Starting phenix.real_space_refine (version: dev) on Sun Feb 19 10:20:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wts_21898/02_2023/6wts_21898.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wts_21898/02_2023/6wts_21898.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/6wts_21898/02_2023/6wts_21898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wts_21898/02_2023/6wts_21898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wts_21898/02_2023/6wts_21898.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wts_21898/02_2023/6wts_21898.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 145": "NH1" <-> "NH2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1455": "OE1" <-> "OE2" Residue "C PHE 1474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1534": "OD1" <-> "OD2" Residue "C PHE 1585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1608": "OD1" <-> "OD2" Residue "C PHE 1622": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9863 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4170 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 508} Chain breaks: 2 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "B" Number of atoms: 3964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3964 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 26, 'TRANS': 505} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 172 Chain: "C" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1589 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 9, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 130 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.01, per 1000 atoms: 0.61 Number of scatterers: 9863 At special positions: 0 Unit cell: (99.91, 108.15, 132.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1835 8.00 N 1645 7.00 C 6317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 117 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 144 " distance=2.03 Simple disulfide: pdb=" SG CYS A 258 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 605 " - " ASN A 33 " " NAG A 606 " - " ASN A 65 " " NAG B1303 " - " ASN B 434 " " NAG B1304 " - " ASN B 65 " " NAG D 1 " - " ASN A 434 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN B 282 " Time building additional restraints: 3.94 Conformation dependent library (CDL) restraints added in 1.7 seconds 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2426 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 27 sheets defined 13.9% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 100 through 109 removed outlier: 4.057A pdb=" N THR A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.664A pdb=" N PHE A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 385 through 395 Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.869A pdb=" N ARG A 408 " --> pdb=" O ILE A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 514 through 519 removed outlier: 4.234A pdb=" N TYR A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 519 " --> pdb=" O CYS A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 514 through 519' Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'B' and resid 100 through 111 removed outlier: 3.611A pdb=" N GLY B 111 " --> pdb=" O CYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 4.116A pdb=" N PHE B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.656A pdb=" N VAL B 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.912A pdb=" N ARG B 408 " --> pdb=" O ILE B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 514 through 519 removed outlier: 3.786A pdb=" N TYR B 518 " --> pdb=" O ARG B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 removed outlier: 3.704A pdb=" N ARG B 529 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 1434 through 1438 removed outlier: 3.657A pdb=" N GLU C1438 " --> pdb=" O LYS C1435 " (cutoff:3.500A) Processing helix chain 'C' and resid 1439 through 1450 Processing helix chain 'C' and resid 1499 through 1502 removed outlier: 3.598A pdb=" N SER C1502 " --> pdb=" O MET C1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1499 through 1502' Processing helix chain 'C' and resid 1560 through 1565 Processing helix chain 'C' and resid 1565 through 1570 Processing helix chain 'C' and resid 1583 through 1589 Processing helix chain 'C' and resid 1590 through 1594 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.514A pdb=" N GLU A 468 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A 422 " --> pdb=" O GLY A 441 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 64 removed outlier: 3.730A pdb=" N MET A 60 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 62 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 93 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 126 Processing sheet with id=AA4, first strand: chain 'A' and resid 174 through 178 removed outlier: 3.561A pdb=" N LEU A 207 " --> pdb=" O ARG A 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 228 removed outlier: 5.306A pdb=" N PHE A 222 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG A 237 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N VAL A 402 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG A 280 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.519A pdb=" N VAL A 285 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE A 291 " --> pdb=" O VAL A 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 295 through 299 removed outlier: 6.683A pdb=" N THR A 314 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL A 299 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 312 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 295 through 299 removed outlier: 6.683A pdb=" N THR A 314 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL A 299 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 312 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 344 through 345 Processing sheet with id=AB1, first strand: chain 'A' and resid 489 through 493 removed outlier: 3.601A pdb=" N GLY A 489 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.536A pdb=" N ALA A 541 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 536 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 29 through 30 removed outlier: 6.971A pdb=" N SER B 30 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N PHE B 465 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU B 451 " --> pdb=" O PHE B 465 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N HIS B 435 " --> pdb=" O ALA B 428 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA B 428 " --> pdb=" O HIS B 435 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS B 422 " --> pdb=" O GLY B 441 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.717A pdb=" N GLY B 489 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 60 through 64 Processing sheet with id=AB6, first strand: chain 'B' and resid 121 through 128 removed outlier: 3.777A pdb=" N LYS B 127 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 174 through 177 removed outlier: 3.784A pdb=" N LEU B 207 " --> pdb=" O ARG B 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 221 through 228 removed outlier: 5.235A pdb=" N PHE B 222 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG B 237 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 277 " --> pdb=" O GLN B 256 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N VAL B 402 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ARG B 280 " --> pdb=" O VAL B 402 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 284 through 285 removed outlier: 3.557A pdb=" N VAL B 285 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE B 291 " --> pdb=" O VAL B 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 295 through 299 removed outlier: 6.619A pdb=" N THR B 314 " --> pdb=" O GLN B 297 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL B 299 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 312 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 295 through 299 removed outlier: 6.619A pdb=" N THR B 314 " --> pdb=" O GLN B 297 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL B 299 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 312 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 344 through 346 Processing sheet with id=AC4, first strand: chain 'B' and resid 533 through 535 Processing sheet with id=AC5, first strand: chain 'C' and resid 1401 through 1402 removed outlier: 3.628A pdb=" N ILE C1402 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C1418 " --> pdb=" O ILE C1402 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C1406 " --> pdb=" O ILE C1414 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1401 through 1402 removed outlier: 3.628A pdb=" N ILE C1402 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C1418 " --> pdb=" O ILE C1402 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1459 through 1466 removed outlier: 3.983A pdb=" N ASP C1466 " --> pdb=" O THR C1469 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU C1487 " --> pdb=" O LYS C1470 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER C1492 " --> pdb=" O SER C1509 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER C1509 " --> pdb=" O SER C1492 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE C1494 " --> pdb=" O ILE C1507 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE C1507 " --> pdb=" O ILE C1494 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASN C1496 " --> pdb=" O LEU C1505 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C1505 " --> pdb=" O ASN C1496 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN C1503 " --> pdb=" O TYR C1498 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1514 through 1518 removed outlier: 5.845A pdb=" N ASP C1515 " --> pdb=" O ASN C1530 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN C1530 " --> pdb=" O ASP C1515 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C1527 " --> pdb=" O PHE C1542 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C1538 " --> pdb=" O TYR C1531 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR C1543 " --> pdb=" O LEU C1552 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU C1552 " --> pdb=" O THR C1543 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU C1545 " --> pdb=" O ILE C1550 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE C1550 " --> pdb=" O GLU C1545 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE C1550 " --> pdb=" O ILE C1606 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1613 through 1614 removed outlier: 6.807A pdb=" N GLU C1623 " --> pdb=" O TYR C1635 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN C1633 " --> pdb=" O ILE C1625 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1586 1.31 - 1.44: 2790 1.44 - 1.56: 5613 1.56 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 10084 Sorted by residual: bond pdb=" C LYS A 110 " pdb=" O LYS A 110 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" CA LYS A 110 " pdb=" CB LYS A 110 " ideal model delta sigma weight residual 1.529 1.494 0.035 1.63e-02 3.76e+03 4.62e+00 bond pdb=" CA LYS A 110 " pdb=" C LYS A 110 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.37e-02 5.33e+03 4.55e+00 bond pdb=" C LYS A 110 " pdb=" N GLY A 111 " ideal model delta sigma weight residual 1.331 1.300 0.030 1.46e-02 4.69e+03 4.32e+00 bond pdb=" C HIS A 212 " pdb=" O HIS A 212 " ideal model delta sigma weight residual 1.233 1.207 0.026 1.28e-02 6.10e+03 4.26e+00 ... (remaining 10079 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.11: 296 107.11 - 113.83: 5580 113.83 - 120.54: 3649 120.54 - 127.26: 4083 127.26 - 133.98: 87 Bond angle restraints: 13695 Sorted by residual: angle pdb=" C HIS A 212 " pdb=" CA HIS A 212 " pdb=" CB HIS A 212 " ideal model delta sigma weight residual 111.89 108.17 3.72 1.42e+00 4.96e-01 6.87e+00 angle pdb=" CA LEU C1540 " pdb=" CB LEU C1540 " pdb=" CG LEU C1540 " ideal model delta sigma weight residual 116.30 125.46 -9.16 3.50e+00 8.16e-02 6.85e+00 angle pdb=" C PRO A 362 " pdb=" N LYS A 363 " pdb=" CA LYS A 363 " ideal model delta sigma weight residual 121.80 115.59 6.21 2.44e+00 1.68e-01 6.49e+00 angle pdb=" C SER C1424 " pdb=" N TYR C1425 " pdb=" CA TYR C1425 " ideal model delta sigma weight residual 120.82 124.11 -3.29 1.47e+00 4.63e-01 5.01e+00 angle pdb=" C LYS C1511 " pdb=" CA LYS C1511 " pdb=" CB LYS C1511 " ideal model delta sigma weight residual 109.65 105.88 3.77 1.74e+00 3.30e-01 4.69e+00 ... (remaining 13690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 5550 16.30 - 32.61: 347 32.61 - 48.91: 79 48.91 - 65.21: 20 65.21 - 81.51: 3 Dihedral angle restraints: 5999 sinusoidal: 2236 harmonic: 3763 Sorted by residual: dihedral pdb=" CA LYS A 363 " pdb=" C LYS A 363 " pdb=" N PRO A 364 " pdb=" CA PRO A 364 " ideal model delta harmonic sigma weight residual 180.00 118.59 61.41 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA PHE B 293 " pdb=" C PHE B 293 " pdb=" N ASN B 294 " pdb=" CA ASN B 294 " ideal model delta harmonic sigma weight residual -180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.53e+00 dihedral pdb=" CA LYS A 248 " pdb=" CB LYS A 248 " pdb=" CG LYS A 248 " pdb=" CD LYS A 248 " ideal model delta sinusoidal sigma weight residual -180.00 -123.22 -56.78 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 5996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1408 0.074 - 0.148: 164 0.148 - 0.223: 2 0.223 - 0.297: 0 0.297 - 0.371: 1 Chirality restraints: 1575 Sorted by residual: chirality pdb=" CA LYS A 110 " pdb=" N LYS A 110 " pdb=" C LYS A 110 " pdb=" CB LYS A 110 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA HIS A 212 " pdb=" N HIS A 212 " pdb=" C HIS A 212 " pdb=" CB HIS A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" C1 NAG A 606 " pdb=" ND2 ASN A 65 " pdb=" C2 NAG A 606 " pdb=" O5 NAG A 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 1572 not shown) Planarity restraints: 1747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 363 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO A 364 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 110 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C LYS A 110 " -0.027 2.00e-02 2.50e+03 pdb=" O LYS A 110 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY A 111 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C1499 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO C1500 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C1500 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C1500 " -0.020 5.00e-02 4.00e+02 ... (remaining 1744 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2483 2.80 - 3.32: 8581 3.32 - 3.85: 15442 3.85 - 4.37: 17617 4.37 - 4.90: 31607 Nonbonded interactions: 75730 Sorted by model distance: nonbonded pdb=" OG1 THR C1547 " pdb=" OD1 ASN C1548 " model vdw 2.272 2.440 nonbonded pdb=" O GLY C1431 " pdb=" OH TYR C1462 " model vdw 2.307 2.440 nonbonded pdb=" O SER B 348 " pdb=" OG SER B 351 " model vdw 2.327 2.440 nonbonded pdb=" OH TYR C1508 " pdb=" O THR C1547 " model vdw 2.340 2.440 nonbonded pdb=" OD2 ASP A 426 " pdb=" OH TYR A 532 " model vdw 2.359 2.440 ... (remaining 75725 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 44 or resid 55 through 73 or (resid 74 and (nam \ e N or name CA or name C or name O or name CB )) or resid 75 through 81 or (resi \ d 82 through 88 and (name N or name CA or name C or name O or name CB )) or resi \ d 89 through 93 or (resid 94 and (name N or name CA or name C or name O or name \ CB )) or resid 95 through 102 or (resid 103 and (name N or name CA or name C or \ name O or name CB )) or resid 104 or (resid 105 and (name N or name CA or name C \ or name O or name CB )) or resid 106 through 107 or (resid 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 through 111 or (resid 112 \ through 114 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 5 or (resid 116 and (name N or name CA or name C or name O or name CB )) or resi \ d 117 through 129 or (resid 130 through 131 and (name N or name CA or name C or \ name O or name CB )) or resid 132 through 147 or (resid 148 and (name N or name \ CA or name C or name O or name CB )) or resid 149 through 150 or (resid 151 and \ (name N or name CA or name C or name O or name CB )) or resid 152 or (resid 153 \ and (name N or name CA or name C or name O or name CB )) or resid 154 through 16 \ 7 or (resid 168 through 169 and (name N or name CA or name C or name O or name C \ B )) or resid 170 through 190 or (resid 191 through 192 and (name N or name CA o \ r name C or name O or name CB )) or resid 193 through 200 or (resid 201 and (nam \ e N or name CA or name C or name O or name CB )) or resid 202 through 213 or (re \ sid 214 through 215 and (name N or name CA or name C or name O or name CB )) or \ resid 216 through 243 or (resid 244 through 245 and (name N or name CA or name C \ or name O or name CB )) or (resid 248 and (name N or name CA or name C or name \ O or name CB )) or resid 249 through 265 or (resid 266 through 267 and (name N o \ r name CA or name C or name O or name CB )) or resid 268 through 269 or (resid 2 \ 70 through 271 and (name N or name CA or name C or name O or name CB )) or resid \ 272 through 308 or (resid 309 and (name N or name CA or name C or name O or nam \ e CB )) or resid 310 through 349 or (resid 350 and (name N or name CA or name C \ or name O or name CB )) or resid 351 through 357 or (resid 358 through 359 and ( \ name N or name CA or name C or name O or name CB )) or resid 360 through 362 or \ (resid 363 and (name N or name CA or name C or name O or name CB )) or resid 364 \ through 375 or (resid 376 through 377 and (name N or name CA or name C or name \ O or name CB )) or resid 378 through 399 or (resid 400 through 401 and (name N o \ r name CA or name C or name O or name CB )) or resid 402 through 443 or (resid 4 \ 44 and (name N or name CA or name C or name O or name CB )) or resid 445 through \ 461 or (resid 462 and (name N or name CA or name C or name O or name CB )) or r \ esid 463 through 466 or (resid 467 and (name N or name CA or name C or name O or \ name CB )) or resid 468 through 479 or (resid 480 and (name N or name CA or nam \ e C or name O or name CB )) or resid 481 through 504 or (resid 505 and (name N o \ r name CA or name C or name O or name CB )) or resid 506 through 513 or (resid 5 \ 14 and (name N or name CA or name C or name O or name CB )) or resid 515 or (res \ id 516 and (name N or name CA or name C or name O or name CB )) or resid 517 thr \ ough 519 or (resid 520 and (name N or name CA or name C or name O or name CB )) \ or resid 521 through 536 or (resid 537 through 538 and (name N or name CA or nam \ e C or name O or name CB )) or resid 539 through 543 or (resid 544 through 551 a \ nd (name N or name CA or name C or name O or name CB )) or resid 552 through 553 \ or (resid 554 and (name N or name CA or name C or name O or name CB )) or resid \ 555 through 564 or (resid 565 and (name N or name CA or name C or name O or nam \ e CB )) or resid 566 or resid 605 through 606)) selection = (chain 'B' and (resid 19 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 319 or (resid 320 and (name N or n \ ame CA or name C or name O or name CB )) or resid 321 through 492 or (resid 493 \ and (name N or name CA or name C or name O or name CB )) or resid 494 through 54 \ 8 or (resid 549 through 551 and (name N or name CA or name C or name O or name C \ B )) or resid 552 through 566 or resid 1303 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6317 2.51 5 N 1645 2.21 5 O 1835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.440 Check model and map are aligned: 0.140 Process input model: 30.320 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.090 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 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 : 0.002 0.046 10084 Z= 0.138 Angle : 0.482 9.158 13695 Z= 0.268 Chirality : 0.044 0.371 1575 Planarity : 0.004 0.064 1740 Dihedral : 11.628 81.514 3531 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -1.65 (0.22), residues: 1265 helix: -1.47 (0.42), residues: 131 sheet: -0.60 (0.26), residues: 342 loop : -1.27 (0.20), residues: 792 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 403 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 405 average time/residue: 0.2348 time to fit residues: 132.2093 Evaluate side-chains 344 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 64 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 0.0270 chunk 60 optimal weight: 30.0000 chunk 74 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 overall best weight: 5.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 224 GLN A 435 HIS A 544 HIS B 224 GLN B 390 ASN B 435 HIS C1444 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.061 10084 Z= 0.437 Angle : 0.671 10.846 13695 Z= 0.355 Chirality : 0.049 0.195 1575 Planarity : 0.005 0.054 1740 Dihedral : 4.777 57.490 1448 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.32 % Favored : 96.60 % Rotamer Outliers : 4.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -1.26 (0.22), residues: 1265 helix: -0.67 (0.47), residues: 122 sheet: -0.56 (0.26), residues: 376 loop : -0.98 (0.21), residues: 767 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 334 time to evaluate : 1.138 Fit side-chains outliers start: 44 outliers final: 29 residues processed: 351 average time/residue: 0.2219 time to fit residues: 109.4539 Evaluate side-chains 351 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 322 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.0997 time to fit residues: 6.9732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 10084 Z= 0.271 Angle : 0.589 9.174 13695 Z= 0.308 Chirality : 0.048 0.503 1575 Planarity : 0.004 0.057 1740 Dihedral : 4.643 54.809 1448 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.44 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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 (0.23), residues: 1265 helix: -0.54 (0.47), residues: 127 sheet: -0.54 (0.26), residues: 371 loop : -0.81 (0.22), residues: 767 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 336 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 345 average time/residue: 0.2219 time to fit residues: 107.4573 Evaluate side-chains 329 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 319 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1033 time to fit residues: 3.5303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 60 optimal weight: 40.0000 chunk 109 optimal weight: 5.9990 chunk 33 optimal weight: 0.0870 overall best weight: 3.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 544 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 10084 Z= 0.334 Angle : 0.592 8.394 13695 Z= 0.310 Chirality : 0.047 0.194 1575 Planarity : 0.004 0.057 1740 Dihedral : 4.728 55.184 1448 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.79 % Favored : 96.13 % Rotamer Outliers : 4.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.95 (0.23), residues: 1265 helix: -0.14 (0.50), residues: 119 sheet: -0.45 (0.26), residues: 371 loop : -0.77 (0.21), residues: 775 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 325 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 25 residues processed: 339 average time/residue: 0.2189 time to fit residues: 104.5164 Evaluate side-chains 308 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 283 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0938 time to fit residues: 5.9518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 30.0000 chunk 69 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 104 optimal weight: 40.0000 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 224 GLN A 544 HIS C1496 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 10084 Z= 0.406 Angle : 0.625 8.524 13695 Z= 0.329 Chirality : 0.048 0.170 1575 Planarity : 0.004 0.060 1740 Dihedral : 4.874 56.090 1448 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.97 (0.23), residues: 1265 helix: -0.12 (0.50), residues: 119 sheet: -0.46 (0.26), residues: 370 loop : -0.79 (0.22), residues: 776 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 320 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 329 average time/residue: 0.2016 time to fit residues: 94.7068 Evaluate side-chains 312 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 292 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1138 time to fit residues: 5.6412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 224 GLN A 544 HIS B 59 GLN B 491 GLN C1444 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 10084 Z= 0.171 Angle : 0.580 12.418 13695 Z= 0.298 Chirality : 0.047 0.340 1575 Planarity : 0.004 0.059 1740 Dihedral : 4.709 52.945 1448 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1265 helix: -0.21 (0.48), residues: 126 sheet: -0.28 (0.27), residues: 371 loop : -0.66 (0.22), residues: 768 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 319 time to evaluate : 1.438 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 324 average time/residue: 0.2126 time to fit residues: 98.2154 Evaluate side-chains 316 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 304 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1259 time to fit residues: 4.1437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 103 optimal weight: 0.0470 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 0.2980 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 224 GLN A 544 HIS B 59 GLN B 212 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10084 Z= 0.187 Angle : 0.576 10.378 13695 Z= 0.295 Chirality : 0.046 0.242 1575 Planarity : 0.004 0.061 1740 Dihedral : 4.608 51.992 1448 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.24 % Favored : 96.68 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.72 (0.23), residues: 1265 helix: 0.08 (0.50), residues: 120 sheet: -0.14 (0.27), residues: 374 loop : -0.71 (0.22), residues: 771 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 305 time to evaluate : 1.190 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 311 average time/residue: 0.2103 time to fit residues: 93.6010 Evaluate side-chains 310 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 298 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1225 time to fit residues: 4.1873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 40.0000 chunk 11 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 224 GLN A 544 HIS B 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10084 Z= 0.175 Angle : 0.592 10.155 13695 Z= 0.301 Chirality : 0.046 0.321 1575 Planarity : 0.004 0.060 1740 Dihedral : 4.607 51.059 1448 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.71 (0.23), residues: 1265 helix: 0.03 (0.48), residues: 126 sheet: -0.14 (0.27), residues: 381 loop : -0.70 (0.22), residues: 758 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 305 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 308 average time/residue: 0.2222 time to fit residues: 99.9054 Evaluate side-chains 305 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 297 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0942 time to fit residues: 3.1094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 106 optimal weight: 0.0670 chunk 114 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 overall best weight: 2.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 544 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10084 Z= 0.233 Angle : 0.584 8.870 13695 Z= 0.300 Chirality : 0.046 0.221 1575 Planarity : 0.004 0.061 1740 Dihedral : 4.599 52.147 1448 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.52 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.68 (0.23), residues: 1265 helix: -0.02 (0.48), residues: 126 sheet: -0.08 (0.27), residues: 374 loop : -0.68 (0.22), residues: 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 301 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 304 average time/residue: 0.2200 time to fit residues: 94.6292 Evaluate side-chains 309 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 298 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1046 time to fit residues: 3.8489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 116 optimal weight: 0.3980 chunk 100 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 0.0570 overall best weight: 1.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 544 HIS B 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10084 Z= 0.177 Angle : 0.578 9.126 13695 Z= 0.296 Chirality : 0.046 0.218 1575 Planarity : 0.004 0.061 1740 Dihedral : 4.537 51.095 1448 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.77 % Favored : 97.15 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.66 (0.23), residues: 1265 helix: -0.04 (0.48), residues: 126 sheet: -0.04 (0.27), residues: 374 loop : -0.69 (0.22), residues: 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 311 time to evaluate : 1.141 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 311 average time/residue: 0.2222 time to fit residues: 97.7410 Evaluate side-chains 305 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1074 time to fit residues: 1.9691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 103 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.0570 overall best weight: 3.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 544 HIS B 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.161963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118546 restraints weight = 12626.296| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.21 r_work: 0.3100 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 10084 Z= 0.323 Angle : 0.614 9.442 13695 Z= 0.316 Chirality : 0.048 0.212 1575 Planarity : 0.004 0.060 1740 Dihedral : 4.714 53.510 1448 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.73 (0.23), residues: 1265 helix: 0.01 (0.49), residues: 126 sheet: -0.18 (0.28), residues: 364 loop : -0.69 (0.22), residues: 775 =============================================================================== Job complete usr+sys time: 2515.04 seconds wall clock time: 46 minutes 31.76 seconds (2791.76 seconds total)