start: 0.8299 (m-30) cc_final: 0.7666 (t0) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.3392 time to fit residues: 93.7173 Evaluate side-chains 119 residues out of total 2831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 253 optimal weight: 0.0980 chunk 207 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 305 optimal weight: 9.9990 chunk 330 optimal weight: 4.9990 chunk 272 optimal weight: 0.0670 chunk 303 optimal weight: 0.0170 chunk 104 optimal weight: 0.4980 chunk 245 optimal weight: 0.9990 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: