Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 05:21:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8v_15241/04_2023/8a8v_15241_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8v_15241/04_2023/8a8v_15241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8v_15241/04_2023/8a8v_15241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8v_15241/04_2023/8a8v_15241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8v_15241/04_2023/8a8v_15241_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8v_15241/04_2023/8a8v_15241_updated.pdb" } resolution = 3.34 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= -0.001 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 66 5.16 5 C 17044 2.51 5 N 4838 2.21 5 O 5196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B GLU 626": "OE1" <-> "OE2" Residue "B GLU 643": "OE1" <-> "OE2" Residue "B GLU 700": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C GLU 217": "OE1" <-> "OE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C GLU 606": "OE1" <-> "OE2" Residue "C GLU 628": "OE1" <-> "OE2" Residue "C GLU 643": "OE1" <-> "OE2" Residue "C GLU 782": "OE1" <-> "OE2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D GLU 327": "OE1" <-> "OE2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D GLU 349": "OE1" <-> "OE2" Residue "D GLU 725": "OE1" <-> "OE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E GLU 357": "OE1" <-> "OE2" Residue "E GLU 367": "OE1" <-> "OE2" Residue "E GLU 478": "OE1" <-> "OE2" Residue "E GLU 501": "OE1" <-> "OE2" Residue "E GLU 503": "OE1" <-> "OE2" Residue "E GLU 633": "OE1" <-> "OE2" Residue "E GLU 643": "OE1" <-> "OE2" Residue "E GLU 700": "OE1" <-> "OE2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F GLU 327": "OE1" <-> "OE2" Residue "F GLU 501": "OE1" <-> "OE2" Residue "F GLU 512": "OE1" <-> "OE2" Residue "F GLU 725": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 27164 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4403 Classifications: {'peptide': 558} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 540} Chain breaks: 4 Chain: "B" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4483 Classifications: {'peptide': 568} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 548} Chain breaks: 3 Chain: "C" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4510 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 553} Chain breaks: 2 Chain: "D" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4530 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 555} Chain breaks: 2 Chain: "E" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4490 Classifications: {'peptide': 569} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 548} Chain breaks: 3 Chain: "F" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4364 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 532} Chain breaks: 5 Chain: "G" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 114 Classifications: {'peptide': 23} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.96, per 1000 atoms: 0.51 Number of scatterers: 27164 At special positions: 0 Unit cell: (123.12, 139.365, 148.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 20 15.00 O 5196 8.00 N 4838 7.00 C 17044 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: 10.86 Conformation dependent library (CDL) restraints added in 4.2 seconds 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6310 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 170 helices and 25 sheets defined 50.7% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 178 through 184 Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 222 through 235 Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 289 through 294 removed outlier: 4.008A pdb=" N VAL A 293 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 Proline residue: A 310 - end of helix Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.899A pdb=" N ARG A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 370 removed outlier: 4.663A pdb=" N ASP A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 4.280A pdb=" N ARG A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 414 Processing helix chain 'A' and resid 481 through 492 Processing helix chain 'A' and resid 496 through 499 No H-bonds generated for 'chain 'A' and resid 496 through 499' Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.555A pdb=" N ARG A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 510 " --> pdb=" O ARG A 506 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLU A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 536 Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.632A pdb=" N ARG A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 616 Processing helix chain 'A' and resid 632 through 644 Processing helix chain 'A' and resid 690 through 704 removed outlier: 3.622A pdb=" N LYS A 694 " --> pdb=" O TYR A 690 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 702 " --> pdb=" O ASN A 698 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'A' and resid 724 through 745 removed outlier: 5.326A pdb=" N SER A 744 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS A 745 " --> pdb=" O GLN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 763 Processing helix chain 'A' and resid 771 through 779 removed outlier: 3.781A pdb=" N ARG A 774 " --> pdb=" O ARG A 771 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 775 " --> pdb=" O PRO A 772 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE A 777 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 790 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 222 through 235 Processing helix chain 'B' and resid 252 through 255 No H-bonds generated for 'chain 'B' and resid 252 through 255' Processing helix chain 'B' and resid 263 through 279 Processing helix chain 'B' and resid 289 through 292 Processing helix chain 'B' and resid 304 through 314 Proline residue: B 310 - end of helix removed outlier: 3.750A pdb=" N ARG B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 352 through 370 removed outlier: 4.669A pdb=" N ASP B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 389 Processing helix chain 'B' and resid 397 through 414 Processing helix chain 'B' and resid 481 through 492 Processing helix chain 'B' and resid 501 through 508 Processing helix chain 'B' and resid 510 through 515 Processing helix chain 'B' and resid 522 through 537 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.939A pdb=" N SER B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 582 through 584 No H-bonds generated for 'chain 'B' and resid 582 through 584' Processing helix chain 'B' and resid 589 through 595 Processing helix chain 'B' and resid 609 through 616 removed outlier: 3.705A pdb=" N LYS B 613 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 629 No H-bonds generated for 'chain 'B' and resid 627 through 629' Processing helix chain 'B' and resid 632 through 643 removed outlier: 3.526A pdb=" N TYR B 635 " --> pdb=" O GLN B 632 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN B 640 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 704 Processing helix chain 'B' and resid 707 through 710 No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 724 through 745 removed outlier: 3.845A pdb=" N ASP B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER B 744 " --> pdb=" O GLY B 740 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS B 745 " --> pdb=" O GLN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 762 Processing helix chain 'B' and resid 771 through 779 Processing helix chain 'B' and resid 782 through 790 Processing helix chain 'C' and resid 171 through 174 No H-bonds generated for 'chain 'C' and resid 171 through 174' Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 222 through 235 removed outlier: 3.557A pdb=" N VAL C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 262 through 279 Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 304 through 314 Proline residue: C 310 - end of helix removed outlier: 3.559A pdb=" N ARG C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'C' and resid 363 through 370 Processing helix chain 'C' and resid 376 through 388 Processing helix chain 'C' and resid 397 through 414 Processing helix chain 'C' and resid 481 through 492 Processing helix chain 'C' and resid 501 through 508 Processing helix chain 'C' and resid 510 through 515 Processing helix chain 'C' and resid 522 through 536 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.923A pdb=" N SER C 563 " --> pdb=" O LYS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 595 removed outlier: 3.865A pdb=" N ALA C 591 " --> pdb=" O ARG C 588 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER C 592 " --> pdb=" O PHE C 589 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 594 " --> pdb=" O ALA C 591 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE C 595 " --> pdb=" O SER C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 616 removed outlier: 3.510A pdb=" N LYS C 613 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 629 No H-bonds generated for 'chain 'C' and resid 627 through 629' Processing helix chain 'C' and resid 632 through 644 removed outlier: 5.007A pdb=" N GLN C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL C 641 " --> pdb=" O SER C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 704 Processing helix chain 'C' and resid 707 through 712 Processing helix chain 'C' and resid 724 through 745 removed outlier: 4.103A pdb=" N SER C 744 " --> pdb=" O GLY C 740 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS C 745 " --> pdb=" O GLN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 763 Processing helix chain 'C' and resid 774 through 780 Processing helix chain 'C' and resid 782 through 790 Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 222 through 235 removed outlier: 3.898A pdb=" N VAL D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 264 through 279 Processing helix chain 'D' and resid 289 through 292 Processing helix chain 'D' and resid 304 through 313 Proline residue: D 310 - end of helix Processing helix chain 'D' and resid 325 through 331 Processing helix chain 'D' and resid 336 through 340 removed outlier: 3.590A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 336 through 340' Processing helix chain 'D' and resid 352 through 370 removed outlier: 4.694A pdb=" N ASP D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARG D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 389 removed outlier: 3.692A pdb=" N VAL D 380 " --> pdb=" O ASP D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 414 Processing helix chain 'D' and resid 481 through 492 Processing helix chain 'D' and resid 501 through 508 Processing helix chain 'D' and resid 510 through 515 Processing helix chain 'D' and resid 522 through 536 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.657A pdb=" N SER D 563 " --> pdb=" O LYS D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 576 No H-bonds generated for 'chain 'D' and resid 574 through 576' Processing helix chain 'D' and resid 582 through 584 No H-bonds generated for 'chain 'D' and resid 582 through 584' Processing helix chain 'D' and resid 588 through 595 removed outlier: 3.803A pdb=" N ALA D 591 " --> pdb=" O ARG D 588 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER D 592 " --> pdb=" O PHE D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 616 Processing helix chain 'D' and resid 632 through 643 removed outlier: 3.784A pdb=" N ASN D 636 " --> pdb=" O GLN D 632 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER D 637 " --> pdb=" O GLU D 633 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 638 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLN D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL D 641 " --> pdb=" O SER D 637 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 704 Processing helix chain 'D' and resid 707 through 710 No H-bonds generated for 'chain 'D' and resid 707 through 710' Processing helix chain 'D' and resid 724 through 745 removed outlier: 3.726A pdb=" N ASP D 732 " --> pdb=" O ILE D 728 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL D 738 " --> pdb=" O MET D 734 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER D 744 " --> pdb=" O GLY D 740 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS D 745 " --> pdb=" O GLN D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 761 Processing helix chain 'D' and resid 771 through 780 Processing helix chain 'D' and resid 782 through 790 Processing helix chain 'E' and resid 169 through 173 Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 194 through 205 removed outlier: 3.746A pdb=" N SER E 205 " --> pdb=" O MET E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 235 removed outlier: 3.745A pdb=" N VAL E 226 " --> pdb=" O LYS E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 264 through 279 Processing helix chain 'E' and resid 289 through 292 Processing helix chain 'E' and resid 304 through 314 removed outlier: 3.859A pdb=" N LEU E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Proline residue: E 310 - end of helix Processing helix chain 'E' and resid 325 through 331 removed outlier: 3.586A pdb=" N ARG E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 339 No H-bonds generated for 'chain 'E' and resid 336 through 339' Processing helix chain 'E' and resid 352 through 361 Processing helix chain 'E' and resid 363 through 370 Processing helix chain 'E' and resid 376 through 389 removed outlier: 3.547A pdb=" N THR E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 414 removed outlier: 3.961A pdb=" N LEU E 402 " --> pdb=" O LYS E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 492 Processing helix chain 'E' and resid 501 through 508 Processing helix chain 'E' and resid 510 through 515 Processing helix chain 'E' and resid 522 through 536 Processing helix chain 'E' and resid 559 through 571 removed outlier: 3.570A pdb=" N SER E 563 " --> pdb=" O LYS E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 576 No H-bonds generated for 'chain 'E' and resid 574 through 576' Processing helix chain 'E' and resid 590 through 595 removed outlier: 3.529A pdb=" N PHE E 595 " --> pdb=" O SER E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 616 Processing helix chain 'E' and resid 627 through 629 No H-bonds generated for 'chain 'E' and resid 627 through 629' Processing helix chain 'E' and resid 632 through 644 removed outlier: 3.568A pdb=" N SER E 637 " --> pdb=" O GLU E 633 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN E 640 " --> pdb=" O ASN E 636 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL E 641 " --> pdb=" O SER E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 691 through 704 Processing helix chain 'E' and resid 707 through 712 removed outlier: 4.003A pdb=" N ARG E 712 " --> pdb=" O GLU E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 745 removed outlier: 4.272A pdb=" N SER E 744 " --> pdb=" O GLY E 740 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYS E 745 " --> pdb=" O GLN E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 753 through 762 Processing helix chain 'E' and resid 771 through 780 Processing helix chain 'E' and resid 782 through 790 removed outlier: 3.696A pdb=" N LEU E 790 " --> pdb=" O SER E 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 174 No H-bonds generated for 'chain 'F' and resid 171 through 174' Processing helix chain 'F' and resid 179 through 184 removed outlier: 4.107A pdb=" N MET F 183 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU F 184 " --> pdb=" O ALA F 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 179 through 184' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 222 through 235 removed outlier: 3.802A pdb=" N VAL F 226 " --> pdb=" O LYS F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 279 Processing helix chain 'F' and resid 289 through 314 removed outlier: 3.635A pdb=" N VAL F 293 " --> pdb=" O HIS F 290 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP F 303 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA F 304 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA F 305 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER F 306 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU F 308 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LYS F 309 " --> pdb=" O SER F 306 " (cutoff:3.500A) Proline residue: F 310 - end of helix Processing helix chain 'F' and resid 325 through 330 Processing helix chain 'F' and resid 352 through 370 removed outlier: 4.723A pdb=" N ASP F 364 " --> pdb=" O LYS F 360 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ARG F 365 " --> pdb=" O GLY F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 389 Processing helix chain 'F' and resid 397 through 414 removed outlier: 3.851A pdb=" N LEU F 402 " --> pdb=" O LYS F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 481 through 492 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 510 through 515 Processing helix chain 'F' and resid 522 through 536 Processing helix chain 'F' and resid 559 through 570 Processing helix chain 'F' and resid 588 through 593 removed outlier: 3.921A pdb=" N ARG F 593 " --> pdb=" O PHE F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 616 Processing helix chain 'F' and resid 627 through 629 No H-bonds generated for 'chain 'F' and resid 627 through 629' Processing helix chain 'F' and resid 632 through 644 Processing helix chain 'F' and resid 688 through 703 Processing helix chain 'F' and resid 707 through 711 Processing helix chain 'F' and resid 724 through 745 removed outlier: 3.720A pdb=" N LEU F 733 " --> pdb=" O ARG F 729 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG F 737 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL F 738 " --> pdb=" O MET F 734 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS F 745 " --> pdb=" O GLN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 753 through 762 Processing helix chain 'F' and resid 771 through 780 removed outlier: 3.830A pdb=" N ARG F 775 " --> pdb=" O ARG F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 782 through 791 removed outlier: 3.552A pdb=" N LEU F 790 " --> pdb=" O SER F 786 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 343 through 346 removed outlier: 8.108A pdb=" N ILE A 320 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 284 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA A 322 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A 286 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN A 246 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N PHE A 285 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N TYR A 248 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP A 287 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU A 250 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 715 through 719 removed outlier: 3.605A pdb=" N ASP A 715 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 578 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASP A 625 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE A 580 " --> pdb=" O ASP A 625 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 646 through 648 Processing sheet with id= D, first strand: chain 'A' and resid 748 through 751 Processing sheet with id= E, first strand: chain 'B' and resid 175 through 177 removed outlier: 5.142A pdb=" N ASP B 287 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 715 through 719 Processing sheet with id= G, first strand: chain 'B' and resid 646 through 648 Processing sheet with id= H, first strand: chain 'B' and resid 748 through 751 Processing sheet with id= I, first strand: chain 'C' and resid 175 through 177 removed outlier: 5.178A pdb=" N ASP C 287 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLN C 343 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE C 215 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL C 345 " --> pdb=" O ILE C 215 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 715 through 719 removed outlier: 6.559A pdb=" N ILE C 578 " --> pdb=" O LEU C 623 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP C 625 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE C 580 " --> pdb=" O ASP C 625 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 646 through 648 Processing sheet with id= L, first strand: chain 'C' and resid 749 through 751 removed outlier: 6.271A pdb=" N VAL C 800 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 175 through 177 removed outlier: 6.255A pdb=" N GLN D 343 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE D 215 " --> pdb=" O GLN D 343 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 345 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 715 through 719 removed outlier: 6.714A pdb=" N ILE D 578 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASP D 625 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE D 580 " --> pdb=" O ASP D 625 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 646 through 648 Processing sheet with id= P, first strand: chain 'D' and resid 747 through 751 removed outlier: 6.953A pdb=" N GLN D 798 " --> pdb=" O ALA D 748 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL D 750 " --> pdb=" O GLN D 798 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL D 800 " --> pdb=" O VAL D 750 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 803 through 805 Processing sheet with id= R, first strand: chain 'E' and resid 175 through 177 removed outlier: 5.000A pdb=" N ASP E 287 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA E 322 " --> pdb=" O ILE E 286 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 715 through 718 removed outlier: 3.753A pdb=" N GLY E 547 " --> pdb=" O THR E 660 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER E 620 " --> pdb=" O VAL E 661 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE E 663 " --> pdb=" O SER E 620 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL E 622 " --> pdb=" O ILE E 663 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N THR E 665 " --> pdb=" O VAL E 622 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE E 624 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE E 578 " --> pdb=" O LEU E 623 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASP E 625 " --> pdb=" O ILE E 578 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE E 580 " --> pdb=" O ASP E 625 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 646 through 648 Processing sheet with id= U, first strand: chain 'E' and resid 749 through 751 removed outlier: 6.281A pdb=" N VAL E 800 " --> pdb=" O VAL E 750 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 175 through 177 removed outlier: 5.370A pdb=" N ASP F 287 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLN F 318 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE F 286 " --> pdb=" O GLN F 318 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE F 320 " --> pdb=" O ILE F 286 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 715 through 718 removed outlier: 6.962A pdb=" N ILE F 578 " --> pdb=" O LEU F 623 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASP F 625 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE F 580 " --> pdb=" O ASP F 625 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 646 through 648 Processing sheet with id= Y, first strand: chain 'F' and resid 748 through 751 removed outlier: 3.729A pdb=" N THR F 801 " --> pdb=" O THR F 821 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR F 821 " --> pdb=" O THR F 801 " (cutoff:3.500A) 1149 hydrogen bonds defined for protein. 3327 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: 10.60 Time building geometry restraints manager: 11.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9245 1.34 - 1.46: 4452 1.46 - 1.58: 13693 1.58 - 1.70: 31 1.70 - 1.82: 132 Bond restraints: 27553 Sorted by residual: bond pdb=" N ASP E 732 " pdb=" CA ASP E 732 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.09e+00 bond pdb=" N MET E 734 " pdb=" CA MET E 734 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.30e-02 5.92e+03 3.75e+00 bond pdb=" N LEU E 733 " pdb=" CA LEU E 733 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.64e+00 bond pdb=" CA ARG F 712 " pdb=" C ARG F 712 " ideal model delta sigma weight residual 1.522 1.549 -0.026 1.43e-02 4.89e+03 3.35e+00 bond pdb=" CB PRO C 495 " pdb=" CG PRO C 495 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.13e+00 ... (remaining 27548 not shown) Histogram of bond angle deviations from ideal: 97.33 - 105.13: 425 105.13 - 112.93: 14952 112.93 - 120.73: 12995 120.73 - 128.53: 8664 128.53 - 136.32: 133 Bond angle restraints: 37169 Sorted by residual: angle pdb=" CA ARG F 509 " pdb=" CB ARG F 509 " pdb=" CG ARG F 509 " ideal model delta sigma weight residual 114.10 123.52 -9.42 2.00e+00 2.50e-01 2.22e+01 angle pdb=" CA PRO C 495 " pdb=" N PRO C 495 " pdb=" CD PRO C 495 " ideal model delta sigma weight residual 112.00 105.51 6.49 1.40e+00 5.10e-01 2.15e+01 angle pdb=" N VAL C 220 " pdb=" CA VAL C 220 " pdb=" C VAL C 220 " ideal model delta sigma weight residual 113.47 109.15 4.32 1.01e+00 9.80e-01 1.83e+01 angle pdb=" N LYS E 543 " pdb=" CA LYS E 543 " pdb=" C LYS E 543 " ideal model delta sigma weight residual 114.64 108.47 6.17 1.52e+00 4.33e-01 1.65e+01 angle pdb=" CB MET E 183 " pdb=" CG MET E 183 " pdb=" SD MET E 183 " ideal model delta sigma weight residual 112.70 124.00 -11.30 3.00e+00 1.11e-01 1.42e+01 ... (remaining 37164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.02: 16247 32.02 - 64.05: 565 64.05 - 96.07: 36 96.07 - 128.09: 7 128.09 - 160.11: 5 Dihedral angle restraints: 16860 sinusoidal: 7103 harmonic: 9757 Sorted by residual: dihedral pdb=" C5' ADP E 901 " pdb=" O5' ADP E 901 " pdb=" PA ADP E 901 " pdb=" O2A ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 100.12 -160.11 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O2A ADP D 902 " pdb=" O3A ADP D 902 " pdb=" PA ADP D 902 " pdb=" PB ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 99.29 -159.29 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 83.19 -143.18 1 2.00e+01 2.50e-03 4.32e+01 ... (remaining 16857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3646 0.066 - 0.133: 563 0.133 - 0.199: 24 0.199 - 0.266: 2 0.266 - 0.332: 4 Chirality restraints: 4239 Sorted by residual: chirality pdb=" CB ILE B 716 " pdb=" CA ILE B 716 " pdb=" CG1 ILE B 716 " pdb=" CG2 ILE B 716 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE B 550 " pdb=" CA ILE B 550 " pdb=" CG1 ILE B 550 " pdb=" CG2 ILE B 550 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB VAL C 767 " pdb=" CA VAL C 767 " pdb=" CG1 VAL C 767 " pdb=" CG2 VAL C 767 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 4236 not shown) Planarity restraints: 4820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 706 " -0.059 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO C 707 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 707 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 707 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 771 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO E 772 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO E 772 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 772 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 811 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO F 812 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 812 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 812 " -0.038 5.00e-02 4.00e+02 ... (remaining 4817 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2782 2.75 - 3.28: 27285 3.28 - 3.82: 45374 3.82 - 4.36: 54205 4.36 - 4.90: 92637 Nonbonded interactions: 222283 Sorted by model distance: nonbonded pdb=" O ILE D 627 " pdb=" OH TYR D 635 " model vdw 2.208 2.440 nonbonded pdb=" NH2 ARG A 775 " pdb=" O LEU F 710 " model vdw 2.212 2.520 nonbonded pdb=" O ILE E 627 " pdb=" OH TYR E 635 " model vdw 2.227 2.440 nonbonded pdb=" NH1 ARG B 262 " pdb=" O UNK G 7 " model vdw 2.241 2.520 nonbonded pdb=" O THR F 560 " pdb=" OG SER F 563 " model vdw 2.242 2.440 ... (remaining 222278 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 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 594 or resid 609 through 668 or resid 691 through 808 or resid 815 through 8 \ 21 or resid 901)) selection = (chain 'B' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'C' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'D' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'E' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'F' and (resid 170 through 415 or resid 477 through 668 or resid 691 thro \ ugh 808 or resid 815 through 821 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.010 Normalize map: mean=0, sd=1: 6.470 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: 0.030 Extract box with map and model: 27.830 Check model and map are aligned: 0.470 Set scattering table: 0.250 Process input model: 68.290 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 : 0.004 0.088 27553 Z= 0.256 Angle : 0.791 11.301 37169 Z= 0.406 Chirality : 0.047 0.332 4239 Planarity : 0.006 0.091 4820 Dihedral : 15.570 160.114 10550 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3346 helix: -0.33 (0.11), residues: 1801 sheet: -0.44 (0.24), residues: 389 loop : -0.11 (0.19), residues: 1156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 370 time to evaluate : 3.148 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 372 average time/residue: 0.4497 time to fit residues: 253.7856 Evaluate side-chains 284 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 3.428 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2267 time to fit residues: 4.7567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 306 optimal weight: 0.0040 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 235 HIS ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN B 211 ASN B 391 ASN B 490 ASN B 640 GLN C 343 GLN C 391 ASN C 640 GLN C 651 GLN D 695 GLN E 640 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 27553 Z= 0.199 Angle : 0.577 8.049 37169 Z= 0.272 Chirality : 0.042 0.158 4239 Planarity : 0.004 0.066 4820 Dihedral : 8.432 173.487 3831 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.04 (0.15), residues: 3346 helix: 0.31 (0.12), residues: 1820 sheet: -0.45 (0.24), residues: 388 loop : 0.02 (0.20), residues: 1138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 310 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 19 residues processed: 332 average time/residue: 0.4506 time to fit residues: 228.7372 Evaluate side-chains 281 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 262 time to evaluate : 3.124 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2445 time to fit residues: 13.2399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 170 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 255 optimal weight: 3.9990 chunk 209 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 307 optimal weight: 0.9980 chunk 332 optimal weight: 0.6980 chunk 273 optimal weight: 0.9980 chunk 304 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 246 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN C 568 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN D 631 HIS E 640 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 27553 Z= 0.172 Angle : 0.553 8.173 37169 Z= 0.259 Chirality : 0.041 0.145 4239 Planarity : 0.004 0.065 4820 Dihedral : 7.951 172.406 3831 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.38 (0.15), residues: 3346 helix: 0.66 (0.12), residues: 1807 sheet: -0.41 (0.24), residues: 394 loop : 0.09 (0.20), residues: 1145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 298 time to evaluate : 3.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 318 average time/residue: 0.4586 time to fit residues: 225.5643 Evaluate side-chains 269 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 260 time to evaluate : 3.259 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2568 time to fit residues: 8.8584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 303 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 146 optimal weight: 0.6980 chunk 206 optimal weight: 0.2980 chunk 308 optimal weight: 0.4980 chunk 326 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 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 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 667 ASN B 391 ASN C 346 GLN C 391 ASN C 568 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN E 798 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 27553 Z= 0.222 Angle : 0.571 6.924 37169 Z= 0.269 Chirality : 0.042 0.201 4239 Planarity : 0.004 0.065 4820 Dihedral : 7.643 167.451 3831 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.36 (0.15), residues: 3346 helix: 0.66 (0.12), residues: 1823 sheet: -0.44 (0.24), residues: 396 loop : 0.06 (0.20), residues: 1127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 291 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 20 residues processed: 321 average time/residue: 0.4513 time to fit residues: 222.3555 Evaluate side-chains 296 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 276 time to evaluate : 3.416 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2618 time to fit residues: 14.4548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 272 optimal weight: 0.7980 chunk 185 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 243 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 278 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 166 optimal weight: 0.5980 chunk 293 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 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 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN B 391 ASN C 568 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 27553 Z= 0.203 Angle : 0.564 7.667 37169 Z= 0.265 Chirality : 0.042 0.189 4239 Planarity : 0.004 0.065 4820 Dihedral : 7.366 167.061 3831 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.45 (0.15), residues: 3346 helix: 0.72 (0.12), residues: 1821 sheet: -0.54 (0.24), residues: 416 loop : 0.19 (0.20), residues: 1109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 283 time to evaluate : 3.131 Fit side-chains outliers start: 30 outliers final: 11 residues processed: 306 average time/residue: 0.4622 time to fit residues: 214.1226 Evaluate side-chains 271 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 260 time to evaluate : 3.235 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3119 time to fit residues: 10.5929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 109 optimal weight: 9.9990 chunk 294 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 327 optimal weight: 0.7980 chunk 271 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN B 391 ASN B 667 ASN C 391 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 27553 Z= 0.221 Angle : 0.580 8.995 37169 Z= 0.273 Chirality : 0.042 0.164 4239 Planarity : 0.004 0.065 4820 Dihedral : 7.268 167.901 3831 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.44 (0.15), residues: 3346 helix: 0.71 (0.12), residues: 1821 sheet: -0.56 (0.24), residues: 416 loop : 0.20 (0.20), residues: 1109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 279 time to evaluate : 3.296 Fit side-chains outliers start: 27 outliers final: 13 residues processed: 294 average time/residue: 0.4480 time to fit residues: 202.6270 Evaluate side-chains 277 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 264 time to evaluate : 3.320 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2575 time to fit residues: 10.7093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 315 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 chunk 185 optimal weight: 0.0000 chunk 275 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 325 optimal weight: 7.9990 chunk 203 optimal weight: 0.1980 chunk 198 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN B 391 ASN B 667 ASN C 391 ASN C 568 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 27553 Z= 0.175 Angle : 0.567 8.894 37169 Z= 0.267 Chirality : 0.041 0.145 4239 Planarity : 0.004 0.063 4820 Dihedral : 7.005 170.769 3831 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3346 helix: 0.85 (0.12), residues: 1824 sheet: -0.51 (0.24), residues: 417 loop : 0.27 (0.21), residues: 1105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 269 time to evaluate : 3.378 Fit side-chains outliers start: 22 outliers final: 6 residues processed: 285 average time/residue: 0.4392 time to fit residues: 193.6819 Evaluate side-chains 265 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 259 time to evaluate : 3.410 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2609 time to fit residues: 7.9074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 201 optimal weight: 0.0040 chunk 130 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 98 optimal weight: 0.0470 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 221 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 256 optimal weight: 0.9980 overall best weight: 0.4890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN B 391 ASN B 667 ASN C 391 ASN C 568 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 27553 Z= 0.162 Angle : 0.569 9.658 37169 Z= 0.266 Chirality : 0.041 0.144 4239 Planarity : 0.004 0.064 4820 Dihedral : 6.820 166.822 3831 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3346 helix: 0.90 (0.12), residues: 1825 sheet: -0.47 (0.24), residues: 417 loop : 0.31 (0.21), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 274 time to evaluate : 3.554 Fit side-chains outliers start: 25 outliers final: 10 residues processed: 289 average time/residue: 0.4464 time to fit residues: 198.5511 Evaluate side-chains 269 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 259 time to evaluate : 3.278 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2481 time to fit residues: 9.1424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 296 optimal weight: 4.9990 chunk 312 optimal weight: 7.9990 chunk 284 optimal weight: 0.7980 chunk 303 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 238 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 chunk 287 optimal weight: 0.8980 chunk 302 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 659 ASN A 667 ASN B 391 ASN C 391 ASN C 568 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN F 579 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 27553 Z= 0.216 Angle : 0.593 10.131 37169 Z= 0.279 Chirality : 0.042 0.299 4239 Planarity : 0.004 0.065 4820 Dihedral : 6.907 166.497 3831 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3346 helix: 0.84 (0.12), residues: 1816 sheet: -0.51 (0.24), residues: 417 loop : 0.25 (0.20), residues: 1113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 269 time to evaluate : 3.591 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 278 average time/residue: 0.4694 time to fit residues: 207.2564 Evaluate side-chains 261 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 253 time to evaluate : 3.558 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3683 time to fit residues: 10.5501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 199 optimal weight: 0.2980 chunk 321 optimal weight: 9.9990 chunk 195 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 223 optimal weight: 0.5980 chunk 336 optimal weight: 6.9990 chunk 309 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 164 optimal weight: 0.0050 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN B 391 ASN C 391 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 27553 Z= 0.164 Angle : 0.579 10.171 37169 Z= 0.269 Chirality : 0.041 0.265 4239 Planarity : 0.004 0.066 4820 Dihedral : 6.672 163.662 3831 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.71 (0.15), residues: 3346 helix: 0.95 (0.13), residues: 1819 sheet: -0.44 (0.24), residues: 413 loop : 0.30 (0.21), residues: 1114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 268 time to evaluate : 3.298 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 276 average time/residue: 0.4507 time to fit residues: 192.4481 Evaluate side-chains 263 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 259 time to evaluate : 3.430 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2572 time to fit residues: 6.6607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 212 optimal weight: 0.6980 chunk 285 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 247 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 275 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 49 optimal weight: 8.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 667 ASN B 391 ASN C 391 ASN C 568 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.174961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137086 restraints weight = 34872.999| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.94 r_work: 0.3597 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 27553 Z= 0.191 Angle : 0.591 10.658 37169 Z= 0.276 Chirality : 0.042 0.260 4239 Planarity : 0.004 0.066 4820 Dihedral : 6.664 162.243 3831 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.70 (0.15), residues: 3346 helix: 0.95 (0.13), residues: 1814 sheet: -0.49 (0.24), residues: 418 loop : 0.31 (0.21), residues: 1114 =============================================================================== Job complete usr+sys time: 5796.24 seconds wall clock time: 106 minutes 12.67 seconds (6372.67 seconds total)