Starting phenix.real_space_refine on Mon Sep 30 00:34:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z11_11026/09_2024/6z11_11026.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z11_11026/09_2024/6z11_11026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z11_11026/09_2024/6z11_11026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z11_11026/09_2024/6z11_11026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z11_11026/09_2024/6z11_11026.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z11_11026/09_2024/6z11_11026.cif" } resolution = 3.36 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= 0.002 sd= 0.024 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 87 5.16 5 C 14991 2.51 5 N 4254 2.21 5 O 4613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 142 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23948 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1700 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 209} Chain: "B" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1783 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 220} Chain: "C" Number of atoms: 8433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8433 Classifications: {'peptide': 1089} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1030} Chain breaks: 1 Chain: "D" Number of atoms: 9826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1254, 9826 Classifications: {'peptide': 1254} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 54, 'TRANS': 1197} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 75} Chain: "H" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1563 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 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 18925 SG CYS D 890 35.486 59.610 77.607 1.00 25.70 S ATOM 19487 SG CYS D 967 38.115 62.172 78.213 1.00 22.34 S ATOM 19529 SG CYS D 974 36.383 60.503 81.055 1.00 21.46 S ATOM 19548 SG CYS D 977 38.738 58.556 79.254 1.00 20.41 S ATOM 12390 SG CYS D 60 41.523 123.724 95.786 1.00 69.43 S ATOM 12408 SG CYS D 62 43.027 127.404 96.225 1.00 73.10 S ATOM 12517 SG CYS D 75 40.569 126.973 93.957 1.00 69.31 S ATOM 12543 SG CYS D 78 43.892 125.420 93.141 1.00 71.22 S Time building chain proxies: 13.74, per 1000 atoms: 0.57 Number of scatterers: 23948 At special positions: 0 Unit cell: (130.483, 145.442, 173.7, 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 87 16.00 Mg 1 11.99 O 4613 8.00 N 4254 7.00 C 14991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.78 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 974 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 890 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 977 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 967 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " Number of angles added : 12 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5672 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 41 sheets defined 35.5% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 31 through 45 Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.534A pdb=" N LYS A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.779A pdb=" N SER A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 151 through 156' Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.919A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 45 Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.677A pdb=" N GLY B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 Processing helix chain 'C' and resid 45 through 56 removed outlier: 3.912A pdb=" N THR C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 76 through 85 removed outlier: 3.847A pdb=" N VAL C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 246 through 254 removed outlier: 4.231A pdb=" N MET C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 273 Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.544A pdb=" N LYS C 310 " --> pdb=" O LYS C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 342 removed outlier: 3.706A pdb=" N GLU C 334 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 396 Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 411 through 424 removed outlier: 3.537A pdb=" N VAL C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 523 through 527 Processing helix chain 'C' and resid 587 through 591 Processing helix chain 'C' and resid 592 through 604 removed outlier: 3.658A pdb=" N ARG C 604 " --> pdb=" O ALA C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 628 Processing helix chain 'C' and resid 721 through 725 removed outlier: 3.962A pdb=" N ASP C 724 " --> pdb=" O ASN C 721 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 725 " --> pdb=" O TYR C 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 721 through 725' Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 768 through 773 removed outlier: 4.382A pdb=" N LEU C 772 " --> pdb=" O SER C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 895 Processing helix chain 'C' and resid 909 through 913 removed outlier: 4.092A pdb=" N GLY C 912 " --> pdb=" O ASN C 909 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 913 " --> pdb=" O THR C 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 909 through 913' Processing helix chain 'C' and resid 919 through 933 removed outlier: 3.631A pdb=" N LEU C 923 " --> pdb=" O ILE C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 948 Processing helix chain 'C' and resid 1027 through 1031 Processing helix chain 'C' and resid 1050 through 1054 Processing helix chain 'C' and resid 1060 through 1069 removed outlier: 3.624A pdb=" N CYS C1064 " --> pdb=" O GLY C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1082 Processing helix chain 'C' and resid 1088 through 1100 Processing helix chain 'C' and resid 1109 through 1120 removed outlier: 3.530A pdb=" N LYS C1113 " --> pdb=" O PRO C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1121 through 1123 No H-bonds generated for 'chain 'C' and resid 1121 through 1123' Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.833A pdb=" N ILE D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.026A pdb=" N LEU D 39 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 40 " --> pdb=" O ARG D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 40' Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.706A pdb=" N PHE D 107 " --> pdb=" O HIS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 123 through 130 removed outlier: 4.209A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 185 removed outlier: 4.157A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ALA D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 4.041A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 Processing helix chain 'D' and resid 260 through 268 removed outlier: 4.420A pdb=" N GLU D 266 " --> pdb=" O LYS D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 288 through 302 removed outlier: 3.642A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 341 through 356 removed outlier: 3.938A pdb=" N ARG D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 382 removed outlier: 3.986A pdb=" N ALA D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU D 381 " --> pdb=" O SER D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 4.870A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 462 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 482 through 491 removed outlier: 4.799A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (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 548 through 558 Processing helix chain 'D' and resid 579 through 590 removed outlier: 3.808A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 removed outlier: 3.526A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 674 removed outlier: 3.755A pdb=" N VAL D 670 " --> pdb=" O THR D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 703 Processing helix chain 'D' and resid 704 through 724 removed outlier: 4.043A pdb=" N VAL D 708 " --> pdb=" O PRO D 704 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN D 710 " --> pdb=" O ILE D 706 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 724 " --> pdb=" O PHE D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 761 removed outlier: 4.015A pdb=" N ILE D 744 " --> pdb=" O GLN D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 792 Processing helix chain 'D' and resid 796 through 804 Processing helix chain 'D' and resid 809 through 818 removed outlier: 3.969A pdb=" N THR D 813 " --> pdb=" O ASN D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 880 removed outlier: 3.968A pdb=" N ALA D 855 " --> pdb=" O ASN D 851 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ALA D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D 864 " --> pdb=" O ALA D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 919 removed outlier: 3.511A pdb=" N SER D 918 " --> pdb=" O HIS D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 954 Processing helix chain 'D' and resid 995 through 1004 removed outlier: 3.563A pdb=" N ALA D 999 " --> pdb=" O GLY D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1009 removed outlier: 3.857A pdb=" N LEU D1009 " --> pdb=" O GLY D1006 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1036 Processing helix chain 'D' and resid 1118 through 1126 Processing helix chain 'D' and resid 1130 through 1145 Processing helix chain 'D' and resid 1155 through 1160 removed outlier: 3.700A pdb=" N ARG D1160 " --> pdb=" O GLU D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1161 through 1163 No H-bonds generated for 'chain 'D' and resid 1161 through 1163' Processing helix chain 'D' and resid 1184 through 1190 Processing helix chain 'D' and resid 1210 through 1217 Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.587A pdb=" N ALA D1224 " --> pdb=" O SER D1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 1229 through 1240 removed outlier: 3.617A pdb=" N VAL D1233 " --> pdb=" O GLU D1229 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN D1240 " --> pdb=" O ASP D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1265 through 1270 Processing helix chain 'E' and resid 30 through 34 removed outlier: 3.545A pdb=" N THR E 33 " --> pdb=" O LEU E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 46 through 67 removed outlier: 4.260A pdb=" N ARG E 57 " --> pdb=" O TYR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 98 Processing helix chain 'H' and resid 4 through 41 removed outlier: 3.706A pdb=" N GLU H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 65 Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 454 through 474 removed outlier: 3.907A pdb=" N ARG H 458 " --> pdb=" O GLU H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 480 removed outlier: 3.822A pdb=" N LEU H 480 " --> pdb=" O ARG H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 494 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 26 removed outlier: 5.942A pdb=" N ARG A 18 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR A 198 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ARG A 20 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL A 196 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL A 22 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE A 194 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLU A 24 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU A 192 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.112A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY A 145 " --> pdb=" O PRO A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.112A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 12 removed outlier: 3.646A pdb=" N GLU B 24 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 22 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ARG B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL B 196 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL B 22 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE B 189 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR B 181 " --> pdb=" O PHE B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.579A pdb=" N VAL B 111 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR B 96 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 106 removed outlier: 3.612A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.685A pdb=" N ASN C 132 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 102 through 103 removed outlier: 3.621A pdb=" N ARG C 102 " --> pdb=" O PHE C 125 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY C 146 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 158 through 159 Processing sheet with id=AB5, first strand: chain 'C' and resid 170 through 172 Processing sheet with id=AB6, first strand: chain 'C' and resid 181 through 182 removed outlier: 3.709A pdb=" N LEU C 190 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AB8, first strand: chain 'C' and resid 346 through 347 Processing sheet with id=AB9, first strand: chain 'C' and resid 496 through 497 removed outlier: 5.451A pdb=" N GLN C 518 " --> pdb=" O LYS C 509 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N GLU C 511 " --> pdb=" O THR C 516 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR C 516 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 496 through 497 Processing sheet with id=AC2, first strand: chain 'C' and resid 532 through 533 removed outlier: 3.873A pdb=" N VAL C 532 " --> pdb=" O ARG C 553 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 617 through 618 Processing sheet with id=AC4, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.732A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 639 through 643 removed outlier: 5.568A pdb=" N ILE C 641 " --> pdb=" O MET C 652 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N MET C 652 " --> pdb=" O ILE C 641 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 699 through 700 removed outlier: 3.722A pdb=" N GLU C 703 " --> pdb=" O GLN C 700 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 883 through 885 removed outlier: 4.559A pdb=" N THR C1015 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 714 " --> pdb=" O THR C1015 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ILE C 906 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 711 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU C 908 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA C 713 " --> pdb=" O LEU C 908 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 883 through 885 Processing sheet with id=AC9, first strand: chain 'C' and resid 740 through 750 removed outlier: 3.665A pdb=" N GLY C 840 " --> pdb=" O TYR C 863 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA C 865 " --> pdb=" O VAL C 838 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL C 838 " --> pdb=" O ALA C 865 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N LYS C 867 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N GLY C 836 " --> pdb=" O LYS C 867 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 836 " --> pdb=" O VAL C 787 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AD2, first strand: chain 'C' and resid 792 through 794 removed outlier: 4.022A pdb=" N VAL C 794 " --> pdb=" O LEU C 828 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1033 through 1035 removed outlier: 3.529A pdb=" N GLY D 426 " --> pdb=" O VAL D 543 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL D 517 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1127 through 1128 Processing sheet with id=AD5, first strand: chain 'D' and resid 93 through 102 removed outlier: 6.330A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 328 through 330 removed outlier: 3.865A pdb=" N ARG D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD8, first strand: chain 'D' and resid 896 through 898 Processing sheet with id=AD9, first strand: chain 'D' and resid 901 through 903 Processing sheet with id=AE1, first strand: chain 'D' and resid 1076 through 1077 removed outlier: 3.603A pdb=" N PHE D1063 " --> pdb=" O LEU D1081 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU D1081 " --> pdb=" O PHE D1063 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1076 through 1077 Processing sheet with id=AE3, first strand: chain 'D' and resid 1182 through 1183 removed outlier: 3.502A pdb=" N THR D1167 " --> pdb=" O ARG D1205 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1272 through 1275 removed outlier: 3.803A pdb=" N GLN D1272 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR E 104 " --> pdb=" O GLN D1272 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN D1274 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 98 through 103 removed outlier: 7.186A pdb=" N ASP H 92 " --> pdb=" O PRO H 99 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU H 88 " --> pdb=" O ASP H 103 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY H 73 " --> pdb=" O ILE H 85 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG H 87 " --> pdb=" O CYS H 71 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N CYS H 71 " --> pdb=" O ARG H 87 " (cutoff:3.500A) 897 hydrogen bonds defined for protein. 2481 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: 9.71 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8291 1.34 - 1.46: 4551 1.46 - 1.58: 11342 1.58 - 1.70: 0 1.70 - 1.81: 155 Bond restraints: 24339 Sorted by residual: bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.48e+00 bond pdb=" CD ARG D 980 " pdb=" NE ARG D 980 " ideal model delta sigma weight residual 1.458 1.440 0.018 1.40e-02 5.10e+03 1.72e+00 bond pdb=" CB VAL C 930 " pdb=" CG1 VAL C 930 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.61e+00 bond pdb=" N VAL D 431 " pdb=" CA VAL D 431 " ideal model delta sigma weight residual 1.459 1.443 0.016 1.25e-02 6.40e+03 1.56e+00 ... (remaining 24334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 31102 1.19 - 2.38: 1566 2.38 - 3.58: 208 3.58 - 4.77: 62 4.77 - 5.96: 10 Bond angle restraints: 32948 Sorted by residual: angle pdb=" N VAL C 225 " pdb=" CA VAL C 225 " pdb=" C VAL C 225 " ideal model delta sigma weight residual 113.42 109.17 4.25 1.17e+00 7.31e-01 1.32e+01 angle pdb=" CA TYR E 53 " pdb=" CB TYR E 53 " pdb=" CG TYR E 53 " ideal model delta sigma weight residual 113.90 119.10 -5.20 1.80e+00 3.09e-01 8.36e+00 angle pdb=" C GLU C 723 " pdb=" N ASP C 724 " pdb=" CA ASP C 724 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 6.99e+00 angle pdb=" C GLY E 83 " pdb=" N LEU E 84 " pdb=" CA LEU E 84 " ideal model delta sigma weight residual 121.54 126.55 -5.01 1.91e+00 2.74e-01 6.89e+00 angle pdb=" C ILE E 52 " pdb=" N TYR E 53 " pdb=" CA TYR E 53 " ideal model delta sigma weight residual 120.60 124.58 -3.98 1.60e+00 3.91e-01 6.18e+00 ... (remaining 32943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 13331 17.74 - 35.48: 1355 35.48 - 53.21: 197 53.21 - 70.95: 39 70.95 - 88.69: 11 Dihedral angle restraints: 14933 sinusoidal: 6123 harmonic: 8810 Sorted by residual: dihedral pdb=" CA GLY E 83 " pdb=" C GLY E 83 " pdb=" N LEU E 84 " pdb=" CA LEU E 84 " ideal model delta harmonic sigma weight residual 180.00 155.00 25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA THR C 404 " pdb=" C THR C 404 " pdb=" N PRO C 405 " pdb=" CA PRO C 405 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA TYR D 130 " pdb=" C TYR D 130 " pdb=" N PHE D 131 " pdb=" CA PHE D 131 " ideal model delta harmonic sigma weight residual 180.00 156.87 23.13 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 14930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2192 0.031 - 0.062: 1037 0.062 - 0.093: 349 0.093 - 0.124: 152 0.124 - 0.155: 15 Chirality restraints: 3745 Sorted by residual: chirality pdb=" CA ILE B 193 " pdb=" N ILE B 193 " pdb=" C ILE B 193 " pdb=" CB ILE B 193 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA VAL C 193 " pdb=" N VAL C 193 " pdb=" C VAL C 193 " pdb=" CB VAL C 193 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE D 34 " pdb=" N ILE D 34 " pdb=" C ILE D 34 " pdb=" CB ILE D 34 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 3742 not shown) Planarity restraints: 4357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 404 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO C 405 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 405 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 405 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 545 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO D 546 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 546 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 546 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 110 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO H 111 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 111 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 111 " 0.029 5.00e-02 4.00e+02 ... (remaining 4354 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 148 2.50 - 3.10: 19032 3.10 - 3.70: 33411 3.70 - 4.30: 50143 4.30 - 4.90: 85328 Nonbonded interactions: 188062 Sorted by model distance: nonbonded pdb=" OD1 ASP D 539 " pdb=" OD1 ASP H 483 " model vdw 1.906 3.040 nonbonded pdb=" OD2 ASP H 483 " pdb="MG MG D2003 " model vdw 1.929 2.170 nonbonded pdb=" NH2 ARG E 57 " pdb=" O GLY E 77 " model vdw 2.071 3.120 nonbonded pdb=" NH1 ARG D 875 " pdb=" OG1 THR D1212 " model vdw 2.078 3.120 nonbonded pdb=" OG SER C 173 " pdb=" OH TYR C 177 " model vdw 2.080 3.040 ... (remaining 188057 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' selection = (chain 'B' and resid 1 through 224) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.330 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: 1.090 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 57.620 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.100 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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 : 0.005 0.046 24339 Z= 0.355 Angle : 0.612 5.962 32948 Z= 0.342 Chirality : 0.042 0.155 3745 Planarity : 0.004 0.056 4357 Dihedral : 14.183 88.688 9261 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 0.04 % Allowed : 2.25 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -5.38 (0.11), residues: 3053 helix: -2.89 (0.12), residues: 1001 sheet: -3.14 (0.23), residues: 346 loop : -4.29 (0.11), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 104 HIS 0.007 0.001 HIS D 505 PHE 0.012 0.001 PHE D 920 TYR 0.032 0.001 TYR E 53 ARG 0.006 0.001 ARG C1090 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 310 average time/residue: 0.4712 time to fit residues: 209.2629 Evaluate side-chains 180 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 749 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 9.9990 chunk 231 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 155 optimal weight: 0.0170 chunk 123 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 145 optimal weight: 0.0040 chunk 177 optimal weight: 10.0000 chunk 276 optimal weight: 0.5980 overall best weight: 0.4430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 880 HIS D 22 ASN D 35 ASN D 766 HIS ** D1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24339 Z= 0.179 Angle : 0.617 11.004 32948 Z= 0.321 Chirality : 0.044 0.189 3745 Planarity : 0.005 0.055 4357 Dihedral : 4.834 37.122 3374 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.85 % Allowed : 8.17 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -3.31 (0.13), residues: 3053 helix: -0.80 (0.16), residues: 1014 sheet: -2.33 (0.25), residues: 344 loop : -3.20 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 58 HIS 0.003 0.001 HIS C 191 PHE 0.015 0.001 PHE B 219 TYR 0.016 0.001 TYR E 53 ARG 0.012 0.001 ARG D 875 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 211 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 319 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6353 (mp) REVERT: C 570 MET cc_start: 0.7168 (ttt) cc_final: 0.6962 (ttt) outliers start: 22 outliers final: 8 residues processed: 225 average time/residue: 0.4025 time to fit residues: 140.8578 Evaluate side-chains 178 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 993 VAL Chi-restraints excluded: chain D residue 211 ARG Chi-restraints excluded: chain D residue 1233 VAL Chi-restraints excluded: chain H residue 479 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 153 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 230 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 277 optimal weight: 0.9990 chunk 299 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 chunk 275 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN C 340 HIS C 512 ASN D 329 GLN D 540 GLN D 932 ASN ** D1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24339 Z= 0.268 Angle : 0.612 9.056 32948 Z= 0.315 Chirality : 0.044 0.273 3745 Planarity : 0.005 0.048 4357 Dihedral : 4.650 43.876 3374 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.59 % Allowed : 11.23 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.14), residues: 3053 helix: 0.08 (0.16), residues: 1016 sheet: -1.69 (0.26), residues: 348 loop : -2.63 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 58 HIS 0.004 0.001 HIS C 470 PHE 0.016 0.001 PHE B 219 TYR 0.021 0.001 TYR E 53 ARG 0.006 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 319 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6251 (mp) REVERT: D 310 MET cc_start: 0.5975 (tmm) cc_final: 0.5761 (tmm) REVERT: D 1085 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.5592 (mm-40) outliers start: 41 outliers final: 22 residues processed: 230 average time/residue: 0.3657 time to fit residues: 131.9408 Evaluate side-chains 191 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 211 ARG Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 1085 GLN Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain H residue 479 ASP Chi-restraints excluded: chain H residue 493 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 274 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 ASN C1026 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 766 HIS D1132 GLN ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 24339 Z= 0.414 Angle : 0.699 11.538 32948 Z= 0.357 Chirality : 0.047 0.185 3745 Planarity : 0.005 0.044 4357 Dihedral : 4.953 47.549 3374 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.36 % Allowed : 13.52 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.15), residues: 3053 helix: 0.11 (0.16), residues: 1018 sheet: -1.48 (0.27), residues: 356 loop : -2.33 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 58 HIS 0.005 0.001 HIS B 231 PHE 0.017 0.002 PHE C1002 TYR 0.028 0.002 TYR E 53 ARG 0.010 0.001 ARG D 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 174 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6149 (tp) REVERT: C 221 ARG cc_start: 0.6413 (mmp80) cc_final: 0.6114 (mmp80) REVERT: C 319 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6251 (mp) REVERT: C 717 TRP cc_start: 0.9007 (OUTLIER) cc_final: 0.8696 (t60) REVERT: D 310 MET cc_start: 0.6371 (tmm) cc_final: 0.6160 (tmm) REVERT: D 1085 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.5619 (mm-40) outliers start: 61 outliers final: 35 residues processed: 225 average time/residue: 0.3802 time to fit residues: 134.8553 Evaluate side-chains 195 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 156 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 211 ARG Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 1085 GLN Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 479 ASP Chi-restraints excluded: chain H residue 493 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 245 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 219 optimal weight: 0.2980 chunk 121 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 264 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- 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** ** D1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN H 130 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24339 Z= 0.175 Angle : 0.555 10.368 32948 Z= 0.285 Chirality : 0.042 0.173 3745 Planarity : 0.004 0.046 4357 Dihedral : 4.562 52.571 3374 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.09 % Allowed : 15.26 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -1.47 (0.15), residues: 3053 helix: 0.64 (0.17), residues: 1019 sheet: -1.31 (0.27), residues: 350 loop : -2.02 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 58 HIS 0.003 0.001 HIS B 124 PHE 0.013 0.001 PHE B 219 TYR 0.019 0.001 TYR C 305 ARG 0.007 0.000 ARG D 474 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 182 time to evaluate : 2.945 Fit side-chains REVERT: C 221 ARG cc_start: 0.6230 (mmp80) cc_final: 0.5925 (mmp80) REVERT: C 319 ILE cc_start: 0.6847 (OUTLIER) cc_final: 0.6085 (mp) REVERT: C 717 TRP cc_start: 0.8902 (OUTLIER) cc_final: 0.8536 (t60) REVERT: D 310 MET cc_start: 0.6234 (tmm) cc_final: 0.5961 (tmm) REVERT: D 627 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8089 (pt) REVERT: D 1085 GLN cc_start: 0.6156 (OUTLIER) cc_final: 0.5688 (mm-40) REVERT: H 123 MET cc_start: 0.5813 (tmm) cc_final: 0.5595 (tmm) REVERT: H 481 MET cc_start: 0.3908 (mtt) cc_final: 0.3656 (mtt) outliers start: 54 outliers final: 28 residues processed: 227 average time/residue: 0.3809 time to fit residues: 136.1913 Evaluate side-chains 193 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 387 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 627 LEU Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1085 GLN Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 479 ASP Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 493 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 8.9990 chunk 265 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 173 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 295 optimal weight: 0.0020 chunk 244 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 857 ASN ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24339 Z= 0.178 Angle : 0.548 10.284 32948 Z= 0.281 Chirality : 0.042 0.167 3745 Planarity : 0.004 0.071 4357 Dihedral : 4.392 53.219 3374 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.13 % Allowed : 16.19 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -1.23 (0.15), residues: 3053 helix: 0.78 (0.17), residues: 1030 sheet: -1.29 (0.27), residues: 374 loop : -1.81 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 58 HIS 0.003 0.001 HIS D 505 PHE 0.011 0.001 PHE B 219 TYR 0.014 0.001 TYR E 64 ARG 0.005 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 171 time to evaluate : 2.953 Fit side-chains REVERT: C 221 ARG cc_start: 0.6276 (mmp80) cc_final: 0.5968 (mmp80) REVERT: C 319 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6204 (mp) REVERT: C 717 TRP cc_start: 0.8909 (OUTLIER) cc_final: 0.8572 (t60) REVERT: D 1085 GLN cc_start: 0.6160 (OUTLIER) cc_final: 0.5702 (mm-40) REVERT: H 481 MET cc_start: 0.3948 (mtt) cc_final: 0.3654 (mtt) outliers start: 55 outliers final: 33 residues processed: 216 average time/residue: 0.3671 time to fit residues: 126.0422 Evaluate side-chains 201 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 387 MET Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1085 GLN Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 479 ASP Chi-restraints excluded: chain H residue 493 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 284 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 chunk 168 optimal weight: 9.9990 chunk 215 optimal weight: 0.5980 chunk 166 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 293 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24339 Z= 0.191 Angle : 0.553 14.512 32948 Z= 0.281 Chirality : 0.042 0.186 3745 Planarity : 0.004 0.062 4357 Dihedral : 4.342 52.837 3374 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.25 % Allowed : 16.62 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -1.08 (0.15), residues: 3053 helix: 0.90 (0.17), residues: 1031 sheet: -1.21 (0.27), residues: 375 loop : -1.71 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 58 HIS 0.003 0.001 HIS D 505 PHE 0.016 0.001 PHE D 131 TYR 0.016 0.001 TYR C 305 ARG 0.006 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 170 time to evaluate : 2.697 Fit side-chains revert: symmetry clash REVERT: C 221 ARG cc_start: 0.6272 (mmp80) cc_final: 0.5972 (mmp80) REVERT: C 319 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6146 (mp) REVERT: C 717 TRP cc_start: 0.8905 (OUTLIER) cc_final: 0.8501 (t60) REVERT: D 268 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.6340 (t80) REVERT: D 1085 GLN cc_start: 0.6149 (OUTLIER) cc_final: 0.5699 (mm-40) REVERT: H 481 MET cc_start: 0.4006 (mtt) cc_final: 0.3719 (mtt) outliers start: 58 outliers final: 38 residues processed: 216 average time/residue: 0.3616 time to fit residues: 124.2123 Evaluate side-chains 206 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 164 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 211 ARG Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1085 GLN Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 493 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 181 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 175 optimal weight: 0.0370 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24339 Z= 0.164 Angle : 0.539 11.436 32948 Z= 0.275 Chirality : 0.042 0.256 3745 Planarity : 0.004 0.058 4357 Dihedral : 4.240 52.685 3374 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.25 % Allowed : 16.77 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -0.91 (0.15), residues: 3053 helix: 0.99 (0.17), residues: 1038 sheet: -1.05 (0.27), residues: 364 loop : -1.59 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 58 HIS 0.002 0.001 HIS D 505 PHE 0.010 0.001 PHE D 920 TYR 0.014 0.001 TYR C 305 ARG 0.008 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 173 time to evaluate : 3.005 Fit side-chains REVERT: C 221 ARG cc_start: 0.6270 (mmp80) cc_final: 0.5969 (mmp80) REVERT: C 319 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6200 (mp) REVERT: C 717 TRP cc_start: 0.8897 (OUTLIER) cc_final: 0.8471 (t60) REVERT: D 215 GLU cc_start: 0.5035 (OUTLIER) cc_final: 0.4054 (pt0) REVERT: D 356 ARG cc_start: 0.6237 (mmp-170) cc_final: 0.5949 (mmp80) REVERT: H 481 MET cc_start: 0.4103 (mtt) cc_final: 0.3827 (mtt) outliers start: 58 outliers final: 36 residues processed: 222 average time/residue: 0.3677 time to fit residues: 129.9606 Evaluate side-chains 201 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 162 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1091 THR Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 493 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 267 optimal weight: 0.8980 chunk 281 optimal weight: 5.9990 chunk 256 optimal weight: 0.4980 chunk 273 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 119 optimal weight: 0.0370 chunk 215 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 247 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24339 Z= 0.172 Angle : 0.544 13.363 32948 Z= 0.278 Chirality : 0.042 0.210 3745 Planarity : 0.004 0.059 4357 Dihedral : 4.217 52.008 3374 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.74 % Allowed : 17.20 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -0.79 (0.15), residues: 3053 helix: 1.08 (0.17), residues: 1032 sheet: -0.95 (0.27), residues: 364 loop : -1.52 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 58 HIS 0.002 0.001 HIS D 505 PHE 0.014 0.001 PHE C 130 TYR 0.013 0.001 TYR E 53 ARG 0.007 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 172 time to evaluate : 2.775 Fit side-chains REVERT: C 221 ARG cc_start: 0.6267 (mmp80) cc_final: 0.5991 (mmp80) REVERT: C 319 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6163 (mp) REVERT: C 717 TRP cc_start: 0.8882 (OUTLIER) cc_final: 0.8455 (t60) REVERT: D 215 GLU cc_start: 0.5037 (OUTLIER) cc_final: 0.4035 (pt0) REVERT: D 356 ARG cc_start: 0.6285 (mmp-170) cc_final: 0.5957 (mmp80) REVERT: H 481 MET cc_start: 0.4157 (mtt) cc_final: 0.3871 (mtt) outliers start: 45 outliers final: 38 residues processed: 209 average time/residue: 0.3716 time to fit residues: 122.7071 Evaluate side-chains 202 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1091 THR Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain D residue 1249 LEU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 483 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 179 optimal weight: 0.9980 chunk 289 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 201 optimal weight: 0.0040 chunk 303 optimal weight: 10.0000 chunk 279 optimal weight: 0.0570 chunk 241 optimal weight: 9.9990 chunk 25 optimal weight: 0.4980 chunk 186 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24339 Z= 0.139 Angle : 0.531 8.954 32948 Z= 0.271 Chirality : 0.041 0.194 3745 Planarity : 0.004 0.076 4357 Dihedral : 4.092 51.862 3374 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.39 % Allowed : 17.62 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -0.59 (0.15), residues: 3053 helix: 1.21 (0.17), residues: 1029 sheet: -0.70 (0.28), residues: 355 loop : -1.40 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 58 HIS 0.002 0.000 HIS C 590 PHE 0.011 0.001 PHE C 243 TYR 0.020 0.001 TYR D 241 ARG 0.010 0.000 ARG D1086 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 180 time to evaluate : 2.980 Fit side-chains REVERT: C 319 ILE cc_start: 0.6667 (OUTLIER) cc_final: 0.6007 (mp) REVERT: C 717 TRP cc_start: 0.8827 (OUTLIER) cc_final: 0.8370 (t60) REVERT: D 215 GLU cc_start: 0.5013 (OUTLIER) cc_final: 0.4065 (pt0) REVERT: D 356 ARG cc_start: 0.6198 (mmp-170) cc_final: 0.5946 (mmp80) REVERT: D 687 MET cc_start: 0.7913 (mmp) cc_final: 0.7486 (mmp) REVERT: H 11 GLN cc_start: 0.6819 (tm-30) cc_final: 0.6348 (tm-30) REVERT: H 481 MET cc_start: 0.4151 (mtt) cc_final: 0.3923 (mtt) outliers start: 36 outliers final: 29 residues processed: 208 average time/residue: 0.3829 time to fit residues: 125.1514 Evaluate side-chains 196 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1091 THR Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1249 LEU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 192 optimal weight: 0.8980 chunk 257 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 223 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 242 optimal weight: 0.2980 chunk 101 optimal weight: 0.3980 chunk 248 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** 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 = 0.3630 r_free = 0.3630 target = 0.085257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.067595 restraints weight = 71943.719| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.75 r_work: 0.3128 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24339 Z= 0.150 Angle : 0.537 12.297 32948 Z= 0.273 Chirality : 0.042 0.223 3745 Planarity : 0.004 0.068 4357 Dihedral : 4.039 50.480 3374 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.55 % Allowed : 17.62 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -0.49 (0.15), residues: 3053 helix: 1.30 (0.17), residues: 1026 sheet: -0.66 (0.28), residues: 355 loop : -1.34 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 58 HIS 0.002 0.000 HIS D 505 PHE 0.025 0.001 PHE D 131 TYR 0.028 0.001 TYR D 241 ARG 0.004 0.000 ARG D 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4704.54 seconds wall clock time: 85 minutes 9.35 seconds (5109.35 seconds total)