Starting phenix.real_space_refine (version: 1.21rc1) on Mon Aug 14 06:53:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6c_31742/08_2023/7v6c_31742.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6c_31742/08_2023/7v6c_31742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6c_31742/08_2023/7v6c_31742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6c_31742/08_2023/7v6c_31742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6c_31742/08_2023/7v6c_31742.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6c_31742/08_2023/7v6c_31742.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 52 5.49 5 S 84 5.16 5 C 9817 2.51 5 N 2651 2.21 5 O 3039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A GLU 732": "OE1" <-> "OE2" Residue "A ARG 759": "NH1" <-> "NH2" Residue "A GLU 878": "OE1" <-> "OE2" Residue "A TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1315": "OE1" <-> "OE2" Residue "A ASP 1401": "OD1" <-> "OD2" Residue "A GLU 1470": "OE1" <-> "OE2" Residue "A GLU 1489": "OE1" <-> "OE2" Residue "A GLU 1544": "OE1" <-> "OE2" Residue "A GLU 1644": "OE1" <-> "OE2" Residue "A GLU 1690": "OE1" <-> "OE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B ASP 297": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 15643 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 12487 Classifications: {'peptide': 1540} Link IDs: {'PTRANS': 65, 'TRANS': 1474} Chain breaks: 12 Chain: "B" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2057 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 111 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna3p_pyr': 7} Link IDs: {'rna3p': 6} Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 435 Classifications: {'DNA': 1, 'RNA': 20} Modifications used: {'5*END': 1, 'rna3p_pur': 13, 'rna3p_pyr': 7} Link IDs: {'rna3p': 20} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan2': 1, ' A%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 413 Classifications: {'DNA': 1, 'RNA': 20} Modifications used: {'5*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 14} Link IDs: {'rna3p': 20} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C%5*END:plan2': 1, ' C%5*END:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 8.05, per 1000 atoms: 0.51 Number of scatterers: 15643 At special positions: 0 Unit cell: (105.841, 156.764, 139.789, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 P 52 15.00 O 3039 8.00 N 2651 7.00 C 9817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.75 Conformation dependent library (CDL) restraints added in 2.0 seconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3450 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 13 sheets defined 52.8% alpha, 11.1% beta 22 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 4.94 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 33 through 45 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 89 through 97 removed outlier: 6.638A pdb=" N VAL A 94 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP A 95 " --> pdb=" O GLN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 141 through 145 removed outlier: 4.238A pdb=" N THR A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 232 through 252 removed outlier: 4.160A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 313 removed outlier: 7.100A pdb=" N ILE A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N TYR A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 345 removed outlier: 3.543A pdb=" N MET A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 364 through 378 Processing helix chain 'A' and resid 394 through 412 removed outlier: 3.760A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 452 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 510 through 534 removed outlier: 3.614A pdb=" N GLN A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 582A removed outlier: 3.550A pdb=" N ALA A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 606 removed outlier: 3.598A pdb=" N ASP A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 605 " --> pdb=" O GLU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 657 Processing helix chain 'A' and resid 667 through 680 removed outlier: 3.577A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.633A pdb=" N GLN A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 810 removed outlier: 4.093A pdb=" N LEU A 796 " --> pdb=" O ASN A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'A' and resid 916 through 925 removed outlier: 4.060A pdb=" N PHE A 920 " --> pdb=" O THR A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1016 removed outlier: 4.408A pdb=" N LEU A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) Proline residue: A 993C - end of helix removed outlier: 3.579A pdb=" N TYR A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1048 removed outlier: 4.122A pdb=" N ASN A1048 " --> pdb=" O PRO A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1084 removed outlier: 3.947A pdb=" N PHE A1082 " --> pdb=" O GLU A1078 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A1083 " --> pdb=" O ILE A1079 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN A1084 " --> pdb=" O THR A1080 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1078 through 1084' Processing helix chain 'A' and resid 1087 through 1091 Processing helix chain 'A' and resid 1103 through 1116 removed outlier: 3.536A pdb=" N LEU A1107 " --> pdb=" O TYR A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1182 Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1200 through 1204 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.792A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1249 Processing helix chain 'A' and resid 1249 through 1260 Processing helix chain 'A' and resid 1285 through 1295 Processing helix chain 'A' and resid 1295 through 1300 removed outlier: 3.624A pdb=" N ALA A1299 " --> pdb=" O ASN A1295 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1295 through 1300' Processing helix chain 'A' and resid 1303 through 1309 Processing helix chain 'A' and resid 1324 through 1339 removed outlier: 3.770A pdb=" N GLY A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1353 Processing helix chain 'A' and resid 1354 through 1356 No H-bonds generated for 'chain 'A' and resid 1354 through 1356' Processing helix chain 'A' and resid 1363 through 1382 removed outlier: 3.757A pdb=" N ALA A1367 " --> pdb=" O ASN A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1393 removed outlier: 3.658A pdb=" N LYS A1388 " --> pdb=" O GLN A1384 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A1389 " --> pdb=" O HIS A1385 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A1390 " --> pdb=" O ALA A1386 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A1391 " --> pdb=" O PHE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 4.420A pdb=" N LEU A1408 " --> pdb=" O THR A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 4.149A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 removed outlier: 3.651A pdb=" N LEU A1436 " --> pdb=" O ASN A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1455 Processing helix chain 'A' and resid 1467 through 1491 removed outlier: 4.302A pdb=" N LEU A1471 " --> pdb=" O SER A1467 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1508 Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1521 through 1525 Processing helix chain 'A' and resid 1529 through 1547 Processing helix chain 'A' and resid 1551 through 1557 Processing helix chain 'A' and resid 1610 through 1628 Processing helix chain 'A' and resid 1629 through 1651 Proline residue: A1643 - end of helix Processing helix chain 'A' and resid 1655 through 1663 Processing helix chain 'A' and resid 1701 through 1720 Processing helix chain 'B' and resid 6 through 18 Processing helix chain 'B' and resid 51 through 69 removed outlier: 3.732A pdb=" N SER B 61 " --> pdb=" O HIS B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 145 through 163 Processing helix chain 'B' and resid 189 through 198 Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.508A pdb=" N LEU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 removed outlier: 3.503A pdb=" N ARG B 223 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N HIS B 224 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B 225 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE B 227 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 244 Processing helix chain 'B' and resid 249 through 261 Processing helix chain 'B' and resid 295 through 311 removed outlier: 4.268A pdb=" N TYR B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 5.894A pdb=" N GLY A 86 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N THR A 115 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N TYR A 88 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA A 60 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N GLY A 114 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE A 62 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ARG A 59 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N ILE A 137 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A 61 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASP A 139 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N MET A 63 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER A 134 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL A 169 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 136 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU A 171 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 138 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY A 24 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR A 172 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 26 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 225 removed outlier: 6.540A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA5, first strand: chain 'A' and resid 702 through 706 Processing sheet with id=AA6, first strand: chain 'A' and resid 768A through 772 Processing sheet with id=AA7, first strand: chain 'A' and resid 768A through 772 removed outlier: 4.549A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 753 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AA9, first strand: chain 'A' and resid 939 through 944 removed outlier: 3.549A pdb=" N LYS A 897 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG A 943 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL A 895 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1070 through 1072 removed outlier: 4.010A pdb=" N LYS A1694 " --> pdb=" O ALA A1072 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 23 through 27 Processing sheet with id=AB3, first strand: chain 'B' and resid 113 through 120 removed outlier: 6.198A pdb=" N ILE B 114 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N SER B 133 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS B 131 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 266 through 270 removed outlier: 4.657A pdb=" N LEU B 278 " --> pdb=" O VAL B 270 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 2064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 7.75 Time building geometry restraints manager: 6.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2452 1.30 - 1.43: 4448 1.43 - 1.57: 8936 1.57 - 1.70: 102 1.70 - 1.84: 130 Bond restraints: 16068 Sorted by residual: bond pdb=" C PRO A1496 " pdb=" O PRO A1496 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.30e-02 5.92e+03 3.21e+01 bond pdb=" C TYR A 396 " pdb=" O TYR A 396 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.32e-02 5.74e+03 2.07e+01 bond pdb=" N THR A 903 " pdb=" CA THR A 903 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.61e+01 bond pdb=" C PRO A 413 " pdb=" O PRO A 413 " ideal model delta sigma weight residual 1.235 1.186 0.050 1.30e-02 5.92e+03 1.45e+01 bond pdb=" CA SER A1467 " pdb=" CB SER A1467 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.49e-02 4.50e+03 1.45e+01 ... (remaining 16063 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.92: 632 105.92 - 113.05: 8226 113.05 - 120.18: 7329 120.18 - 127.31: 5577 127.31 - 134.44: 202 Bond angle restraints: 21966 Sorted by residual: angle pdb=" N TYR A 11 " pdb=" CA TYR A 11 " pdb=" C TYR A 11 " ideal model delta sigma weight residual 111.82 103.42 8.40 1.16e+00 7.43e-01 5.24e+01 angle pdb=" C PRO A1188 " pdb=" CA PRO A1188 " pdb=" CB PRO A1188 " ideal model delta sigma weight residual 111.23 102.55 8.68 1.28e+00 6.10e-01 4.60e+01 angle pdb=" N ASP A1347 " pdb=" CA ASP A1347 " pdb=" C ASP A1347 " ideal model delta sigma weight residual 112.97 106.33 6.64 1.06e+00 8.90e-01 3.93e+01 angle pdb=" CA TYR B 204 " pdb=" C TYR B 204 " pdb=" O TYR B 204 " ideal model delta sigma weight residual 120.24 113.89 6.35 1.11e+00 8.12e-01 3.27e+01 angle pdb=" N TYR B 305 " pdb=" CA TYR B 305 " pdb=" C TYR B 305 " ideal model delta sigma weight residual 111.07 105.06 6.01 1.07e+00 8.73e-01 3.15e+01 ... (remaining 21961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8802 17.94 - 35.87: 625 35.87 - 53.81: 155 53.81 - 71.75: 27 71.75 - 89.69: 9 Dihedral angle restraints: 9618 sinusoidal: 4311 harmonic: 5307 Sorted by residual: dihedral pdb=" C PRO A1496 " pdb=" N PRO A1496 " pdb=" CA PRO A1496 " pdb=" CB PRO A1496 " ideal model delta harmonic sigma weight residual -120.70 -110.87 -9.83 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" C PHE B 306 " pdb=" N PHE B 306 " pdb=" CA PHE B 306 " pdb=" CB PHE B 306 " ideal model delta harmonic sigma weight residual -122.60 -132.03 9.43 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" C ILE A1431 " pdb=" N ILE A1431 " pdb=" CA ILE A1431 " pdb=" CB ILE A1431 " ideal model delta harmonic sigma weight residual -122.00 -131.02 9.02 0 2.50e+00 1.60e-01 1.30e+01 ... (remaining 9615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1264 0.063 - 0.126: 881 0.126 - 0.188: 312 0.188 - 0.251: 57 0.251 - 0.314: 7 Chirality restraints: 2521 Sorted by residual: chirality pdb=" P G C 2 " pdb=" OP1 G C 2 " pdb=" OP2 G C 2 " pdb=" O5' G C 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" P G E 4 " pdb=" OP1 G E 4 " pdb=" OP2 G E 4 " pdb=" O5' G E 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA PHE B 306 " pdb=" N PHE B 306 " pdb=" C PHE B 306 " pdb=" CB PHE B 306 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 2518 not shown) Planarity restraints: 2608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 412 " 0.025 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C THR A 412 " -0.080 2.00e-02 2.50e+03 pdb=" O THR A 412 " 0.029 2.00e-02 2.50e+03 pdb=" N PRO A 413 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1000 " -0.033 2.00e-02 2.50e+03 2.11e-02 8.92e+00 pdb=" CG TYR A1000 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A1000 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A1000 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A1000 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A1000 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A1000 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR A1000 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 204 " 0.014 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" C TYR B 204 " -0.051 2.00e-02 2.50e+03 pdb=" O TYR B 204 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP B 205 " 0.018 2.00e-02 2.50e+03 ... (remaining 2605 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1576 2.76 - 3.30: 15447 3.30 - 3.83: 24136 3.83 - 4.37: 33827 4.37 - 4.90: 51207 Nonbonded interactions: 126193 Sorted by model distance: nonbonded pdb=" O ASN A 253 " pdb=" OD1 ASN A 253 " model vdw 2.230 3.040 nonbonded pdb=" O SER B 124 " pdb=" O2' U C 9 " model vdw 2.306 2.440 nonbonded pdb=" NH1 ARG B 150 " pdb=" OP1 A D 2 " model vdw 2.312 2.520 nonbonded pdb=" O THR A 412 " pdb=" N GLU A 414 " model vdw 2.351 2.520 nonbonded pdb=" O PHE A1542 " pdb=" OG SER A1545 " model vdw 2.401 2.440 ... (remaining 126188 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 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: 0.400 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: 3.440 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 46.550 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.012 0.074 16068 Z= 0.768 Angle : 1.558 8.680 21966 Z= 1.181 Chirality : 0.088 0.314 2521 Planarity : 0.006 0.064 2608 Dihedral : 13.329 89.685 6168 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.18), residues: 1766 helix: 0.42 (0.17), residues: 826 sheet: -0.80 (0.36), residues: 162 loop : -1.21 (0.20), residues: 778 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 424 time to evaluate : 1.697 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 11 residues processed: 466 average time/residue: 0.3163 time to fit residues: 209.1269 Evaluate side-chains 236 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 225 time to evaluate : 1.669 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2034 time to fit residues: 5.8926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 10.0000 chunk 139 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 167 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 HIS A 339 GLN A 407 ASN A 448 GLN A 456 ASN A 520 GLN A 562 ASN A 619 ASN A 623 ASN A 734 GLN A 884 GLN A 888 ASN A 899 HIS A 913 GLN A1143 ASN A1286 HIS A1305 HIS A1329 ASN A1384 GLN A1543 GLN B 11 GLN B 91 ASN B 151 GLN B 229 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 16068 Z= 0.163 Angle : 0.527 8.975 21966 Z= 0.282 Chirality : 0.039 0.232 2521 Planarity : 0.004 0.037 2608 Dihedral : 5.427 53.074 2563 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 1766 helix: 1.82 (0.18), residues: 831 sheet: -0.36 (0.34), residues: 187 loop : -0.62 (0.21), residues: 748 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 252 time to evaluate : 1.722 Fit side-chains outliers start: 39 outliers final: 23 residues processed: 281 average time/residue: 0.2800 time to fit residues: 119.1229 Evaluate side-chains 222 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 199 time to evaluate : 1.976 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1597 time to fit residues: 9.1941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 149 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 HIS A 865 GLN A1076 ASN A1490 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 16068 Z= 0.289 Angle : 0.593 9.718 21966 Z= 0.309 Chirality : 0.042 0.326 2521 Planarity : 0.005 0.039 2608 Dihedral : 5.582 56.708 2563 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.19), residues: 1766 helix: 1.74 (0.18), residues: 817 sheet: -0.02 (0.33), residues: 195 loop : -0.68 (0.21), residues: 754 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 218 time to evaluate : 1.806 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 254 average time/residue: 0.2954 time to fit residues: 111.6166 Evaluate side-chains 211 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 189 time to evaluate : 1.573 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1591 time to fit residues: 9.1730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 210 ASN A 456 ASN A 865 GLN A1076 ASN A1490 ASN A1704 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 16068 Z= 0.241 Angle : 0.544 9.831 21966 Z= 0.282 Chirality : 0.040 0.325 2521 Planarity : 0.004 0.051 2608 Dihedral : 5.384 55.833 2563 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1766 helix: 1.71 (0.18), residues: 827 sheet: 0.12 (0.33), residues: 202 loop : -0.69 (0.21), residues: 737 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 200 time to evaluate : 1.658 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 217 average time/residue: 0.3038 time to fit residues: 97.4980 Evaluate side-chains 195 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 183 time to evaluate : 1.765 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1685 time to fit residues: 6.1537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 159 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN A1076 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16068 Z= 0.161 Angle : 0.496 10.248 21966 Z= 0.254 Chirality : 0.038 0.326 2521 Planarity : 0.004 0.054 2608 Dihedral : 5.005 54.461 2563 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 1.30 % 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: 1.07 (0.19), residues: 1766 helix: 1.95 (0.18), residues: 827 sheet: 0.21 (0.34), residues: 202 loop : -0.56 (0.21), residues: 737 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 1.903 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 209 average time/residue: 0.3032 time to fit residues: 94.1189 Evaluate side-chains 188 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 1.716 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1577 time to fit residues: 4.6184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.9990 chunk 160 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 147 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 456 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 16068 Z= 0.154 Angle : 0.488 10.108 21966 Z= 0.249 Chirality : 0.038 0.331 2521 Planarity : 0.004 0.053 2608 Dihedral : 4.834 54.130 2563 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.87 % 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: 1.21 (0.20), residues: 1766 helix: 2.04 (0.18), residues: 828 sheet: 0.33 (0.34), residues: 212 loop : -0.50 (0.22), residues: 726 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 1.900 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 204 average time/residue: 0.3101 time to fit residues: 93.8876 Evaluate side-chains 183 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 177 time to evaluate : 1.799 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1506 time to fit residues: 4.0620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 16068 Z= 0.260 Angle : 0.566 11.144 21966 Z= 0.289 Chirality : 0.040 0.339 2521 Planarity : 0.004 0.054 2608 Dihedral : 5.197 57.954 2563 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 1766 helix: 1.77 (0.18), residues: 824 sheet: 0.30 (0.35), residues: 202 loop : -0.57 (0.22), residues: 740 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 185 time to evaluate : 1.704 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 198 average time/residue: 0.2986 time to fit residues: 87.4649 Evaluate side-chains 193 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 180 time to evaluate : 1.695 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1459 time to fit residues: 5.8598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 16068 Z= 0.293 Angle : 0.593 11.634 21966 Z= 0.303 Chirality : 0.041 0.314 2521 Planarity : 0.004 0.056 2608 Dihedral : 5.411 61.092 2563 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 1766 helix: 1.41 (0.17), residues: 839 sheet: 0.14 (0.34), residues: 202 loop : -0.72 (0.22), residues: 725 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 180 time to evaluate : 1.737 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 188 average time/residue: 0.3136 time to fit residues: 86.2568 Evaluate side-chains 173 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1559 time to fit residues: 3.0579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 16068 Z= 0.244 Angle : 0.557 12.075 21966 Z= 0.284 Chirality : 0.040 0.288 2521 Planarity : 0.004 0.056 2608 Dihedral : 5.250 61.161 2563 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.19), residues: 1766 helix: 1.52 (0.18), residues: 834 sheet: 0.16 (0.34), residues: 204 loop : -0.71 (0.22), residues: 728 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 1.747 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 177 average time/residue: 0.2945 time to fit residues: 77.8739 Evaluate side-chains 174 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 169 time to evaluate : 1.627 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1469 time to fit residues: 3.5978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 16068 Z= 0.318 Angle : 0.615 12.912 21966 Z= 0.314 Chirality : 0.042 0.289 2521 Planarity : 0.005 0.056 2608 Dihedral : 5.480 63.057 2563 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1766 helix: 1.26 (0.17), residues: 839 sheet: 0.10 (0.34), residues: 204 loop : -0.81 (0.22), residues: 723 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.592 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3074 time to fit residues: 79.7021 Evaluate side-chains 170 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 128 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS A1462 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.158257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128310 restraints weight = 20648.964| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.54 r_work: 0.3333 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 16068 Z= 0.142 Angle : 0.508 12.548 21966 Z= 0.256 Chirality : 0.037 0.208 2521 Planarity : 0.004 0.056 2608 Dihedral : 4.846 60.174 2563 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1766 helix: 1.71 (0.18), residues: 846 sheet: 0.15 (0.34), residues: 208 loop : -0.59 (0.22), residues: 712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3209.59 seconds wall clock time: 59 minutes 21.99 seconds (3561.99 seconds total)