Starting phenix.real_space_refine on Tue Feb 20 07:40:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8v_15241/02_2024/8a8v_15241_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8v_15241/02_2024/8a8v_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_15241/02_2024/8a8v_15241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8v_15241/02_2024/8a8v_15241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8v_15241/02_2024/8a8v_15241_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8v_15241/02_2024/8a8v_15241_updated.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-dev-5238/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: 14.77, per 1000 atoms: 0.54 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: 10.77 Conformation dependent library (CDL) restraints added in 5.7 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: 6.96 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: 11.80 Time building geometry restraints manager: 11.29 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: 0.000 Normalize map: mean=0, sd=1: 7.530 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: 0.020 Extract box with map and model: 27.170 Check model and map are aligned: 0.440 Set scattering table: 0.240 Process input model: 79.100 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.060 ------------------------------------------------------------------------------- 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 % Allowed : 0.35 % Favored : 99.54 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 807 HIS 0.005 0.001 HIS D 720 PHE 0.030 0.002 PHE A 265 TYR 0.040 0.002 TYR F 389 ARG 0.018 0.001 ARG F 729 *********************** 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 : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 582 MET cc_start: 0.4675 (ppp) cc_final: 0.4459 (mmt) REVERT: A 779 ARG cc_start: 0.7434 (mmt180) cc_final: 0.7229 (mmm160) REVERT: B 415 MET cc_start: 0.3682 (mmm) cc_final: 0.3198 (mtt) REVERT: B 606 GLU cc_start: 0.7438 (pp20) cc_final: 0.7172 (pt0) REVERT: B 774 ARG cc_start: 0.6169 (mmm-85) cc_final: 0.5875 (mtp85) REVERT: D 331 TYR cc_start: 0.8320 (m-10) cc_final: 0.8090 (m-10) REVERT: D 518 ILE cc_start: 0.8666 (mm) cc_final: 0.8444 (mm) REVERT: D 695 GLN cc_start: 0.7710 (tp40) cc_final: 0.7477 (tp-100) REVERT: E 582 MET cc_start: 0.8037 (mmm) cc_final: 0.7805 (mmt) REVERT: E 589 PHE cc_start: 0.5554 (m-10) cc_final: 0.5033 (m-10) REVERT: E 727 ILE cc_start: 0.7575 (mm) cc_final: 0.7337 (mm) REVERT: E 734 MET cc_start: 0.8235 (mtt) cc_final: 0.7976 (mtt) outliers start: 3 outliers final: 1 residues processed: 372 average time/residue: 0.4382 time to fit residues: 246.6003 Evaluate side-chains 285 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 284 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 568 ASN 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: 0.7980 chunk 102 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 197 optimal weight: 0.5980 chunk 306 optimal weight: 0.0040 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 E 640 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27553 Z= 0.189 Angle : 0.574 8.029 37169 Z= 0.270 Chirality : 0.042 0.152 4239 Planarity : 0.004 0.066 4820 Dihedral : 8.384 172.906 3833 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.12 % Allowed : 7.79 % Favored : 91.08 % 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: 0.07 (0.15), residues: 3346 helix: 0.35 (0.12), residues: 1814 sheet: -0.44 (0.24), residues: 388 loop : 0.02 (0.20), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 807 HIS 0.011 0.001 HIS D 290 PHE 0.020 0.001 PHE C 497 TYR 0.015 0.001 TYR A 635 ARG 0.008 0.000 ARG A 329 *********************** 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 344 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 312 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 ASN cc_start: 0.6993 (m110) cc_final: 0.6627 (m110) REVERT: B 281 ASP cc_start: 0.8203 (p0) cc_final: 0.7927 (p0) REVERT: B 339 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7993 (tt0) REVERT: B 415 MET cc_start: 0.3625 (mmm) cc_final: 0.3156 (mtt) REVERT: B 634 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7211 (mt) REVERT: D 695 GLN cc_start: 0.7653 (tp40) cc_final: 0.7430 (tp-100) REVERT: E 201 MET cc_start: 0.7289 (mmt) cc_final: 0.7061 (mmt) REVERT: E 215 ILE cc_start: 0.8914 (mm) cc_final: 0.8549 (mt) REVERT: E 581 ASP cc_start: 0.7527 (p0) cc_final: 0.7195 (p0) REVERT: E 589 PHE cc_start: 0.5528 (m-10) cc_final: 0.4970 (m-10) REVERT: E 732 ASP cc_start: 0.7797 (t0) cc_final: 0.7541 (m-30) REVERT: F 623 LEU cc_start: 0.7386 (tt) cc_final: 0.7074 (tt) REVERT: F 783 ASP cc_start: 0.6905 (t70) cc_final: 0.6564 (t0) outliers start: 32 outliers final: 17 residues processed: 335 average time/residue: 0.4464 time to fit residues: 227.8173 Evaluate side-chains 293 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 275 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 733 LEU 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: 3.9990 chunk 255 optimal weight: 0.8980 chunk 209 optimal weight: 0.0970 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: 0.9990 chunk 104 optimal weight: 7.9990 chunk 246 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 391 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1241 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= 0.184 Angle : 0.558 8.251 37169 Z= 0.262 Chirality : 0.041 0.146 4239 Planarity : 0.004 0.065 4820 Dihedral : 7.988 171.970 3831 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.40 % Allowed : 10.81 % Favored : 87.79 % 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: 0.34 (0.15), residues: 3346 helix: 0.61 (0.12), residues: 1813 sheet: -0.44 (0.25), residues: 388 loop : 0.10 (0.20), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 807 HIS 0.009 0.001 HIS D 290 PHE 0.018 0.001 PHE C 497 TYR 0.018 0.001 TYR A 635 ARG 0.008 0.000 ARG A 329 *********************** 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 339 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 299 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7269 (t0) cc_final: 0.6926 (m-30) REVERT: A 391 ASN cc_start: 0.6994 (m110) cc_final: 0.6636 (m110) REVERT: A 510 MET cc_start: 0.7914 (ptm) cc_final: 0.7671 (ptm) REVERT: A 734 MET cc_start: 0.8151 (ptm) cc_final: 0.7799 (ptp) REVERT: A 747 MET cc_start: 0.3880 (tpt) cc_final: 0.3536 (mmm) REVERT: B 281 ASP cc_start: 0.8207 (p0) cc_final: 0.7920 (p0) REVERT: B 339 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8040 (tt0) REVERT: B 415 MET cc_start: 0.3393 (mmm) cc_final: 0.2936 (mtt) REVERT: B 634 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7267 (mt) REVERT: D 379 MET cc_start: 0.7497 (mtm) cc_final: 0.7035 (mtm) REVERT: D 695 GLN cc_start: 0.7627 (tp40) cc_final: 0.7281 (tp-100) REVERT: E 201 MET cc_start: 0.7358 (mmt) cc_final: 0.7093 (mmt) REVERT: E 589 PHE cc_start: 0.5518 (m-10) cc_final: 0.4880 (m-10) REVERT: E 732 ASP cc_start: 0.7772 (t0) cc_final: 0.7462 (m-30) REVERT: F 623 LEU cc_start: 0.7334 (tt) cc_final: 0.7013 (tt) REVERT: F 730 MET cc_start: 0.6830 (mmt) cc_final: 0.6522 (mmt) REVERT: F 783 ASP cc_start: 0.6785 (t70) cc_final: 0.6449 (t0) outliers start: 40 outliers final: 21 residues processed: 330 average time/residue: 0.4526 time to fit residues: 231.9467 Evaluate side-chains 299 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 277 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 587 ASP Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 303 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 146 optimal weight: 0.0770 chunk 206 optimal weight: 0.2980 chunk 308 optimal weight: 2.9990 chunk 326 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 292 optimal weight: 0.0270 chunk 88 optimal weight: 0.9980 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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** C 651 GLN E 640 GLN E 798 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27553 Z= 0.137 Angle : 0.530 7.097 37169 Z= 0.247 Chirality : 0.040 0.201 4239 Planarity : 0.004 0.066 4820 Dihedral : 7.484 169.883 3831 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.76 % Allowed : 12.32 % Favored : 85.92 % 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: 0.57 (0.15), residues: 3346 helix: 0.80 (0.12), residues: 1826 sheet: -0.34 (0.24), residues: 384 loop : 0.20 (0.20), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 807 HIS 0.007 0.000 HIS D 290 PHE 0.016 0.001 PHE A 265 TYR 0.019 0.001 TYR A 635 ARG 0.007 0.000 ARG A 329 *********************** 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 357 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 307 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 779 ARG cc_start: 0.7798 (mmm160) cc_final: 0.7582 (mpt180) REVERT: B 281 ASP cc_start: 0.8146 (p0) cc_final: 0.7901 (p0) REVERT: B 339 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7997 (tt0) REVERT: B 415 MET cc_start: 0.3253 (mmm) cc_final: 0.2872 (mtt) REVERT: B 626 GLU cc_start: 0.7536 (tp30) cc_final: 0.7122 (tp30) REVERT: B 628 GLU cc_start: 0.7758 (pt0) cc_final: 0.7419 (pt0) REVERT: B 634 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7288 (mt) REVERT: D 379 MET cc_start: 0.7485 (mtm) cc_final: 0.7151 (mtt) REVERT: D 695 GLN cc_start: 0.7606 (tp40) cc_final: 0.7266 (tp-100) REVERT: E 589 PHE cc_start: 0.5562 (m-10) cc_final: 0.4890 (m-10) REVERT: E 732 ASP cc_start: 0.7739 (t0) cc_final: 0.7456 (m-30) REVERT: F 623 LEU cc_start: 0.7273 (tt) cc_final: 0.6974 (tt) outliers start: 50 outliers final: 27 residues processed: 347 average time/residue: 0.4413 time to fit residues: 234.0201 Evaluate side-chains 305 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 277 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 587 ASP Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 715 ASP Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 819 THR 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: 1.9990 chunk 4 optimal weight: 0.7980 chunk 243 optimal weight: 0.2980 chunk 134 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 166 optimal weight: 0.5980 chunk 293 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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** C 651 GLN E 640 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 27553 Z= 0.160 Angle : 0.537 7.532 37169 Z= 0.252 Chirality : 0.041 0.176 4239 Planarity : 0.004 0.067 4820 Dihedral : 7.166 170.419 3831 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.72 % Allowed : 13.79 % Favored : 84.49 % 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: 0.66 (0.15), residues: 3346 helix: 0.90 (0.12), residues: 1822 sheet: -0.40 (0.24), residues: 402 loop : 0.26 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 807 HIS 0.012 0.001 HIS D 290 PHE 0.028 0.001 PHE C 497 TYR 0.018 0.001 TYR A 635 ARG 0.009 0.000 ARG A 329 *********************** 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 345 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 296 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7153 (t0) cc_final: 0.6718 (m-30) REVERT: A 582 MET cc_start: 0.4604 (ppp) cc_final: 0.4136 (mpp) REVERT: B 281 ASP cc_start: 0.8208 (p0) cc_final: 0.7918 (p0) REVERT: B 339 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8003 (tt0) REVERT: B 415 MET cc_start: 0.3234 (mmm) cc_final: 0.2940 (mtt) REVERT: B 626 GLU cc_start: 0.7472 (tp30) cc_final: 0.7110 (tp30) REVERT: B 628 GLU cc_start: 0.7757 (pt0) cc_final: 0.7484 (pt0) REVERT: B 634 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7455 (mt) REVERT: D 379 MET cc_start: 0.7541 (mtm) cc_final: 0.7206 (mtm) REVERT: D 695 GLN cc_start: 0.7630 (tp40) cc_final: 0.7260 (tp-100) REVERT: E 201 MET cc_start: 0.7456 (mmt) cc_final: 0.7139 (mmt) REVERT: E 589 PHE cc_start: 0.5517 (m-10) cc_final: 0.4872 (m-10) REVERT: E 732 ASP cc_start: 0.7716 (t0) cc_final: 0.7436 (m-30) REVERT: F 389 TYR cc_start: 0.6817 (m-80) cc_final: 0.6605 (m-80) REVERT: F 623 LEU cc_start: 0.7257 (tt) cc_final: 0.6979 (tt) outliers start: 49 outliers final: 31 residues processed: 333 average time/residue: 0.4246 time to fit residues: 219.1974 Evaluate side-chains 309 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 277 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 587 ASP Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 715 ASP Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 109 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 327 optimal weight: 2.9990 chunk 271 optimal weight: 0.7980 chunk 151 optimal weight: 0.0570 chunk 27 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 171 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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** C 651 GLN D 391 ASN E 640 GLN F 586 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27553 Z= 0.178 Angle : 0.553 9.731 37169 Z= 0.258 Chirality : 0.041 0.168 4239 Planarity : 0.004 0.066 4820 Dihedral : 7.034 171.583 3831 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.18 % Allowed : 13.90 % Favored : 83.92 % 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: 0.92 (0.12), residues: 1816 sheet: -0.41 (0.24), residues: 402 loop : 0.28 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 807 HIS 0.009 0.001 HIS D 290 PHE 0.023 0.001 PHE C 497 TYR 0.018 0.001 TYR A 635 ARG 0.008 0.000 ARG A 329 *********************** 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 348 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 286 time to evaluate : 3.579 Fit side-chains revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7208 (t0) cc_final: 0.6798 (m-30) REVERT: A 582 MET cc_start: 0.4551 (ppp) cc_final: 0.4237 (mpp) REVERT: B 171 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7895 (tp) REVERT: B 281 ASP cc_start: 0.8199 (p0) cc_final: 0.7911 (p0) REVERT: B 339 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7899 (tt0) REVERT: B 415 MET cc_start: 0.3293 (mmm) cc_final: 0.2923 (mtt) REVERT: B 626 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7113 (tp30) REVERT: B 628 GLU cc_start: 0.7746 (pt0) cc_final: 0.7488 (pt0) REVERT: B 634 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7511 (mt) REVERT: B 667 ASN cc_start: 0.7294 (t0) cc_final: 0.7071 (t0) REVERT: D 379 MET cc_start: 0.7506 (mtm) cc_final: 0.7221 (mtm) REVERT: D 695 GLN cc_start: 0.7655 (tp40) cc_final: 0.7188 (tp-100) REVERT: E 201 MET cc_start: 0.7473 (mmt) cc_final: 0.7185 (mmt) REVERT: E 732 ASP cc_start: 0.7728 (t0) cc_final: 0.7437 (m-30) REVERT: F 389 TYR cc_start: 0.6917 (m-80) cc_final: 0.6701 (m-80) REVERT: F 585 PHE cc_start: 0.5793 (m-80) cc_final: 0.5532 (m-80) REVERT: F 623 LEU cc_start: 0.7202 (tt) cc_final: 0.7000 (mt) REVERT: F 624 PHE cc_start: 0.7623 (m-80) cc_final: 0.7198 (m-80) outliers start: 62 outliers final: 36 residues processed: 330 average time/residue: 0.4654 time to fit residues: 237.8942 Evaluate side-chains 316 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 277 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 587 ASP Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 715 ASP Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 315 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 186 optimal weight: 0.0470 chunk 238 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 275 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 325 optimal weight: 8.9990 chunk 203 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- 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 C 343 GLN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 27553 Z= 0.274 Angle : 0.607 8.332 37169 Z= 0.288 Chirality : 0.043 0.274 4239 Planarity : 0.004 0.065 4820 Dihedral : 7.209 168.231 3831 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.11 % Allowed : 14.78 % Favored : 83.12 % 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: 0.42 (0.15), residues: 3346 helix: 0.72 (0.12), residues: 1823 sheet: -0.56 (0.24), residues: 414 loop : 0.12 (0.20), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 491 HIS 0.010 0.001 HIS D 290 PHE 0.021 0.001 PHE C 497 TYR 0.017 0.002 TYR A 635 ARG 0.007 0.000 ARG A 646 *********************** 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 342 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 282 time to evaluate : 3.152 Fit side-chains REVERT: A 387 ASP cc_start: 0.7312 (t0) cc_final: 0.6866 (m-30) REVERT: A 570 LEU cc_start: 0.8218 (mt) cc_final: 0.7976 (mt) REVERT: A 582 MET cc_start: 0.4546 (ppp) cc_final: 0.4086 (mpp) REVERT: A 734 MET cc_start: 0.8186 (ptm) cc_final: 0.7861 (ptp) REVERT: A 774 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7171 (tmm160) REVERT: B 171 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7811 (tp) REVERT: B 281 ASP cc_start: 0.8251 (p0) cc_final: 0.7966 (p0) REVERT: B 339 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7899 (tt0) REVERT: B 634 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7615 (mt) REVERT: D 201 MET cc_start: 0.8402 (mmm) cc_final: 0.7871 (mtt) REVERT: E 201 MET cc_start: 0.7485 (mmt) cc_final: 0.7260 (mmt) REVERT: E 732 ASP cc_start: 0.7797 (t0) cc_final: 0.7484 (m-30) REVERT: F 582 MET cc_start: 0.4899 (mmm) cc_final: 0.4640 (mmm) REVERT: F 585 PHE cc_start: 0.5830 (m-80) cc_final: 0.5450 (m-80) REVERT: F 624 PHE cc_start: 0.7674 (m-80) cc_final: 0.7220 (m-80) outliers start: 60 outliers final: 44 residues processed: 323 average time/residue: 0.4240 time to fit residues: 210.3282 Evaluate side-chains 304 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 257 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 587 ASP Chi-restraints excluded: chain E residue 604 TYR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 715 ASP Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 716 ILE Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 201 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 194 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 207 optimal weight: 0.4980 chunk 221 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 256 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 343 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2031 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= 0.174 Angle : 0.564 9.405 37169 Z= 0.265 Chirality : 0.041 0.233 4239 Planarity : 0.004 0.062 4820 Dihedral : 6.917 167.601 3831 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.04 % Allowed : 15.20 % Favored : 82.77 % 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: 0.63 (0.15), residues: 3346 helix: 0.88 (0.12), residues: 1822 sheet: -0.50 (0.24), residues: 411 loop : 0.27 (0.21), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 807 HIS 0.007 0.001 HIS D 290 PHE 0.019 0.001 PHE C 497 TYR 0.016 0.001 TYR A 635 ARG 0.007 0.000 ARG A 329 *********************** 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 334 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 276 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7225 (t0) cc_final: 0.6814 (m-30) REVERT: A 570 LEU cc_start: 0.8207 (mt) cc_final: 0.7958 (mt) REVERT: A 582 MET cc_start: 0.4695 (ppp) cc_final: 0.4376 (mpp) REVERT: A 774 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7564 (tmm160) REVERT: B 281 ASP cc_start: 0.8224 (p0) cc_final: 0.7947 (p0) REVERT: B 339 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7876 (tt0) REVERT: B 415 MET cc_start: 0.3097 (mmm) cc_final: 0.2819 (mtm) REVERT: B 634 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7676 (mt) REVERT: D 201 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7866 (mtt) REVERT: D 331 TYR cc_start: 0.8299 (m-10) cc_final: 0.7903 (m-10) REVERT: E 201 MET cc_start: 0.7418 (mmt) cc_final: 0.7132 (mmt) REVERT: E 589 PHE cc_start: 0.5626 (m-10) cc_final: 0.5243 (m-80) REVERT: E 732 ASP cc_start: 0.7750 (t0) cc_final: 0.7424 (m-30) REVERT: F 585 PHE cc_start: 0.5865 (m-80) cc_final: 0.5465 (m-80) REVERT: F 623 LEU cc_start: 0.7681 (mt) cc_final: 0.7419 (pp) outliers start: 58 outliers final: 43 residues processed: 316 average time/residue: 0.4377 time to fit residues: 212.8800 Evaluate side-chains 311 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 265 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 667 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 581 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 587 ASP Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 715 ASP Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 296 optimal weight: 2.9990 chunk 312 optimal weight: 3.9990 chunk 284 optimal weight: 0.4980 chunk 303 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 238 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 287 optimal weight: 4.9990 chunk 302 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 568 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN E 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27553 Z= 0.187 Angle : 0.577 10.086 37169 Z= 0.269 Chirality : 0.042 0.209 4239 Planarity : 0.004 0.063 4820 Dihedral : 6.840 166.123 3831 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.07 % Allowed : 15.58 % Favored : 82.34 % 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: 0.68 (0.15), residues: 3346 helix: 0.92 (0.12), residues: 1813 sheet: -0.50 (0.24), residues: 411 loop : 0.30 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 807 HIS 0.008 0.001 HIS D 290 PHE 0.030 0.001 PHE A 265 TYR 0.017 0.001 TYR F 635 ARG 0.010 0.000 ARG A 329 *********************** 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 328 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 269 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 570 LEU cc_start: 0.8203 (mt) cc_final: 0.7918 (mt) REVERT: A 582 MET cc_start: 0.4702 (ppp) cc_final: 0.4416 (mpp) REVERT: A 774 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7791 (tmm160) REVERT: B 171 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7714 (tp) REVERT: B 281 ASP cc_start: 0.8234 (p0) cc_final: 0.7953 (p0) REVERT: B 339 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7865 (tt0) REVERT: B 634 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7701 (mt) REVERT: D 201 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7862 (mtt) REVERT: E 201 MET cc_start: 0.7394 (mmt) cc_final: 0.7117 (mmt) REVERT: E 732 ASP cc_start: 0.7753 (t0) cc_final: 0.7432 (m-30) REVERT: F 582 MET cc_start: 0.4763 (mmm) cc_final: 0.4457 (mmm) REVERT: F 585 PHE cc_start: 0.5835 (m-80) cc_final: 0.5395 (m-80) REVERT: F 623 LEU cc_start: 0.7680 (mt) cc_final: 0.7339 (pp) REVERT: F 624 PHE cc_start: 0.7207 (m-80) cc_final: 0.6987 (m-80) REVERT: F 646 ARG cc_start: 0.7142 (tpp80) cc_final: 0.6786 (tpp80) outliers start: 59 outliers final: 44 residues processed: 313 average time/residue: 0.4161 time to fit residues: 202.1246 Evaluate side-chains 311 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 263 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 581 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 587 ASP Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 715 ASP Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 199 optimal weight: 0.0070 chunk 321 optimal weight: 7.9990 chunk 195 optimal weight: 0.0970 chunk 152 optimal weight: 0.9990 chunk 223 optimal weight: 0.6980 chunk 336 optimal weight: 6.9990 chunk 309 optimal weight: 8.9990 chunk 268 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 164 optimal weight: 0.0670 overall best weight: 0.3334 ------------------------------------------------------------------------------- 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 C 391 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 27553 Z= 0.147 Angle : 0.562 10.307 37169 Z= 0.262 Chirality : 0.041 0.234 4239 Planarity : 0.004 0.063 4820 Dihedral : 6.620 161.995 3831 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.76 % Allowed : 16.15 % Favored : 82.10 % 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: 0.80 (0.15), residues: 3346 helix: 1.01 (0.13), residues: 1818 sheet: -0.45 (0.24), residues: 419 loop : 0.37 (0.21), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 491 HIS 0.007 0.000 HIS D 290 PHE 0.025 0.001 PHE C 497 TYR 0.015 0.001 TYR A 635 ARG 0.010 0.000 ARG A 329 ********************** 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 328 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 278 time to evaluate : 3.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 ASN cc_start: 0.6861 (m110) cc_final: 0.6510 (m-40) REVERT: A 510 MET cc_start: 0.7983 (ptm) cc_final: 0.7739 (ptm) REVERT: A 570 LEU cc_start: 0.8212 (mt) cc_final: 0.7983 (mt) REVERT: A 582 MET cc_start: 0.4686 (ppp) cc_final: 0.4484 (mpp) REVERT: B 281 ASP cc_start: 0.8173 (p0) cc_final: 0.7907 (p0) REVERT: B 339 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7873 (tt0) REVERT: B 634 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7679 (mt) REVERT: B 668 LEU cc_start: 0.7628 (tp) cc_final: 0.7009 (pt) REVERT: B 787 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6792 (mt-10) REVERT: D 201 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7843 (mtt) REVERT: E 201 MET cc_start: 0.7414 (mmt) cc_final: 0.7070 (mmt) REVERT: E 732 ASP cc_start: 0.7785 (t0) cc_final: 0.7474 (m-30) REVERT: F 582 MET cc_start: 0.4802 (mmm) cc_final: 0.4503 (mmm) REVERT: F 585 PHE cc_start: 0.5896 (m-80) cc_final: 0.5509 (m-80) REVERT: F 623 LEU cc_start: 0.7536 (mt) cc_final: 0.7279 (pp) REVERT: F 624 PHE cc_start: 0.7252 (m-80) cc_final: 0.7017 (m-80) REVERT: F 646 ARG cc_start: 0.7207 (tpp80) cc_final: 0.6844 (tpp80) outliers start: 50 outliers final: 38 residues processed: 309 average time/residue: 0.4592 time to fit residues: 224.5439 Evaluate side-chains 308 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 267 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 587 ASP Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 715 ASP Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 212 optimal weight: 0.9990 chunk 285 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 247 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 112 optimal weight: 0.0970 chunk 275 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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** D 391 ASN E 640 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.175911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.142431 restraints weight = 34898.611| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.70 r_work: 0.3622 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 27553 Z= 0.204 Angle : 0.587 10.190 37169 Z= 0.275 Chirality : 0.042 0.201 4239 Planarity : 0.004 0.066 4820 Dihedral : 6.686 161.492 3831 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.90 % Allowed : 16.25 % Favored : 81.85 % 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: 0.72 (0.15), residues: 3346 helix: 0.96 (0.13), residues: 1815 sheet: -0.52 (0.24), residues: 411 loop : 0.32 (0.21), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 807 HIS 0.012 0.001 HIS E 290 PHE 0.028 0.001 PHE A 265 TYR 0.016 0.001 TYR A 635 ARG 0.009 0.000 ARG A 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6278.50 seconds wall clock time: 114 minutes 54.00 seconds (6894.00 seconds total)