Starting phenix.real_space_refine (version: dev) on Tue Feb 21 16:47:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gu6_34270/02_2023/8gu6_34270.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gu6_34270/02_2023/8gu6_34270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gu6_34270/02_2023/8gu6_34270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gu6_34270/02_2023/8gu6_34270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gu6_34270/02_2023/8gu6_34270.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gu6_34270/02_2023/8gu6_34270.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.036 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 "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 195": "OD1" <-> "OD2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 475": "OD1" <-> "OD2" Residue "D PHE 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ASP 520": "OD1" <-> "OD2" Residue "A ASP 542": "OD1" <-> "OD2" Residue "A ASP 771": "OD1" <-> "OD2" Residue "A ASP 806": "OD1" <-> "OD2" Residue "A PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1557": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15261 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 4880 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 19, 'TRANS': 639} Chain breaks: 4 Unresolved non-hydrogen bonds: 479 Unresolved non-hydrogen angles: 598 Unresolved non-hydrogen dihedrals: 391 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 15, 'TRP:plan': 1, 'ASP:plan': 22, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 316 Chain: "A" Number of atoms: 9314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1211, 9314 Classifications: {'peptide': 1211} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 59, 'TRANS': 1151} Chain breaks: 13 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 485 Unresolved non-hydrogen angles: 598 Unresolved non-hydrogen dihedrals: 385 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 26, 'TYR:plan': 2, 'ASN:plan1': 14, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 34, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 337 Chain: "C" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 689 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 2, 'rna3p_pyr': 12} Link IDs: {'rna2p': 18, 'rna3p': 14} Chain: "J" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 374 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 15} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8188 SG CYS A 491 42.410 50.382 109.592 1.00 56.88 S ATOM 8256 SG CYS A 501 42.340 50.002 113.239 1.00 43.26 S ATOM 8270 SG CYS A 503 39.054 50.135 111.347 1.00 51.40 S ATOM 8292 SG CYS A 506 41.174 47.041 110.957 1.00 42.41 S ATOM 5526 SG CYS A 88 41.869 29.986 135.607 1.00 52.94 S ATOM 5769 SG CYS A 121 42.592 27.562 138.440 1.00 80.14 S ATOM 5800 SG CYS A 127 41.344 26.344 135.032 1.00 50.36 S ATOM 5824 SG CYS A 130 44.895 27.615 135.412 1.00 49.35 S ATOM 10157 SG CYS A 750 48.196 66.675 85.818 1.00 94.35 S ATOM 10170 SG CYS A 752 45.399 65.843 83.413 1.00 72.34 S ATOM 10192 SG CYS A 755 47.298 62.993 84.983 1.00 66.08 S ATOM 12065 SG CYS A1018 57.375 61.363 49.287 1.00 82.93 S ATOM 12218 SG CYS A1406 57.984 62.296 52.978 1.00 87.64 S ATOM 12269 SG CYS A1414 57.266 64.947 50.377 1.00 79.23 S ATOM 12286 SG CYS A1417 54.544 62.425 51.493 1.00 64.66 S Time building chain proxies: 9.45, per 1000 atoms: 0.62 Number of scatterers: 15261 At special positions: 0 Unit cell: (101.65, 95, 158.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 51 16.00 P 50 15.00 O 2896 8.00 N 2670 7.00 C 9590 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: 6.20 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 506 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 121 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 130 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " Number of angles added : 21 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3464 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 22 sheets defined 41.7% alpha, 11.9% beta 11 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'D' and resid 15 through 33 Processing helix chain 'D' and resid 37 through 59 removed outlier: 3.938A pdb=" N LYS D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU D 58 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 82 removed outlier: 3.643A pdb=" N ILE D 82 " --> pdb=" O VAL D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 110 removed outlier: 3.550A pdb=" N LYS D 94 " --> pdb=" O PRO D 90 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA D 107 " --> pdb=" O PHE D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 136 Processing helix chain 'D' and resid 141 through 156 Processing helix chain 'D' and resid 163 through 176 removed outlier: 3.611A pdb=" N ILE D 167 " --> pdb=" O TYR D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 183 through 190 removed outlier: 3.942A pdb=" N LYS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.703A pdb=" N LYS D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 246 removed outlier: 4.095A pdb=" N ASP D 234 " --> pdb=" O HIS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 269 removed outlier: 3.602A pdb=" N PHE D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR D 269 " --> pdb=" O GLN D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 297 Processing helix chain 'D' and resid 302 through 322 removed outlier: 3.559A pdb=" N LYS D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 339 through 359 removed outlier: 3.601A pdb=" N GLU D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN D 357 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 448 Processing helix chain 'D' and resid 451 through 453 No H-bonds generated for 'chain 'D' and resid 451 through 453' Processing helix chain 'D' and resid 454 through 469 Processing helix chain 'D' and resid 470 through 473 removed outlier: 3.501A pdb=" N PHE D 473 " --> pdb=" O PRO D 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 470 through 473' Processing helix chain 'D' and resid 496 through 500 Processing helix chain 'D' and resid 509 through 514 removed outlier: 4.261A pdb=" N ASN D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS D 514 " --> pdb=" O PHE D 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 509 through 514' Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 566 through 572 Processing helix chain 'D' and resid 592 through 595 Processing helix chain 'D' and resid 607 through 613 Processing helix chain 'D' and resid 628 through 632 removed outlier: 3.550A pdb=" N VAL D 632 " --> pdb=" O THR D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 653 removed outlier: 3.684A pdb=" N ALA D 648 " --> pdb=" O SER D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 removed outlier: 3.851A pdb=" N THR D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 691 removed outlier: 4.165A pdb=" N LYS D 689 " --> pdb=" O ASN D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 708 removed outlier: 3.999A pdb=" N ALA D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.404A pdb=" N LYS A 30 " --> pdb=" O TRP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 59 through 78 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.563A pdb=" N ILE A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.548A pdb=" N LEU A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 Processing helix chain 'A' and resid 292 through 303 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 350 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.582A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 617 through 624 removed outlier: 3.631A pdb=" N TYR A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.579A pdb=" N LEU A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 657 Processing helix chain 'A' and resid 658 through 665 Processing helix chain 'A' and resid 687 through 693 removed outlier: 3.546A pdb=" N LEU A 691 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 873 through 881 removed outlier: 3.670A pdb=" N MET A 879 " --> pdb=" O ASP A 875 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.889A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 removed outlier: 3.745A pdb=" N LEU A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1399 removed outlier: 3.574A pdb=" N LYS A1398 " --> pdb=" O LEU A1395 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A1399 " --> pdb=" O GLY A1396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1395 through 1399' Processing helix chain 'A' and resid 1408 through 1412 removed outlier: 3.625A pdb=" N ASP A1411 " --> pdb=" O GLY A1408 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 4.064A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.791A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1499 Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.779A pdb=" N GLY A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1583 through 1588 Processing helix chain 'A' and resid 1590 through 1601 removed outlier: 3.541A pdb=" N GLU A1600 " --> pdb=" O GLN A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1618 Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1675 through 1681 Processing sheet with id=AA1, first strand: chain 'D' and resid 425 through 431 removed outlier: 3.765A pdb=" N ASP D 420 " --> pdb=" O SER D 425 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N CYS D 516 " --> pdb=" O PHE D 709 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER D 711 " --> pdb=" O CYS D 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 562 through 563 removed outlier: 6.583A pdb=" N VAL D 537 " --> pdb=" O THR D 581 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU D 583 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU D 539 " --> pdb=" O LEU D 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 597 through 598 Processing sheet with id=AA4, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.507A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.507A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.008A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 176 through 181 removed outlier: 3.701A pdb=" N PHE A 192 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AB1, first strand: chain 'A' and resid 512 through 514 removed outlier: 3.515A pdb=" N PHE A 557 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.258A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.587A pdb=" N SER A 517 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 526 through 530 Processing sheet with id=AB5, first strand: chain 'A' and resid 721 through 722 removed outlier: 3.872A pdb=" N GLU A 773 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 721 through 722 removed outlier: 3.872A pdb=" N GLU A 773 " --> pdb=" O LYS A 821 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.161A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 920 through 921 removed outlier: 3.672A pdb=" N TYR A 921 " --> pdb=" O ASP A1642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AC1, first strand: chain 'A' and resid 1519 through 1522 removed outlier: 6.819A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 985 through 987 removed outlier: 3.917A pdb=" N GLU A1510 " --> pdb=" O TYR A 987 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR A1509 " --> pdb=" O LEU A1454 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 991 through 992 Processing sheet with id=AC4, first strand: chain 'A' and resid 1647 through 1648 removed outlier: 6.753A pdb=" N VAL A1647 " --> pdb=" O TYR A1663 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 589 hydrogen bonds defined for protein. 1647 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 6.34 Time building geometry restraints manager: 6.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4328 1.33 - 1.45: 2854 1.45 - 1.57: 8353 1.57 - 1.69: 98 1.69 - 1.81: 69 Bond restraints: 15702 Sorted by residual: bond pdb=" C SER A 910 " pdb=" N PRO A 911 " ideal model delta sigma weight residual 1.336 1.350 -0.014 9.80e-03 1.04e+04 1.96e+00 bond pdb=" CB GLU D 398 " pdb=" CG GLU D 398 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.16e-01 bond pdb=" C PRO D 700 " pdb=" N PRO D 701 " ideal model delta sigma weight residual 1.336 1.345 -0.010 1.23e-02 6.61e+03 6.44e-01 bond pdb=" CG1 ILE D 45 " pdb=" CD1 ILE D 45 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 5.92e-01 bond pdb=" CB GLU D 23 " pdb=" CG GLU D 23 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.85e-01 ... (remaining 15697 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.48: 672 106.48 - 113.44: 8573 113.44 - 120.41: 5791 120.41 - 127.38: 6202 127.38 - 134.34: 268 Bond angle restraints: 21506 Sorted by residual: angle pdb=" O4' G C 11 " pdb=" C1' G C 11 " pdb=" N9 G C 11 " ideal model delta sigma weight residual 108.20 115.61 -7.41 1.50e+00 4.44e-01 2.44e+01 angle pdb=" CA LEU A 366 " pdb=" CB LEU A 366 " pdb=" CG LEU A 366 " ideal model delta sigma weight residual 116.30 131.40 -15.10 3.50e+00 8.16e-02 1.86e+01 angle pdb=" O4' A C -2 " pdb=" C1' A C -2 " pdb=" N9 A C -2 " ideal model delta sigma weight residual 108.20 112.52 -4.32 1.50e+00 4.44e-01 8.29e+00 angle pdb=" N GLU A1441 " pdb=" CA GLU A1441 " pdb=" C GLU A1441 " ideal model delta sigma weight residual 110.97 114.10 -3.13 1.09e+00 8.42e-01 8.23e+00 angle pdb=" N LEU A 366 " pdb=" CA LEU A 366 " pdb=" CB LEU A 366 " ideal model delta sigma weight residual 110.28 114.68 -4.40 1.55e+00 4.16e-01 8.07e+00 ... (remaining 21501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 8837 35.68 - 71.36: 339 71.36 - 107.04: 9 107.04 - 142.72: 2 142.72 - 178.40: 2 Dihedral angle restraints: 9189 sinusoidal: 3813 harmonic: 5376 Sorted by residual: dihedral pdb=" O4' U C -9 " pdb=" C1' U C -9 " pdb=" N1 U C -9 " pdb=" C2 U C -9 " ideal model delta sinusoidal sigma weight residual 232.00 53.60 178.40 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U C 10 " pdb=" C1' U C 10 " pdb=" N1 U C 10 " pdb=" C2 U C 10 " ideal model delta sinusoidal sigma weight residual -128.00 44.11 -172.11 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' U C -15 " pdb=" C1' U C -15 " pdb=" N1 U C -15 " pdb=" C2 U C -15 " ideal model delta sinusoidal sigma weight residual -160.00 -91.17 -68.83 1 1.50e+01 4.44e-03 2.73e+01 ... (remaining 9186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2239 0.073 - 0.146: 186 0.146 - 0.218: 6 0.218 - 0.291: 0 0.291 - 0.364: 1 Chirality restraints: 2432 Sorted by residual: chirality pdb=" C1' G C 11 " pdb=" O4' G C 11 " pdb=" C2' G C 11 " pdb=" N9 G C 11 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C1' A C -2 " pdb=" O4' A C -2 " pdb=" C2' A C -2 " pdb=" N9 A C -2 " both_signs ideal model delta sigma weight residual False 2.44 2.25 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CB ILE D 80 " pdb=" CA ILE D 80 " pdb=" CG1 ILE D 80 " pdb=" CG2 ILE D 80 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 2429 not shown) Planarity restraints: 2558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 11 " -0.047 2.00e-02 2.50e+03 2.16e-02 1.40e+01 pdb=" N9 G C 11 " 0.056 2.00e-02 2.50e+03 pdb=" C8 G C 11 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G C 11 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C 11 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G C 11 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G C 11 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G C 11 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G C 11 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G C 11 " 0.008 2.00e-02 2.50e+03 pdb=" N3 G C 11 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G C 11 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1475 " -0.051 5.00e-02 4.00e+02 7.76e-02 9.63e+00 pdb=" N PRO A1476 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A1476 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1476 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A C 3 " -0.031 2.00e-02 2.50e+03 1.45e-02 5.78e+00 pdb=" N9 A C 3 " 0.036 2.00e-02 2.50e+03 pdb=" C8 A C 3 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A C 3 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A C 3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A C 3 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A C 3 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A C 3 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A C 3 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A C 3 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A C 3 " 0.006 2.00e-02 2.50e+03 ... (remaining 2555 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 295 2.65 - 3.21: 14000 3.21 - 3.78: 25283 3.78 - 4.34: 34607 4.34 - 4.90: 56189 Nonbonded interactions: 130374 Sorted by model distance: nonbonded pdb=" O GLY A 186 " pdb=" O2' C C -1 " model vdw 2.091 2.440 nonbonded pdb=" O LYS D 321 " pdb=" OH TYR D 643 " model vdw 2.136 2.440 nonbonded pdb=" O ALA A 685 " pdb=" O2' U C 5 " model vdw 2.163 2.440 nonbonded pdb=" O ASN A 179 " pdb=" O2' G C -4 " model vdw 2.189 2.440 nonbonded pdb=" N THR D 629 " pdb=" O THR D 660 " model vdw 2.194 2.520 ... (remaining 130369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 50 5.49 5 S 51 5.16 5 C 9590 2.51 5 N 2670 2.21 5 O 2896 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 7.130 Check model and map are aligned: 0.220 Process input model: 48.090 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 0.033 15702 Z= 0.157 Angle : 0.534 15.101 21506 Z= 0.283 Chirality : 0.040 0.364 2432 Planarity : 0.004 0.078 2558 Dihedral : 17.376 178.395 5725 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.14 % 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: -0.34 (0.19), residues: 1832 helix: 1.28 (0.21), residues: 647 sheet: -0.79 (0.35), residues: 221 loop : -1.15 (0.19), residues: 964 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 1.698 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 169 average time/residue: 0.3230 time to fit residues: 78.6463 Evaluate side-chains 153 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 1.717 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1587 time to fit residues: 2.9468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 57 optimal weight: 0.0070 chunk 90 optimal weight: 0.9990 chunk 110 optimal weight: 0.0470 chunk 172 optimal weight: 3.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A1494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15702 Z= 0.197 Angle : 0.516 8.384 21506 Z= 0.271 Chirality : 0.041 0.377 2432 Planarity : 0.004 0.060 2558 Dihedral : 11.063 175.207 2594 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 3.47 % 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: -0.24 (0.19), residues: 1832 helix: 1.35 (0.20), residues: 663 sheet: -0.81 (0.35), residues: 219 loop : -1.11 (0.19), residues: 950 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 156 time to evaluate : 1.676 Fit side-chains outliers start: 48 outliers final: 21 residues processed: 190 average time/residue: 0.3026 time to fit residues: 84.0808 Evaluate side-chains 162 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1465 time to fit residues: 8.0712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 153 optimal weight: 0.0970 chunk 171 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 HIS ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 15702 Z= 0.248 Angle : 0.534 8.813 21506 Z= 0.278 Chirality : 0.042 0.375 2432 Planarity : 0.004 0.055 2558 Dihedral : 11.056 173.301 2594 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 3.47 % 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: -0.32 (0.19), residues: 1832 helix: 1.32 (0.20), residues: 663 sheet: -0.94 (0.35), residues: 221 loop : -1.15 (0.19), residues: 948 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 161 time to evaluate : 1.709 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 16 residues processed: 201 average time/residue: 0.2950 time to fit residues: 88.0135 Evaluate side-chains 165 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.678 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1795 time to fit residues: 7.5553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 183 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS A 586 ASN ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 15702 Z= 0.268 Angle : 0.543 9.435 21506 Z= 0.282 Chirality : 0.042 0.376 2432 Planarity : 0.004 0.051 2558 Dihedral : 11.072 173.339 2594 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 3.25 % 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: -0.37 (0.19), residues: 1832 helix: 1.27 (0.20), residues: 665 sheet: -1.00 (0.34), residues: 219 loop : -1.18 (0.19), residues: 948 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 153 time to evaluate : 1.555 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 17 residues processed: 188 average time/residue: 0.2984 time to fit residues: 82.5618 Evaluate side-chains 165 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 1.587 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1419 time to fit residues: 6.7790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 0.1980 chunk 104 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 156 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 93 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 46 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A1494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 15702 Z= 0.161 Angle : 0.499 11.599 21506 Z= 0.258 Chirality : 0.040 0.367 2432 Planarity : 0.004 0.052 2558 Dihedral : 10.958 177.134 2594 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer Outliers : 2.02 % 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: -0.21 (0.19), residues: 1832 helix: 1.45 (0.20), residues: 667 sheet: -0.96 (0.34), residues: 221 loop : -1.12 (0.19), residues: 944 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 1.903 Fit side-chains outliers start: 28 outliers final: 6 residues processed: 181 average time/residue: 0.3008 time to fit residues: 81.2092 Evaluate side-chains 155 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 1.677 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2145 time to fit residues: 4.4384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 0.0060 chunk 45 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 15702 Z= 0.248 Angle : 0.537 9.673 21506 Z= 0.276 Chirality : 0.042 0.371 2432 Planarity : 0.004 0.052 2558 Dihedral : 10.958 173.119 2594 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 2.02 % 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: -0.28 (0.19), residues: 1832 helix: 1.38 (0.20), residues: 666 sheet: -1.00 (0.34), residues: 221 loop : -1.15 (0.19), residues: 945 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 1.736 Fit side-chains outliers start: 28 outliers final: 17 residues processed: 177 average time/residue: 0.2969 time to fit residues: 78.6213 Evaluate side-chains 165 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 1.695 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1478 time to fit residues: 7.0663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 183 optimal weight: 20.0000 chunk 114 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 113 optimal weight: 0.1980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN A 762 HIS A 984 HIS A1494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15702 Z= 0.178 Angle : 0.515 12.764 21506 Z= 0.263 Chirality : 0.040 0.366 2432 Planarity : 0.004 0.051 2558 Dihedral : 10.908 176.340 2594 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 1.59 % 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: -0.17 (0.19), residues: 1832 helix: 1.51 (0.20), residues: 667 sheet: -0.90 (0.35), residues: 215 loop : -1.13 (0.19), residues: 950 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 1.765 Fit side-chains outliers start: 22 outliers final: 3 residues processed: 174 average time/residue: 0.2947 time to fit residues: 75.5735 Evaluate side-chains 156 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1344 time to fit residues: 2.9681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 166 optimal weight: 0.4980 chunk 175 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 15702 Z= 0.240 Angle : 0.546 11.226 21506 Z= 0.278 Chirality : 0.042 0.366 2432 Planarity : 0.004 0.051 2558 Dihedral : 10.926 173.369 2594 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 1832 helix: 1.41 (0.20), residues: 668 sheet: -0.98 (0.34), residues: 223 loop : -1.17 (0.19), residues: 941 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 1.742 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 171 average time/residue: 0.3097 time to fit residues: 78.5371 Evaluate side-chains 159 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.538 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1328 time to fit residues: 4.7707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.0020 chunk 170 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15702 Z= 0.173 Angle : 0.523 13.147 21506 Z= 0.265 Chirality : 0.041 0.362 2432 Planarity : 0.004 0.051 2558 Dihedral : 10.881 176.516 2594 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.58 % 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: -0.19 (0.20), residues: 1832 helix: 1.49 (0.20), residues: 673 sheet: -0.85 (0.35), residues: 215 loop : -1.16 (0.19), residues: 944 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 1.716 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 157 average time/residue: 0.2998 time to fit residues: 70.0986 Evaluate side-chains 156 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 1.685 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1572 time to fit residues: 3.6924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 15702 Z= 0.206 Angle : 0.540 13.134 21506 Z= 0.274 Chirality : 0.041 0.362 2432 Planarity : 0.004 0.051 2558 Dihedral : 10.867 174.541 2594 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 0.43 % 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: -0.22 (0.19), residues: 1832 helix: 1.45 (0.20), residues: 673 sheet: -0.86 (0.35), residues: 215 loop : -1.18 (0.19), residues: 944 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 1.987 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 148 average time/residue: 0.3128 time to fit residues: 68.7748 Evaluate side-chains 148 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 1.713 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1631 time to fit residues: 3.0552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.0040 chunk 138 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 155 optimal weight: 0.3980 chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.178277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132639 restraints weight = 16933.637| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.92 r_work: 0.3407 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 15702 Z= 0.165 Angle : 0.517 13.407 21506 Z= 0.263 Chirality : 0.040 0.359 2432 Planarity : 0.004 0.050 2558 Dihedral : 10.793 176.933 2594 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer Outliers : 0.36 % 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 (0.20), residues: 1832 helix: 1.57 (0.20), residues: 667 sheet: -0.87 (0.35), residues: 219 loop : -1.12 (0.19), residues: 946 =============================================================================== Job complete usr+sys time: 3179.13 seconds wall clock time: 58 minutes 30.30 seconds (3510.30 seconds total)