Starting phenix.real_space_refine on Tue Apr 9 06:48:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6c_31742/04_2024/7v6c_31742.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6c_31742/04_2024/7v6c_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_31742/04_2024/7v6c_31742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6c_31742/04_2024/7v6c_31742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6c_31742/04_2024/7v6c_31742.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6c_31742/04_2024/7v6c_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-dev-5288/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: 24 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: 8.91, per 1000 atoms: 0.57 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: 6.44 Conformation dependent library (CDL) restraints added in 2.6 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: 6.71 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: 7.90 Time building geometry restraints manager: 7.02 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: 8862 17.94 - 35.87: 637 35.87 - 53.81: 198 53.81 - 71.75: 82 71.75 - 89.69: 21 Dihedral angle restraints: 9800 sinusoidal: 4493 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 9797 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: 0.630 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: 0.040 Extract box with map and model: 3.360 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 51.430 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.200 ------------------------------------------------------------------------------- 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 : 15.168 89.685 6350 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 % Allowed : 7.37 % Favored : 88.73 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP A 885 HIS 0.014 0.003 HIS A1433 PHE 0.033 0.005 PHE A 502 TYR 0.041 0.005 TYR A1000 ARG 0.008 0.001 ARG A1097 *********************** 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 : 1.718 Fit side-chains revert: symmetry clash REVERT: A 9 ARG cc_start: 0.6835 (mtp180) cc_final: 0.6577 (ttt180) REVERT: A 75 MET cc_start: 0.7319 (mtt) cc_final: 0.7116 (mtm) REVERT: A 98 THR cc_start: 0.7148 (m) cc_final: 0.6743 (p) REVERT: A 105 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 126 THR cc_start: 0.7564 (OUTLIER) cc_final: 0.7154 (p) REVERT: A 222 MET cc_start: 0.7654 (tpt) cc_final: 0.7154 (tpp) REVERT: A 236 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.7400 (mmm-85) REVERT: A 237 LEU cc_start: 0.7769 (tp) cc_final: 0.7389 (mt) REVERT: A 241 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7087 (mm-30) REVERT: A 279 GLN cc_start: 0.6848 (tt0) cc_final: 0.6596 (tm-30) REVERT: A 290 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7338 (tp30) REVERT: A 310 LYS cc_start: 0.7745 (mmtm) cc_final: 0.7229 (mmmm) REVERT: A 315 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6983 (mp0) REVERT: A 339 GLN cc_start: 0.7593 (tt0) cc_final: 0.7351 (mt0) REVERT: A 344 MET cc_start: 0.6416 (ttp) cc_final: 0.5754 (ttt) REVERT: A 356 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7210 (tm-30) REVERT: A 360 MET cc_start: 0.7803 (mmm) cc_final: 0.7557 (mmm) REVERT: A 382 ASP cc_start: 0.7123 (m-30) cc_final: 0.6405 (t70) REVERT: A 393 GLU cc_start: 0.7828 (tt0) cc_final: 0.7267 (tt0) REVERT: A 410 GLN cc_start: 0.8007 (tt0) cc_final: 0.7785 (tt0) REVERT: A 412 THR cc_start: 0.7945 (p) cc_final: 0.7600 (p) REVERT: A 418 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8185 (t) REVERT: A 424 MET cc_start: 0.8223 (ptm) cc_final: 0.7994 (ptp) REVERT: A 439 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6674 (mp0) REVERT: A 444 LYS cc_start: 0.7398 (mttt) cc_final: 0.7154 (ttpp) REVERT: A 458 MET cc_start: 0.8383 (tpp) cc_final: 0.7658 (tpp) REVERT: A 469 ASP cc_start: 0.7459 (p0) cc_final: 0.7068 (p0) REVERT: A 487 MET cc_start: 0.7999 (tpt) cc_final: 0.7603 (tpt) REVERT: A 499 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6301 (mp0) REVERT: A 519 TYR cc_start: 0.7126 (m-80) cc_final: 0.6835 (t80) REVERT: A 633 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6942 (m-30) REVERT: A 664 VAL cc_start: 0.7807 (t) cc_final: 0.7492 (p) REVERT: A 675 ILE cc_start: 0.7446 (mm) cc_final: 0.7049 (pt) REVERT: A 708 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7448 (tt0) REVERT: A 711 LEU cc_start: 0.7722 (tt) cc_final: 0.7278 (mt) REVERT: A 728 GLU cc_start: 0.8594 (tt0) cc_final: 0.8355 (tt0) REVERT: A 744 MET cc_start: 0.8149 (tpp) cc_final: 0.7747 (mmt) REVERT: A 831 VAL cc_start: 0.8995 (t) cc_final: 0.8683 (m) REVERT: A 854 ARG cc_start: 0.8094 (ttm110) cc_final: 0.7795 (ttm170) REVERT: A 931 ASP cc_start: 0.6896 (m-30) cc_final: 0.6467 (p0) REVERT: A 939 MET cc_start: 0.6347 (mmp) cc_final: 0.5926 (mmm) REVERT: A 947 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7746 (pm20) REVERT: A 948 GLN cc_start: 0.6607 (tt0) cc_final: 0.6227 (tp-100) REVERT: A 1020 LEU cc_start: 0.8617 (mt) cc_final: 0.8234 (tp) REVERT: A 1087 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: A 1090 MET cc_start: 0.8128 (mtt) cc_final: 0.7752 (mtp) REVERT: A 1108 ASP cc_start: 0.7698 (m-30) cc_final: 0.7119 (t0) REVERT: A 1183 LYS cc_start: 0.6670 (mttt) cc_final: 0.5926 (tptm) REVERT: A 1251 ARG cc_start: 0.7375 (mtp85) cc_final: 0.7159 (ttt90) REVERT: A 1287 ASN cc_start: 0.7680 (m110) cc_final: 0.7339 (m110) REVERT: A 1389 MET cc_start: 0.8406 (mmm) cc_final: 0.8190 (mmp) REVERT: A 1411 GLU cc_start: 0.5413 (tt0) cc_final: 0.4740 (mp0) REVERT: A 1520 ARG cc_start: 0.7924 (mmt180) cc_final: 0.7716 (mmt180) REVERT: A 1555 ARG cc_start: 0.7309 (mtt180) cc_final: 0.6430 (mtp-110) REVERT: A 1559 GLU cc_start: 0.6289 (pt0) cc_final: 0.5870 (mt-10) REVERT: A 1607 ASP cc_start: 0.7440 (p0) cc_final: 0.6558 (m-30) REVERT: A 1651 LYS cc_start: 0.7989 (tptp) cc_final: 0.7361 (mptt) REVERT: A 1719 LYS cc_start: 0.6523 (ttpt) cc_final: 0.6261 (ttpp) REVERT: B 118 GLN cc_start: 0.7746 (mm110) cc_final: 0.7367 (mm110) REVERT: B 119 GLN cc_start: 0.6868 (mt0) cc_final: 0.6436 (mp10) REVERT: B 151 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7230 (mm110) REVERT: B 152 ARG cc_start: 0.7112 (mmm-85) cc_final: 0.6908 (mmt-90) REVERT: B 157 MET cc_start: 0.8267 (tpt) cc_final: 0.7786 (tpt) REVERT: B 190 MET cc_start: 0.5025 (mtp) cc_final: 0.4715 (tpt) REVERT: B 240 GLU cc_start: 0.6439 (pt0) cc_final: 0.6129 (pt0) outliers start: 63 outliers final: 11 residues processed: 466 average time/residue: 0.3261 time to fit residues: 213.9085 Evaluate side-chains 264 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 248 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 925 TYR Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 323 HIS 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 A1287 ASN A1305 HIS A1329 ASN A1384 GLN A1462 ASN A1543 GLN B 11 GLN B 91 ASN B 229 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16068 Z= 0.156 Angle : 0.516 9.011 21966 Z= 0.275 Chirality : 0.039 0.223 2521 Planarity : 0.004 0.037 2608 Dihedral : 12.555 73.330 2775 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.66 % Allowed : 12.88 % Favored : 84.46 % 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: 0.85 (0.19), residues: 1766 helix: 1.85 (0.18), residues: 828 sheet: -0.43 (0.34), residues: 192 loop : -0.61 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 885 HIS 0.005 0.001 HIS A1519 PHE 0.015 0.001 PHE A1481 TYR 0.018 0.001 TYR A1000 ARG 0.004 0.000 ARG A 853 *********************** 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 313 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 270 time to evaluate : 1.789 Fit side-chains REVERT: A 50 ASP cc_start: 0.7988 (t0) cc_final: 0.7414 (p0) REVERT: A 236 ARG cc_start: 0.7669 (mmm-85) cc_final: 0.7442 (mmm-85) REVERT: A 237 LEU cc_start: 0.7711 (tp) cc_final: 0.7442 (mt) REVERT: A 279 GLN cc_start: 0.7058 (tt0) cc_final: 0.6681 (tp40) REVERT: A 310 LYS cc_start: 0.7634 (mmtm) cc_final: 0.7267 (mmmm) REVERT: A 315 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6969 (mp0) REVERT: A 339 GLN cc_start: 0.7437 (tt0) cc_final: 0.7194 (tm-30) REVERT: A 356 GLU cc_start: 0.7427 (pt0) cc_final: 0.6938 (tm-30) REVERT: A 382 ASP cc_start: 0.7281 (m-30) cc_final: 0.6633 (t0) REVERT: A 393 GLU cc_start: 0.7720 (tt0) cc_final: 0.7327 (tt0) REVERT: A 412 THR cc_start: 0.7741 (p) cc_final: 0.7291 (p) REVERT: A 424 MET cc_start: 0.7890 (ptm) cc_final: 0.7615 (ptp) REVERT: A 469 ASP cc_start: 0.7812 (p0) cc_final: 0.7329 (p0) REVERT: A 499 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6370 (mp0) REVERT: A 519 TYR cc_start: 0.7288 (m-80) cc_final: 0.6889 (t80) REVERT: A 534 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7845 (t0) REVERT: A 577 ARG cc_start: 0.7062 (mtm-85) cc_final: 0.6170 (mmm160) REVERT: A 674 SER cc_start: 0.6718 (m) cc_final: 0.6494 (p) REVERT: A 675 ILE cc_start: 0.7217 (mm) cc_final: 0.6859 (pt) REVERT: A 706 LYS cc_start: 0.8023 (tttm) cc_final: 0.7765 (ttmt) REVERT: A 708 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7414 (tt0) REVERT: A 711 LEU cc_start: 0.7764 (tt) cc_final: 0.7391 (mt) REVERT: A 728 GLU cc_start: 0.8560 (tt0) cc_final: 0.8150 (tt0) REVERT: A 847 GLU cc_start: 0.6864 (tp30) cc_final: 0.6471 (mp0) REVERT: A 854 ARG cc_start: 0.7949 (ttm110) cc_final: 0.7666 (ttt90) REVERT: A 947 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7761 (pm20) REVERT: A 1020 LEU cc_start: 0.8684 (mt) cc_final: 0.8404 (tp) REVERT: A 1042 ASN cc_start: 0.5535 (m-40) cc_final: 0.4936 (p0) REVERT: A 1078 GLU cc_start: 0.5957 (mt-10) cc_final: 0.5467 (tt0) REVERT: A 1087 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7337 (mp10) REVERT: A 1143 ASN cc_start: 0.7317 (m-40) cc_final: 0.6660 (t0) REVERT: A 1213 GLU cc_start: 0.7944 (tt0) cc_final: 0.7711 (tm-30) REVERT: A 1411 GLU cc_start: 0.5370 (tt0) cc_final: 0.4869 (mt-10) REVERT: A 1491 ASN cc_start: 0.8323 (m-40) cc_final: 0.7963 (m110) REVERT: A 1507 VAL cc_start: 0.7958 (t) cc_final: 0.7652 (m) REVERT: A 1555 ARG cc_start: 0.7477 (mtt180) cc_final: 0.6591 (mtp-110) REVERT: A 1651 LYS cc_start: 0.7824 (tptp) cc_final: 0.7199 (mptt) REVERT: B 93 ASN cc_start: 0.6503 (m-40) cc_final: 0.6122 (m-40) REVERT: B 103 TYR cc_start: 0.7637 (t80) cc_final: 0.7364 (t80) REVERT: B 118 GLN cc_start: 0.7662 (mm110) cc_final: 0.7202 (mm110) REVERT: B 119 GLN cc_start: 0.6990 (mt0) cc_final: 0.6414 (mp10) REVERT: B 152 ARG cc_start: 0.7259 (mmm-85) cc_final: 0.6970 (mmt-90) REVERT: B 190 MET cc_start: 0.4964 (mtp) cc_final: 0.4611 (tpp) REVERT: B 240 GLU cc_start: 0.6380 (pt0) cc_final: 0.6093 (pt0) REVERT: B 305 TYR cc_start: 0.8043 (t80) cc_final: 0.7839 (t80) outliers start: 43 outliers final: 21 residues processed: 302 average time/residue: 0.3020 time to fit residues: 133.1360 Evaluate side-chains 240 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 217 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 287 PHE 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: 2.9990 chunk 139 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 149 optimal weight: 0.5980 chunk 165 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 865 GLN ** A1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1322 ASN A1462 ASN A1490 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16068 Z= 0.279 Angle : 0.595 9.957 21966 Z= 0.310 Chirality : 0.042 0.317 2521 Planarity : 0.005 0.039 2608 Dihedral : 12.384 73.752 2752 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.96 % Allowed : 13.44 % Favored : 82.60 % 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: 0.77 (0.19), residues: 1766 helix: 1.71 (0.17), residues: 818 sheet: 0.02 (0.34), residues: 202 loop : -0.67 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 885 HIS 0.006 0.001 HIS A 899 PHE 0.022 0.002 PHE A 423 TYR 0.026 0.002 TYR A1000 ARG 0.005 0.001 ARG A 703 *********************** 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 299 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 235 time to evaluate : 1.789 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7033 (tp30) cc_final: 0.6799 (tt0) REVERT: A 98 THR cc_start: 0.6783 (OUTLIER) cc_final: 0.6319 (p) REVERT: A 124 THR cc_start: 0.7817 (m) cc_final: 0.7529 (p) REVERT: A 125 GLN cc_start: 0.6843 (mp10) cc_final: 0.6628 (mp10) REVERT: A 126 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7456 (p) REVERT: A 209 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6571 (pt0) REVERT: A 279 GLN cc_start: 0.7232 (tt0) cc_final: 0.7009 (tm-30) REVERT: A 310 LYS cc_start: 0.7791 (mmtm) cc_final: 0.7398 (mmmm) REVERT: A 315 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6941 (mp0) REVERT: A 360 MET cc_start: 0.7418 (mmm) cc_final: 0.7164 (mmm) REVERT: A 364 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7902 (m) REVERT: A 374 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7440 (mp) REVERT: A 382 ASP cc_start: 0.7453 (m-30) cc_final: 0.6834 (t0) REVERT: A 393 GLU cc_start: 0.8059 (tt0) cc_final: 0.7710 (tt0) REVERT: A 412 THR cc_start: 0.8161 (p) cc_final: 0.7916 (p) REVERT: A 414 GLU cc_start: 0.7098 (mp0) cc_final: 0.6547 (mp0) REVERT: A 469 ASP cc_start: 0.7701 (p0) cc_final: 0.7155 (p0) REVERT: A 499 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6266 (tp30) REVERT: A 519 TYR cc_start: 0.7453 (m-80) cc_final: 0.6892 (t80) REVERT: A 534 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7495 (t0) REVERT: A 674 SER cc_start: 0.6542 (m) cc_final: 0.6285 (p) REVERT: A 675 ILE cc_start: 0.7096 (mm) cc_final: 0.6666 (pt) REVERT: A 706 LYS cc_start: 0.8140 (tttm) cc_final: 0.7836 (ttmt) REVERT: A 711 LEU cc_start: 0.7878 (tt) cc_final: 0.7435 (mt) REVERT: A 824 SER cc_start: 0.7492 (OUTLIER) cc_final: 0.7176 (p) REVERT: A 854 ARG cc_start: 0.7975 (ttm110) cc_final: 0.7646 (ttt90) REVERT: A 908 MET cc_start: 0.4160 (mtt) cc_final: 0.3732 (mmm) REVERT: A 918 TYR cc_start: 0.6878 (t80) cc_final: 0.6672 (t80) REVERT: A 947 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7434 (pm20) REVERT: A 952 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.5736 (p90) REVERT: A 1020 LEU cc_start: 0.8664 (mt) cc_final: 0.8246 (tp) REVERT: A 1042 ASN cc_start: 0.5773 (m-40) cc_final: 0.5001 (p0) REVERT: A 1065 MET cc_start: 0.5722 (OUTLIER) cc_final: 0.5139 (ptp) REVERT: A 1078 GLU cc_start: 0.5996 (mt-10) cc_final: 0.5451 (tt0) REVERT: A 1087 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: A 1112 HIS cc_start: 0.7188 (m-70) cc_final: 0.6951 (m-70) REVERT: A 1143 ASN cc_start: 0.7230 (m-40) cc_final: 0.6577 (t0) REVERT: A 1275 TYR cc_start: 0.8344 (m-80) cc_final: 0.8054 (m-80) REVERT: A 1348 PHE cc_start: 0.5135 (m-80) cc_final: 0.4675 (m-10) REVERT: A 1411 GLU cc_start: 0.5522 (tt0) cc_final: 0.5112 (mt-10) REVERT: A 1489 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7455 (tt0) REVERT: A 1491 ASN cc_start: 0.8310 (m-40) cc_final: 0.8087 (m110) REVERT: A 1549 ARG cc_start: 0.7123 (ptp-170) cc_final: 0.6662 (ptt90) REVERT: A 1555 ARG cc_start: 0.7646 (mtt180) cc_final: 0.6860 (mtp-110) REVERT: B 93 ASN cc_start: 0.6208 (m-40) cc_final: 0.5802 (m-40) REVERT: B 109 MET cc_start: 0.7430 (mtt) cc_final: 0.7073 (mtt) REVERT: B 118 GLN cc_start: 0.7798 (mm110) cc_final: 0.7478 (mm110) REVERT: B 119 GLN cc_start: 0.7259 (mt0) cc_final: 0.6463 (mp10) REVERT: B 163 SER cc_start: 0.5433 (t) cc_final: 0.4980 (p) REVERT: B 190 MET cc_start: 0.5265 (mtp) cc_final: 0.4899 (tpp) REVERT: B 240 GLU cc_start: 0.6312 (pt0) cc_final: 0.5999 (pt0) REVERT: B 252 ASP cc_start: 0.6977 (m-30) cc_final: 0.6736 (m-30) outliers start: 64 outliers final: 37 residues processed: 286 average time/residue: 0.2959 time to fit residues: 125.3700 Evaluate side-chains 255 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 209 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1065 MET Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1562 ASP Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 273 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 865 GLN ** A1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1490 ASN A1704 GLN B 151 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3676 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= 0.156 Angle : 0.494 9.625 21966 Z= 0.252 Chirality : 0.038 0.322 2521 Planarity : 0.004 0.041 2608 Dihedral : 12.131 73.535 2751 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.91 % Allowed : 14.98 % Favored : 82.11 % 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: 1.09 (0.19), residues: 1766 helix: 1.97 (0.18), residues: 827 sheet: 0.26 (0.35), residues: 202 loop : -0.57 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 885 HIS 0.004 0.001 HIS A1519 PHE 0.013 0.001 PHE B 306 TYR 0.021 0.001 TYR A1000 ARG 0.008 0.000 ARG A1397 *********************** 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 260 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 213 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: A 124 THR cc_start: 0.7831 (m) cc_final: 0.7525 (p) REVERT: A 126 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7276 (p) REVERT: A 209 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6728 (pt0) REVERT: A 279 GLN cc_start: 0.7172 (tt0) cc_final: 0.6966 (tm-30) REVERT: A 287 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7847 (mm-40) REVERT: A 315 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6999 (mp0) REVERT: A 382 ASP cc_start: 0.7359 (m-30) cc_final: 0.6750 (t0) REVERT: A 414 GLU cc_start: 0.7100 (mp0) cc_final: 0.6612 (mp0) REVERT: A 469 ASP cc_start: 0.7760 (p0) cc_final: 0.7283 (p0) REVERT: A 499 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6253 (mp0) REVERT: A 519 TYR cc_start: 0.7439 (m-80) cc_final: 0.6826 (t80) REVERT: A 534 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.6888 (p0) REVERT: A 675 ILE cc_start: 0.7073 (mm) cc_final: 0.6823 (pt) REVERT: A 706 LYS cc_start: 0.8173 (tttm) cc_final: 0.7863 (ttmt) REVERT: A 711 LEU cc_start: 0.7952 (tt) cc_final: 0.7514 (mt) REVERT: A 831 VAL cc_start: 0.8955 (t) cc_final: 0.8729 (m) REVERT: A 854 ARG cc_start: 0.7913 (ttm110) cc_final: 0.7623 (ttt90) REVERT: A 918 TYR cc_start: 0.6696 (t80) cc_final: 0.6484 (t80) REVERT: A 947 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7417 (pm20) REVERT: A 1020 LEU cc_start: 0.8671 (mt) cc_final: 0.8248 (tp) REVERT: A 1078 GLU cc_start: 0.6079 (mt-10) cc_final: 0.5495 (tt0) REVERT: A 1143 ASN cc_start: 0.7306 (m-40) cc_final: 0.6741 (t0) REVERT: A 1278 LEU cc_start: 0.8116 (pt) cc_final: 0.7908 (pp) REVERT: A 1348 PHE cc_start: 0.5060 (m-80) cc_final: 0.4436 (m-10) REVERT: A 1489 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7474 (tt0) REVERT: A 1507 VAL cc_start: 0.8127 (t) cc_final: 0.7927 (m) REVERT: A 1549 ARG cc_start: 0.6981 (ptp-170) cc_final: 0.6573 (ptt90) REVERT: B 93 ASN cc_start: 0.6112 (m-40) cc_final: 0.5843 (m110) REVERT: B 109 MET cc_start: 0.7404 (mtt) cc_final: 0.7065 (mtt) REVERT: B 118 GLN cc_start: 0.7757 (mm110) cc_final: 0.7439 (mm110) REVERT: B 119 GLN cc_start: 0.7298 (mt0) cc_final: 0.6323 (mp10) REVERT: B 190 MET cc_start: 0.4971 (mtp) cc_final: 0.4646 (tpp) REVERT: B 240 GLU cc_start: 0.6200 (pt0) cc_final: 0.5866 (pt0) REVERT: B 252 ASP cc_start: 0.7019 (m-30) cc_final: 0.6806 (m-30) outliers start: 47 outliers final: 28 residues processed: 249 average time/residue: 0.2814 time to fit residues: 105.5275 Evaluate side-chains 233 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 203 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 273 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.0980 chunk 100 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 456 ASN A 865 GLN ** A1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 HIS B 151 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16068 Z= 0.157 Angle : 0.488 9.630 21966 Z= 0.249 Chirality : 0.038 0.329 2521 Planarity : 0.004 0.042 2608 Dihedral : 11.996 73.576 2748 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.03 % Allowed : 15.42 % Favored : 81.55 % 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: 1.20 (0.19), residues: 1766 helix: 2.02 (0.18), residues: 827 sheet: 0.35 (0.35), residues: 202 loop : -0.48 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1634 HIS 0.004 0.001 HIS A1519 PHE 0.014 0.001 PHE A 977 TYR 0.022 0.001 TYR A1000 ARG 0.006 0.000 ARG A 853 *********************** 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 253 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 204 time to evaluate : 1.757 Fit side-chains REVERT: A 124 THR cc_start: 0.7635 (m) cc_final: 0.7323 (p) REVERT: A 126 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.7233 (p) REVERT: A 140 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7698 (mt-10) REVERT: A 209 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6622 (pt0) REVERT: A 382 ASP cc_start: 0.7331 (m-30) cc_final: 0.6709 (t0) REVERT: A 414 GLU cc_start: 0.6977 (mp0) cc_final: 0.6567 (mp0) REVERT: A 469 ASP cc_start: 0.7747 (p0) cc_final: 0.7310 (p0) REVERT: A 519 TYR cc_start: 0.7451 (m-80) cc_final: 0.6798 (t80) REVERT: A 534 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.6740 (p0) REVERT: A 706 LYS cc_start: 0.8163 (tttm) cc_final: 0.7870 (ttmt) REVERT: A 711 LEU cc_start: 0.7931 (tt) cc_final: 0.7488 (mt) REVERT: A 799 LEU cc_start: 0.8163 (mt) cc_final: 0.7848 (mm) REVERT: A 854 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7600 (ttt90) REVERT: A 873 ARG cc_start: 0.4898 (mmt180) cc_final: 0.4439 (mmm160) REVERT: A 947 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7392 (pm20) REVERT: A 952 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.6127 (p90) REVERT: A 1020 LEU cc_start: 0.8635 (mt) cc_final: 0.8212 (tp) REVERT: A 1078 GLU cc_start: 0.6104 (mt-10) cc_final: 0.5517 (tt0) REVERT: A 1143 ASN cc_start: 0.7316 (m-40) cc_final: 0.6843 (t0) REVERT: A 1489 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7501 (tt0) REVERT: A 1549 ARG cc_start: 0.7026 (ptp-170) cc_final: 0.6621 (ptt90) REVERT: A 1689 MET cc_start: 0.6631 (mmt) cc_final: 0.6417 (mmm) REVERT: B 93 ASN cc_start: 0.6101 (m-40) cc_final: 0.5854 (m110) REVERT: B 109 MET cc_start: 0.7392 (mtt) cc_final: 0.7039 (mtt) REVERT: B 190 MET cc_start: 0.4994 (mtp) cc_final: 0.4658 (tpp) REVERT: B 240 GLU cc_start: 0.6245 (pt0) cc_final: 0.5908 (pt0) REVERT: B 252 ASP cc_start: 0.7014 (m-30) cc_final: 0.6786 (m-30) outliers start: 49 outliers final: 30 residues processed: 243 average time/residue: 0.2900 time to fit residues: 105.7251 Evaluate side-chains 225 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 192 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1562 ASP Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 273 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 147 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 456 ASN A 679 HIS A 865 GLN ** A1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16068 Z= 0.209 Angle : 0.530 10.173 21966 Z= 0.270 Chirality : 0.039 0.342 2521 Planarity : 0.004 0.042 2608 Dihedral : 12.046 73.723 2748 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.41 % Allowed : 15.54 % Favored : 81.05 % 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: 1.11 (0.20), residues: 1766 helix: 1.91 (0.18), residues: 827 sheet: 0.32 (0.35), residues: 202 loop : -0.47 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1292 HIS 0.004 0.001 HIS B 215 PHE 0.018 0.002 PHE A 423 TYR 0.024 0.001 TYR A1000 ARG 0.007 0.000 ARG A1397 *********************** 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 248 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 193 time to evaluate : 1.638 Fit side-chains REVERT: A 75 MET cc_start: 0.7613 (mtm) cc_final: 0.7051 (tpp) REVERT: A 126 THR cc_start: 0.7656 (OUTLIER) cc_final: 0.7291 (p) REVERT: A 209 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6771 (pt0) REVERT: A 364 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7838 (m) REVERT: A 382 ASP cc_start: 0.7360 (m-30) cc_final: 0.6724 (t0) REVERT: A 414 GLU cc_start: 0.6926 (mp0) cc_final: 0.6576 (mp0) REVERT: A 469 ASP cc_start: 0.7727 (p0) cc_final: 0.7297 (p0) REVERT: A 534 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.6734 (p0) REVERT: A 706 LYS cc_start: 0.8168 (tttm) cc_final: 0.7863 (ttmt) REVERT: A 799 LEU cc_start: 0.8155 (mt) cc_final: 0.7840 (mm) REVERT: A 854 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7602 (ttt90) REVERT: A 873 ARG cc_start: 0.4827 (mmt180) cc_final: 0.4423 (mmm160) REVERT: A 908 MET cc_start: 0.4573 (mtt) cc_final: 0.4104 (mmm) REVERT: A 947 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7306 (pm20) REVERT: A 952 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.5911 (p90) REVERT: A 1020 LEU cc_start: 0.8615 (mt) cc_final: 0.8161 (tp) REVERT: A 1078 GLU cc_start: 0.6035 (mt-10) cc_final: 0.5521 (tt0) REVERT: A 1143 ASN cc_start: 0.7310 (m-40) cc_final: 0.6855 (t0) REVERT: A 1213 GLU cc_start: 0.8263 (tt0) cc_final: 0.7852 (tm-30) REVERT: A 1278 LEU cc_start: 0.8173 (pt) cc_final: 0.7944 (pp) REVERT: A 1348 PHE cc_start: 0.5071 (m-80) cc_final: 0.4366 (m-10) REVERT: A 1489 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7457 (tt0) REVERT: A 1549 ARG cc_start: 0.7169 (ptp-170) cc_final: 0.6699 (ptt90) REVERT: A 1689 MET cc_start: 0.6597 (mmt) cc_final: 0.6283 (mmm) REVERT: B 93 ASN cc_start: 0.6148 (m-40) cc_final: 0.5670 (m-40) REVERT: B 109 MET cc_start: 0.7370 (mtt) cc_final: 0.7045 (mtt) REVERT: B 118 GLN cc_start: 0.7904 (mm110) cc_final: 0.7681 (mm-40) REVERT: B 190 MET cc_start: 0.4985 (mtp) cc_final: 0.4641 (tpt) REVERT: B 252 ASP cc_start: 0.6961 (m-30) cc_final: 0.6739 (m-30) REVERT: B 255 MET cc_start: 0.8036 (mmt) cc_final: 0.7628 (mmt) outliers start: 55 outliers final: 37 residues processed: 234 average time/residue: 0.2813 time to fit residues: 99.7016 Evaluate side-chains 226 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 185 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1287 ASN Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1562 ASP Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 273 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 456 ASN ** A1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4197 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= 0.136 Angle : 0.479 11.910 21966 Z= 0.241 Chirality : 0.037 0.301 2521 Planarity : 0.004 0.056 2608 Dihedral : 11.912 73.511 2748 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.60 % Allowed : 16.47 % Favored : 80.93 % 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: 1.32 (0.20), residues: 1766 helix: 2.14 (0.18), residues: 828 sheet: 0.32 (0.35), residues: 212 loop : -0.41 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1634 HIS 0.003 0.000 HIS A1519 PHE 0.011 0.001 PHE A1481 TYR 0.022 0.001 TYR A1000 ARG 0.011 0.000 ARG A1397 *********************** 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 241 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 199 time to evaluate : 1.686 Fit side-chains REVERT: A 75 MET cc_start: 0.7535 (mtm) cc_final: 0.7030 (tpp) REVERT: A 126 THR cc_start: 0.7514 (OUTLIER) cc_final: 0.7109 (p) REVERT: A 140 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7611 (mt-10) REVERT: A 209 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6715 (pt0) REVERT: A 364 THR cc_start: 0.8087 (m) cc_final: 0.7806 (m) REVERT: A 382 ASP cc_start: 0.7235 (m-30) cc_final: 0.6611 (t0) REVERT: A 414 GLU cc_start: 0.6938 (mp0) cc_final: 0.6577 (mp0) REVERT: A 469 ASP cc_start: 0.7730 (p0) cc_final: 0.7335 (p0) REVERT: A 534 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.6750 (p0) REVERT: A 671 ARG cc_start: 0.6699 (mtt-85) cc_final: 0.6478 (mtt-85) REVERT: A 706 LYS cc_start: 0.8180 (tttm) cc_final: 0.7874 (ttmt) REVERT: A 799 LEU cc_start: 0.8163 (mt) cc_final: 0.7902 (mm) REVERT: A 854 ARG cc_start: 0.7821 (ttm110) cc_final: 0.7559 (ttt90) REVERT: A 873 ARG cc_start: 0.4762 (mmt180) cc_final: 0.4440 (tpt-90) REVERT: A 908 MET cc_start: 0.4506 (mtt) cc_final: 0.4142 (mmm) REVERT: A 947 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7235 (pm20) REVERT: A 952 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.6081 (p90) REVERT: A 1020 LEU cc_start: 0.8585 (mt) cc_final: 0.8134 (tp) REVERT: A 1078 GLU cc_start: 0.6119 (mt-10) cc_final: 0.5633 (tt0) REVERT: A 1143 ASN cc_start: 0.7323 (m-40) cc_final: 0.6912 (t0) REVERT: A 1489 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7455 (tt0) REVERT: A 1549 ARG cc_start: 0.6949 (ptp-170) cc_final: 0.6732 (mtm110) REVERT: B 93 ASN cc_start: 0.5972 (m-40) cc_final: 0.5541 (m-40) REVERT: B 103 TYR cc_start: 0.7599 (t80) cc_final: 0.7339 (t80) REVERT: B 190 MET cc_start: 0.4977 (mtp) cc_final: 0.4629 (tpt) REVERT: B 252 ASP cc_start: 0.7001 (m-30) cc_final: 0.6791 (m-30) outliers start: 42 outliers final: 27 residues processed: 235 average time/residue: 0.2877 time to fit residues: 101.0859 Evaluate side-chains 221 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 273 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 253 ASN A 456 ASN ** A1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4293 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= 0.261 Angle : 0.552 11.282 21966 Z= 0.282 Chirality : 0.040 0.306 2521 Planarity : 0.004 0.041 2608 Dihedral : 12.076 73.745 2748 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.22 % Allowed : 15.85 % Favored : 80.93 % 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: 1.01 (0.20), residues: 1766 helix: 1.84 (0.18), residues: 826 sheet: 0.13 (0.34), residues: 206 loop : -0.49 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 885 HIS 0.005 0.001 HIS B 215 PHE 0.021 0.002 PHE A 423 TYR 0.026 0.001 TYR A1000 ARG 0.004 0.001 ARG B 94 *********************** 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 245 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 193 time to evaluate : 1.796 Fit side-chains REVERT: A 364 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7866 (m) REVERT: A 382 ASP cc_start: 0.7336 (m-30) cc_final: 0.6691 (t0) REVERT: A 534 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.6792 (p0) REVERT: A 706 LYS cc_start: 0.8182 (tttm) cc_final: 0.7869 (ttmt) REVERT: A 854 ARG cc_start: 0.7835 (ttm110) cc_final: 0.7537 (ttt90) REVERT: A 873 ARG cc_start: 0.4921 (mmt180) cc_final: 0.4617 (tpt90) REVERT: A 908 MET cc_start: 0.4609 (mtt) cc_final: 0.4106 (mmm) REVERT: A 947 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7283 (pm20) REVERT: A 952 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.5736 (p90) REVERT: A 1078 GLU cc_start: 0.6543 (mt-10) cc_final: 0.5962 (pm20) REVERT: A 1143 ASN cc_start: 0.7374 (m-40) cc_final: 0.6948 (t0) REVERT: A 1278 LEU cc_start: 0.8132 (pt) cc_final: 0.7898 (pp) REVERT: A 1348 PHE cc_start: 0.5140 (m-80) cc_final: 0.4519 (m-10) REVERT: A 1489 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7503 (tt0) REVERT: B 93 ASN cc_start: 0.6069 (m-40) cc_final: 0.5616 (m-40) REVERT: B 190 MET cc_start: 0.5043 (mtp) cc_final: 0.4658 (tpt) REVERT: B 252 ASP cc_start: 0.6993 (m-30) cc_final: 0.6764 (m-30) REVERT: B 255 MET cc_start: 0.8108 (mmt) cc_final: 0.7821 (mmt) outliers start: 52 outliers final: 39 residues processed: 235 average time/residue: 0.2932 time to fit residues: 102.3357 Evaluate side-chains 228 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 186 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1562 ASP Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 273 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 99 optimal weight: 0.0050 chunk 71 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 156 optimal weight: 0.5980 chunk 164 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 overall best weight: 2.9200 ------------------------------------------------------------------------------- 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** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16068 Z= 0.306 Angle : 0.597 10.970 21966 Z= 0.305 Chirality : 0.042 0.304 2521 Planarity : 0.005 0.042 2608 Dihedral : 12.207 73.882 2748 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.97 % Allowed : 16.28 % Favored : 80.74 % 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: 0.60 (0.19), residues: 1766 helix: 1.43 (0.17), residues: 840 sheet: 0.05 (0.34), residues: 206 loop : -0.69 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 885 HIS 0.005 0.001 HIS A 899 PHE 0.025 0.002 PHE A 423 TYR 0.027 0.002 TYR A1000 ARG 0.008 0.001 ARG A 853 *********************** 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 230 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 182 time to evaluate : 1.780 Fit side-chains REVERT: A 75 MET cc_start: 0.7631 (mtm) cc_final: 0.7112 (tpp) REVERT: A 252 MET cc_start: 0.6705 (ttp) cc_final: 0.6492 (ttt) REVERT: A 382 ASP cc_start: 0.7366 (m-30) cc_final: 0.6770 (t0) REVERT: A 534 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.6800 (p0) REVERT: A 706 LYS cc_start: 0.8210 (tttm) cc_final: 0.7887 (ttmt) REVERT: A 854 ARG cc_start: 0.7772 (ttm110) cc_final: 0.7147 (ttp-110) REVERT: A 873 ARG cc_start: 0.5066 (mmt180) cc_final: 0.4755 (tpt90) REVERT: A 878 GLU cc_start: 0.7205 (tt0) cc_final: 0.6657 (tm-30) REVERT: A 908 MET cc_start: 0.4551 (mtt) cc_final: 0.4064 (mmm) REVERT: A 947 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7092 (pm20) REVERT: A 952 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.5579 (p90) REVERT: A 1078 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6132 (pm20) REVERT: A 1112 HIS cc_start: 0.7258 (m-70) cc_final: 0.7031 (m-70) REVERT: A 1143 ASN cc_start: 0.7448 (m-40) cc_final: 0.7246 (t0) REVERT: A 1348 PHE cc_start: 0.5220 (m-80) cc_final: 0.4573 (m-10) REVERT: A 1689 MET cc_start: 0.6572 (mmt) cc_final: 0.6308 (mmt) REVERT: A 1690 GLU cc_start: 0.6453 (mm-30) cc_final: 0.6008 (mt-10) REVERT: B 93 ASN cc_start: 0.6403 (m-40) cc_final: 0.5921 (m-40) REVERT: B 190 MET cc_start: 0.5088 (mtp) cc_final: 0.4687 (mmt) REVERT: B 252 ASP cc_start: 0.7041 (m-30) cc_final: 0.6815 (m-30) REVERT: B 255 MET cc_start: 0.8082 (mmt) cc_final: 0.7799 (mmt) outliers start: 48 outliers final: 38 residues processed: 222 average time/residue: 0.2850 time to fit residues: 95.6584 Evaluate side-chains 218 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 178 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1562 ASP Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 273 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16068 Z= 0.405 Angle : 0.671 12.098 21966 Z= 0.344 Chirality : 0.045 0.311 2521 Planarity : 0.005 0.056 2608 Dihedral : 12.359 74.009 2748 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.91 % Allowed : 16.59 % Favored : 80.50 % 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: 0.12 (0.19), residues: 1766 helix: 0.97 (0.17), residues: 847 sheet: -0.13 (0.34), residues: 211 loop : -0.89 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 885 HIS 0.007 0.002 HIS A 679 PHE 0.029 0.003 PHE A 423 TYR 0.028 0.002 TYR A1000 ARG 0.008 0.001 ARG A 853 ********************** 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 233 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 186 time to evaluate : 1.820 Fit side-chains REVERT: A 75 MET cc_start: 0.7576 (mtm) cc_final: 0.7045 (tpp) REVERT: A 252 MET cc_start: 0.6650 (ttp) cc_final: 0.6445 (ttt) REVERT: A 342 GLN cc_start: 0.7436 (tp40) cc_final: 0.6893 (mm-40) REVERT: A 382 ASP cc_start: 0.7424 (m-30) cc_final: 0.6830 (t0) REVERT: A 509 LYS cc_start: 0.5995 (mttt) cc_final: 0.5784 (pttm) REVERT: A 534 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7390 (t0) REVERT: A 706 LYS cc_start: 0.8210 (tttm) cc_final: 0.7883 (ttmt) REVERT: A 854 ARG cc_start: 0.7802 (ttm110) cc_final: 0.7159 (ttp-110) REVERT: A 873 ARG cc_start: 0.4979 (mmt180) cc_final: 0.4687 (tpt90) REVERT: A 878 GLU cc_start: 0.7193 (tt0) cc_final: 0.6646 (tm-30) REVERT: A 908 MET cc_start: 0.4568 (mtt) cc_final: 0.4252 (mmm) REVERT: A 947 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7028 (pm20) REVERT: A 952 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.5002 (p90) REVERT: A 1078 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6133 (pm20) REVERT: A 1112 HIS cc_start: 0.7324 (m-70) cc_final: 0.7094 (m-70) REVERT: A 1143 ASN cc_start: 0.7331 (m-40) cc_final: 0.7090 (t0) REVERT: B 93 ASN cc_start: 0.6517 (m-40) cc_final: 0.6024 (m-40) REVERT: B 190 MET cc_start: 0.5280 (mtp) cc_final: 0.4812 (mmm) REVERT: B 252 ASP cc_start: 0.7051 (m-30) cc_final: 0.6815 (m-30) REVERT: B 255 MET cc_start: 0.7942 (mmt) cc_final: 0.7738 (mmt) REVERT: B 265 PRO cc_start: 0.6487 (Cg_exo) cc_final: 0.6233 (Cg_endo) outliers start: 47 outliers final: 40 residues processed: 225 average time/residue: 0.2818 time to fit residues: 95.7496 Evaluate side-chains 220 residues out of total 1615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 178 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1562 ASP Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 273 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 128 optimal weight: 0.0170 overall best weight: 0.8018 ------------------------------------------------------------------------------- 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** ** A1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.157617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126567 restraints weight = 20672.597| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.67 r_work: 0.3286 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16068 Z= 0.147 Angle : 0.509 12.534 21966 Z= 0.258 Chirality : 0.038 0.226 2521 Planarity : 0.004 0.049 2608 Dihedral : 12.133 73.710 2748 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.23 % Allowed : 17.65 % Favored : 80.12 % 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 (0.20), residues: 1766 helix: 1.64 (0.18), residues: 841 sheet: -0.01 (0.34), residues: 203 loop : -0.62 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1634 HIS 0.008 0.001 HIS A1019 PHE 0.019 0.001 PHE A 977 TYR 0.026 0.001 TYR A1000 ARG 0.009 0.000 ARG A 853 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3358.12 seconds wall clock time: 62 minutes 32.23 seconds (3752.23 seconds total)