Starting phenix.real_space_refine (version: dev) on Mon Feb 20 09:27:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roh_4972/02_2023/6roh_4972_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roh_4972/02_2023/6roh_4972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roh_4972/02_2023/6roh_4972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roh_4972/02_2023/6roh_4972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roh_4972/02_2023/6roh_4972_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roh_4972/02_2023/6roh_4972_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Process input model Symmetric amino acids flipped Residue "A ARG 183": "NH1" <-> "NH2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ASP 606": "OD1" <-> "OD2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 704": "NH1" <-> "NH2" Residue "A ASP 724": "OD1" <-> "OD2" Residue "A ARG 730": "NH1" <-> "NH2" Residue "A GLU 734": "OE1" <-> "OE2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 784": "OD1" <-> "OD2" Residue "A ARG 786": "NH1" <-> "NH2" Residue "A ASP 815": "OD1" <-> "OD2" Residue "A ARG 838": "NH1" <-> "NH2" Residue "A ARG 850": "NH1" <-> "NH2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "A ASP 889": "OD1" <-> "OD2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A PHE 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A TYR 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1228": "NH1" <-> "NH2" Residue "A ARG 1264": "NH1" <-> "NH2" Residue "A GLU 1282": "OE1" <-> "OE2" Residue "A GLU 1286": "OE1" <-> "OE2" Residue "A ASP 1293": "OD1" <-> "OD2" Residue "A ARG 1298": "NH1" <-> "NH2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11758 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8895 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 30, 'TRANS': 1081} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2738 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 20, 'TRANS': 316} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'PSF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 7.00, per 1000 atoms: 0.60 Number of scatterers: 11758 At special positions: 0 Unit cell: (74.313, 96.93, 173.397, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 48 16.00 P 1 15.00 Mg 1 11.99 F 3 9.00 O 2207 8.00 N 1917 7.00 C 7580 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA D 3 " - " BMA D 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG C 503 " - " ASN C 216 " " NAG D 1 " - " ASN C 199 " Time building additional restraints: 4.76 Conformation dependent library (CDL) restraints added in 1.8 seconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 9 sheets defined 34.5% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 211 through 222 removed outlier: 4.431A pdb=" N LEU A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 3.679A pdb=" N LEU A 218 " --> pdb=" O PRO A 215 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 219 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 222 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.658A pdb=" N LEU A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 269 removed outlier: 3.587A pdb=" N THR A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 274 No H-bonds generated for 'chain 'A' and resid 271 through 274' Processing helix chain 'A' and resid 277 through 280 No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 439 through 472 removed outlier: 3.758A pdb=" N ARG A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 501 removed outlier: 3.903A pdb=" N THR A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 511 through 525 removed outlier: 3.508A pdb=" N LEU A 516 " --> pdb=" O VAL A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 549 through 552 Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 618 through 630 Proline residue: A 621 - end of helix removed outlier: 4.149A pdb=" N ASP A 625 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 627 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR A 628 " --> pdb=" O ASP A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.510A pdb=" N VAL A 659 " --> pdb=" O GLU A 655 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 727 No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'A' and resid 739 through 752 removed outlier: 3.767A pdb=" N ARG A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 752 " --> pdb=" O ASP A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 780 removed outlier: 3.747A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 794 Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 839 through 848 removed outlier: 3.533A pdb=" N ASN A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 880 removed outlier: 3.759A pdb=" N GLU A 870 " --> pdb=" O ARG A 866 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 892 No H-bonds generated for 'chain 'A' and resid 890 through 892' Processing helix chain 'A' and resid 899 through 904 removed outlier: 3.546A pdb=" N PHE A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 918 removed outlier: 3.591A pdb=" N VAL A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.969A pdb=" N VAL A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 958 No H-bonds generated for 'chain 'A' and resid 956 through 958' Processing helix chain 'A' and resid 960 through 963 No H-bonds generated for 'chain 'A' and resid 960 through 963' Processing helix chain 'A' and resid 990 through 998 removed outlier: 3.533A pdb=" N LYS A 994 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 995 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 996 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 997 " --> pdb=" O LYS A 994 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A 998 " --> pdb=" O LYS A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1018 removed outlier: 3.667A pdb=" N ILE A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1023 No H-bonds generated for 'chain 'A' and resid 1020 through 1023' Processing helix chain 'A' and resid 1025 through 1031 removed outlier: 3.690A pdb=" N VAL A1030 " --> pdb=" O GLN A1026 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE A1031 " --> pdb=" O PHE A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1051 removed outlier: 3.969A pdb=" N SER A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN A1050 " --> pdb=" O MET A1046 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1064 removed outlier: 3.558A pdb=" N GLY A1062 " --> pdb=" O PRO A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1075 removed outlier: 3.640A pdb=" N GLU A1074 " --> pdb=" O SER A1070 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A1075 " --> pdb=" O ARG A1071 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1070 through 1075' Processing helix chain 'A' and resid 1077 through 1084 removed outlier: 3.596A pdb=" N LYS A1081 " --> pdb=" O GLN A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1114 removed outlier: 3.629A pdb=" N ASN A1100 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1153 removed outlier: 3.685A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A1146 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1152 " --> pdb=" O GLY A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1179 Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1195 through 1200 Processing helix chain 'A' and resid 1203 through 1208 Processing helix chain 'A' and resid 1212 through 1216 Processing helix chain 'A' and resid 1218 through 1229 Processing helix chain 'A' and resid 1254 through 1257 No H-bonds generated for 'chain 'A' and resid 1254 through 1257' Processing helix chain 'A' and resid 1260 through 1262 No H-bonds generated for 'chain 'A' and resid 1260 through 1262' Processing helix chain 'A' and resid 1281 through 1283 No H-bonds generated for 'chain 'A' and resid 1281 through 1283' Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 64 through 69 removed outlier: 3.821A pdb=" N LYS C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 192 through 195 No H-bonds generated for 'chain 'C' and resid 192 through 195' Processing helix chain 'C' and resid 227 through 230 No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 267 through 273 removed outlier: 3.749A pdb=" N VAL C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 345 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.814A pdb=" N LEU C 354 " --> pdb=" O PHE C 350 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 350 through 355' Processing sheet with id= A, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= B, first strand: chain 'A' and resid 283 through 288 removed outlier: 3.612A pdb=" N SER A 288 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP A 293 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.570A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1266 through 1268 removed outlier: 6.540A pdb=" N ALA A 923 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILE A 897 " --> pdb=" O ALA A 923 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A 925 " --> pdb=" O ILE A 897 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 924 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU A 948 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE A 557 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU A 950 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N SER A 559 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 952 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 967 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLY A 953 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 969 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A 985 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 580 through 583 removed outlier: 6.942A pdb=" N ALA A 808 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS A 575 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA A 806 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE A 577 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ILE A 804 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 694 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 671 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU A 680 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N PHE A 669 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 637 through 640 Processing sheet with id= G, first strand: chain 'A' and resid 319 through 321 removed outlier: 3.532A pdb=" N PHE A 419 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE A 321 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL A 417 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.013A pdb=" N LEU C 73 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 137 " --> pdb=" O ASN C 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE C 143 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR C 282 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 110 through 113 removed outlier: 3.638A pdb=" N GLY C 296 " --> pdb=" O ILE C 129 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 858 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: 3.82 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3276 1.33 - 1.46: 2850 1.46 - 1.58: 5813 1.58 - 1.71: 2 1.71 - 1.83: 77 Bond restraints: 12018 Sorted by residual: bond pdb=" OD1 BFD A 560 " pdb="BE BFD A 560 " ideal model delta sigma weight residual 1.737 1.527 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" O2 PSF A2101 " pdb=" P PSF A2101 " ideal model delta sigma weight residual 1.637 1.701 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " ideal model delta sigma weight residual 1.523 1.555 -0.032 1.35e-02 5.49e+03 5.59e+00 bond pdb=" CA BFD A 560 " pdb=" C BFD A 560 " ideal model delta sigma weight residual 1.525 1.570 -0.045 2.10e-02 2.27e+03 4.52e+00 bond pdb=" F1 BFD A 560 " pdb="BE BFD A 560 " ideal model delta sigma weight residual 1.542 1.504 0.038 2.00e-02 2.50e+03 3.54e+00 ... (remaining 12013 not shown) Histogram of bond angle deviations from ideal: 95.99 - 103.83: 138 103.83 - 111.68: 5293 111.68 - 119.52: 4887 119.52 - 127.37: 5848 127.37 - 135.21: 117 Bond angle restraints: 16283 Sorted by residual: angle pdb=" N ILE A1174 " pdb=" CA ILE A1174 " pdb=" C ILE A1174 " ideal model delta sigma weight residual 111.90 107.86 4.04 8.10e-01 1.52e+00 2.48e+01 angle pdb=" C ASP A 784 " pdb=" N ASN A 785 " pdb=" CA ASN A 785 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C CYS C 176 " pdb=" N SER C 177 " pdb=" CA SER C 177 " ideal model delta sigma weight residual 119.78 125.42 -5.64 1.24e+00 6.50e-01 2.07e+01 angle pdb=" CA CYS C 176 " pdb=" CB CYS C 176 " pdb=" SG CYS C 176 " ideal model delta sigma weight residual 114.40 123.44 -9.04 2.30e+00 1.89e-01 1.55e+01 angle pdb=" C PRO A 240 " pdb=" N HIS A 241 " pdb=" CA HIS A 241 " ideal model delta sigma weight residual 123.47 129.36 -5.89 1.53e+00 4.27e-01 1.48e+01 ... (remaining 16278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 6377 16.66 - 33.31: 643 33.31 - 49.97: 116 49.97 - 66.63: 18 66.63 - 83.28: 8 Dihedral angle restraints: 7162 sinusoidal: 2914 harmonic: 4248 Sorted by residual: dihedral pdb=" CA LEU A1114 " pdb=" C LEU A1114 " pdb=" N ILE A1115 " pdb=" CA ILE A1115 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA THR C 320 " pdb=" C THR C 320 " pdb=" N THR C 321 " pdb=" CA THR C 321 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA LEU A 490 " pdb=" C LEU A 490 " pdb=" N PHE A 491 " pdb=" CA PHE A 491 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 7159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1209 0.046 - 0.092: 473 0.092 - 0.137: 135 0.137 - 0.183: 29 0.183 - 0.229: 9 Chirality restraints: 1855 Sorted by residual: chirality pdb=" CG LEU A 480 " pdb=" CB LEU A 480 " pdb=" CD1 LEU A 480 " pdb=" CD2 LEU A 480 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN C 199 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE A 764 " pdb=" CA ILE A 764 " pdb=" CG1 ILE A 764 " pdb=" CG2 ILE A 764 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1852 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 111 " 0.026 2.00e-02 2.50e+03 2.60e-02 1.68e+01 pdb=" CG TRP C 111 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP C 111 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 111 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 111 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 111 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 111 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 111 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 111 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 111 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1057 " 0.049 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO A1058 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 977 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.37e+00 pdb=" C MET A 977 " -0.047 2.00e-02 2.50e+03 pdb=" O MET A 977 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN A 978 " 0.016 2.00e-02 2.50e+03 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 20 2.35 - 2.99: 5561 2.99 - 3.62: 16880 3.62 - 4.26: 28513 4.26 - 4.90: 46273 Nonbonded interactions: 97247 Sorted by model distance: nonbonded pdb=" F2 BFD A 560 " pdb="MG MG A2102 " model vdw 1.709 2.120 nonbonded pdb="MG MG A2102 " pdb=" O HOH A2201 " model vdw 1.742 2.170 nonbonded pdb="MG MG A2102 " pdb=" O HOH A2202 " model vdw 1.906 2.170 nonbonded pdb=" O THR A 562 " pdb=" O HOH A2201 " model vdw 1.909 2.440 nonbonded pdb=" O THR A 562 " pdb="MG MG A2102 " model vdw 2.042 2.170 ... (remaining 97242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 1 5.49 5 Mg 1 5.21 5 S 48 5.16 5 Be 1 3.05 5 C 7580 2.51 5 N 1917 2.21 5 O 2207 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.010 Extract box with map and model: 4.380 Check model and map are aligned: 0.180 Process input model: 32.120 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.110 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.006 0.210 12018 Z= 0.392 Angle : 0.878 10.208 16283 Z= 0.501 Chirality : 0.054 0.229 1855 Planarity : 0.006 0.073 2039 Dihedral : 13.665 83.283 4416 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.17), residues: 1440 helix: -4.68 (0.08), residues: 565 sheet: -1.21 (0.33), residues: 234 loop : -2.22 (0.20), residues: 641 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 223 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 225 average time/residue: 1.3333 time to fit residues: 325.2884 Evaluate side-chains 123 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 1.455 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1669 time to fit residues: 2.3341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 130 optimal weight: 0.0370 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 HIS A 422 HIS A 466 ASN A 580 HIS A 649 GLN A 694 ASN A 839 GLN A 862 ASN A 891 ASN A1019 ASN A1038 GLN A1050 ASN C 30 GLN C 37 GLN C 121 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 12018 Z= 0.208 Angle : 0.579 10.161 16283 Z= 0.306 Chirality : 0.044 0.181 1855 Planarity : 0.004 0.044 2039 Dihedral : 6.853 84.677 1628 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.19), residues: 1440 helix: -3.14 (0.16), residues: 562 sheet: -0.77 (0.34), residues: 232 loop : -1.71 (0.21), residues: 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 1.247 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 10 residues processed: 154 average time/residue: 1.1565 time to fit residues: 196.3268 Evaluate side-chains 130 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.364 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.1492 time to fit residues: 2.6280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 HIS A 374 GLN A1254 GLN A1258 ASN C 148 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 12018 Z= 0.399 Angle : 0.652 10.600 16283 Z= 0.341 Chirality : 0.048 0.237 1855 Planarity : 0.004 0.039 2039 Dihedral : 6.860 85.138 1628 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.20), residues: 1440 helix: -2.46 (0.18), residues: 587 sheet: -0.78 (0.32), residues: 254 loop : -1.28 (0.23), residues: 599 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 130 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 17 residues processed: 161 average time/residue: 1.2212 time to fit residues: 215.6628 Evaluate side-chains 135 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.422 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.5697 time to fit residues: 5.2154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 839 GLN A 862 ASN C 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12018 Z= 0.176 Angle : 0.526 8.779 16283 Z= 0.274 Chirality : 0.043 0.161 1855 Planarity : 0.003 0.038 2039 Dihedral : 6.471 87.570 1628 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.21), residues: 1440 helix: -1.88 (0.20), residues: 586 sheet: -0.57 (0.33), residues: 239 loop : -1.05 (0.24), residues: 615 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 19 residues processed: 161 average time/residue: 1.2038 time to fit residues: 212.9038 Evaluate side-chains 141 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 3 average time/residue: 0.2099 time to fit residues: 2.9171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.0170 chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 839 GLN A 862 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 12018 Z= 0.263 Angle : 0.567 10.846 16283 Z= 0.292 Chirality : 0.045 0.177 1855 Planarity : 0.003 0.035 2039 Dihedral : 6.425 87.333 1628 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.21), residues: 1440 helix: -1.66 (0.20), residues: 583 sheet: -0.49 (0.33), residues: 239 loop : -0.94 (0.24), residues: 618 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 122 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 21 residues processed: 155 average time/residue: 1.1320 time to fit residues: 192.6400 Evaluate side-chains 140 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.1618 time to fit residues: 2.1104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: