Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 15:58:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/04_2023/6whu_21676_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/04_2023/6whu_21676.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/04_2023/6whu_21676_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/04_2023/6whu_21676_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/04_2023/6whu_21676_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/04_2023/6whu_21676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/04_2023/6whu_21676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/04_2023/6whu_21676_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/04_2023/6whu_21676_updated.pdb" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.781 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 138 5.16 5 Cl 8 4.86 5 C 14988 2.51 5 N 3780 2.21 5 O 4452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A GLU 642": "OE1" <-> "OE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B GLU 790": "OE1" <-> "OE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ARG 489": "NH1" <-> "NH2" Residue "C GLU 543": "OE1" <-> "OE2" Residue "C GLU 642": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D GLU 790": "OE1" <-> "OE2" Residue "D GLU 791": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 23368 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 5804 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 4 Unresolved non-hydrogen bonds: 435 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 280 Chain: "B" Number of atoms: 5745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5745 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 28, 'TRANS': 742} Chain breaks: 5 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 213 Chain: "C" Number of atoms: 5804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 5804 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 4 Unresolved non-hydrogen bonds: 435 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 280 Chain: "D" Number of atoms: 5745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5745 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 28, 'TRANS': 742} Chain breaks: 5 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 213 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.30, per 1000 atoms: 0.53 Number of scatterers: 23368 At special positions: 0 Unit cell: (141.11, 149.33, 186.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 8 17.00 S 138 16.00 P 2 15.00 O 4452 8.00 N 3780 7.00 C 14988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.02 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.04 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=2.02 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.04 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.02 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.04 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1002 " - " ASN A 297 " " NAG A1003 " - " ASN A 224 " " NAG B 902 " - " ASN B 74 " " NAG B 905 " - " ASN B 688 " " NAG C1002 " - " ASN C 297 " " NAG C1003 " - " ASN C 224 " " NAG D 902 " - " ASN D 74 " " NAG D 905 " - " ASN D 688 " " NAG E 1 " - " ASN B 542 " " NAG F 1 " - " ASN D 542 " Time building additional restraints: 10.12 Conformation dependent library (CDL) restraints added in 3.7 seconds 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QGM A1001 " pdb=" CB QGM C1001 " Number of C-beta restraints generated: 5824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 103 helices and 28 sheets defined 36.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 107 through 114 removed outlier: 4.681A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 157 removed outlier: 4.009A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 246 through 261 removed outlier: 4.673A pdb=" N MET A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N MET A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 277 through 282 removed outlier: 5.154A pdb=" N TYR A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 316 Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 479 through 490 Processing helix chain 'A' and resid 521 through 527 Processing helix chain 'A' and resid 544 through 547 No H-bonds generated for 'chain 'A' and resid 544 through 547' Processing helix chain 'A' and resid 575 through 578 Proline residue: A 578 - end of helix No H-bonds generated for 'chain 'A' and resid 575 through 578' Processing helix chain 'A' and resid 583 through 602 removed outlier: 3.825A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 636 Processing helix chain 'A' and resid 648 through 679 removed outlier: 4.107A pdb=" N ILE A 652 " --> pdb=" O PHE A 648 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 694 No H-bonds generated for 'chain 'A' and resid 691 through 694' Processing helix chain 'A' and resid 709 through 715 Processing helix chain 'A' and resid 722 through 728 Processing helix chain 'A' and resid 736 through 743 Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.552A pdb=" N LYS A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 802 Processing helix chain 'A' and resid 805 through 813 Processing helix chain 'A' and resid 836 through 861 removed outlier: 3.857A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.644A pdb=" N SER B 90 " --> pdb=" O CYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.556A pdb=" N ALA B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 163 Processing helix chain 'B' and resid 180 through 190 Processing helix chain 'B' and resid 214 through 222 removed outlier: 3.516A pdb=" N LYS B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 246 removed outlier: 3.545A pdb=" N SER B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 289 through 309 Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.618A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 471 removed outlier: 3.788A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 517 through 522 Processing helix chain 'B' and resid 558 through 580 removed outlier: 5.006A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 569 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 575 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE B 580 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 613 removed outlier: 3.703A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 653 Processing helix chain 'B' and resid 669 through 672 No H-bonds generated for 'chain 'B' and resid 669 through 672' Processing helix chain 'B' and resid 674 through 676 No H-bonds generated for 'chain 'B' and resid 674 through 676' Processing helix chain 'B' and resid 691 through 695 Processing helix chain 'B' and resid 701 through 709 removed outlier: 3.519A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N PHE B 709 " --> pdb=" O TYR B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 722 Processing helix chain 'B' and resid 734 through 741 removed outlier: 4.377A pdb=" N GLY B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 786 Processing helix chain 'B' and resid 789 through 796 Processing helix chain 'B' and resid 816 through 843 removed outlier: 3.784A pdb=" N GLY B 820 " --> pdb=" O ASN B 817 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE B 842 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 107 through 114 removed outlier: 4.629A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 157 removed outlier: 4.000A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 182 Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 246 through 261 removed outlier: 4.652A pdb=" N MET C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N MET C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 273 through 275 No H-bonds generated for 'chain 'C' and resid 273 through 275' Processing helix chain 'C' and resid 277 through 282 removed outlier: 5.223A pdb=" N TYR C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 316 Processing helix chain 'C' and resid 339 through 346 Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 479 through 490 Processing helix chain 'C' and resid 521 through 527 Processing helix chain 'C' and resid 544 through 547 No H-bonds generated for 'chain 'C' and resid 544 through 547' Processing helix chain 'C' and resid 575 through 578 Proline residue: C 578 - end of helix No H-bonds generated for 'chain 'C' and resid 575 through 578' Processing helix chain 'C' and resid 583 through 602 removed outlier: 3.823A pdb=" N GLY C 588 " --> pdb=" O TRP C 584 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 636 Processing helix chain 'C' and resid 648 through 679 removed outlier: 4.118A pdb=" N ILE C 652 " --> pdb=" O PHE C 648 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 678 " --> pdb=" O ALA C 674 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP C 679 " --> pdb=" O PHE C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 694 No H-bonds generated for 'chain 'C' and resid 691 through 694' Processing helix chain 'C' and resid 709 through 715 Processing helix chain 'C' and resid 722 through 728 Processing helix chain 'C' and resid 736 through 743 Processing helix chain 'C' and resid 754 through 764 removed outlier: 3.660A pdb=" N LYS C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 802 Processing helix chain 'C' and resid 805 through 813 Processing helix chain 'C' and resid 836 through 861 removed outlier: 3.840A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 854 " --> pdb=" O PHE C 850 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 857 " --> pdb=" O PHE C 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.645A pdb=" N SER D 90 " --> pdb=" O CYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 116 removed outlier: 3.555A pdb=" N ALA D 109 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'D' and resid 214 through 222 removed outlier: 3.517A pdb=" N LYS D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 246 removed outlier: 3.545A pdb=" N SER D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 289 through 309 Processing helix chain 'D' and resid 329 through 338 removed outlier: 3.618A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 471 removed outlier: 3.788A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 502 Processing helix chain 'D' and resid 517 through 522 Processing helix chain 'D' and resid 558 through 580 removed outlier: 5.006A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL D 569 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 572 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE D 575 " --> pdb=" O ALA D 571 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE D 580 " --> pdb=" O VAL D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 613 removed outlier: 3.703A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 653 Processing helix chain 'D' and resid 669 through 672 No H-bonds generated for 'chain 'D' and resid 669 through 672' Processing helix chain 'D' and resid 674 through 676 No H-bonds generated for 'chain 'D' and resid 674 through 676' Processing helix chain 'D' and resid 691 through 695 Processing helix chain 'D' and resid 701 through 709 removed outlier: 3.519A pdb=" N TYR D 705 " --> pdb=" O GLU D 701 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS D 708 " --> pdb=" O ALA D 704 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N PHE D 709 " --> pdb=" O TYR D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 722 Processing helix chain 'D' and resid 734 through 741 removed outlier: 4.376A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 786 Processing helix chain 'D' and resid 789 through 796 Processing helix chain 'D' and resid 816 through 843 removed outlier: 3.784A pdb=" N GLY D 820 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE D 842 " --> pdb=" O GLU D 839 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 30 through 32 Processing sheet with id= B, first strand: chain 'A' and resid 239 through 243 removed outlier: 4.061A pdb=" N VAL A 239 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 243 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LYS A 211 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LEU A 165 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU A 213 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 12.670A pdb=" N VAL A 167 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 9.472A pdb=" N VAL A 215 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 289 through 292 Processing sheet with id= D, first strand: chain 'A' and resid 375 through 377 Processing sheet with id= E, first strand: chain 'A' and resid 420 through 422 removed outlier: 6.709A pdb=" N GLU A 496 " --> pdb=" O ILE A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 455 through 458 Processing sheet with id= G, first strand: chain 'A' and resid 749 through 753 Processing sheet with id= H, first strand: chain 'B' and resid 38 through 42 removed outlier: 3.763A pdb=" N ILE B 40 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 100 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 42 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 256 through 258 removed outlier: 6.958A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE B 171 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL B 202 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR B 173 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 279 through 281 removed outlier: 4.072A pdb=" N LEU B 366 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 405 through 409 removed outlier: 6.834A pdb=" N THR B 475 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE B 408 " --> pdb=" O THR B 475 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP B 477 " --> pdb=" O ILE B 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 488 through 490 Processing sheet with id= M, first strand: chain 'B' and resid 530 through 532 Processing sheet with id= N, first strand: chain 'B' and resid 534 through 537 Processing sheet with id= O, first strand: chain 'C' and resid 30 through 32 Processing sheet with id= P, first strand: chain 'C' and resid 239 through 243 removed outlier: 4.022A pdb=" N VAL C 239 " --> pdb=" O HIS C 162 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 243 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LYS C 211 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N LEU C 165 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N GLU C 213 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 12.660A pdb=" N VAL C 167 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N VAL C 215 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 289 through 292 Processing sheet with id= R, first strand: chain 'C' and resid 375 through 377 Processing sheet with id= S, first strand: chain 'C' and resid 420 through 422 removed outlier: 6.696A pdb=" N GLU C 496 " --> pdb=" O ILE C 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'C' and resid 455 through 458 Processing sheet with id= U, first strand: chain 'C' and resid 750 through 753 Processing sheet with id= V, first strand: chain 'D' and resid 38 through 42 removed outlier: 3.762A pdb=" N ILE D 40 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 100 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D 42 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 256 through 258 removed outlier: 6.957A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE D 171 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL D 202 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR D 173 " --> pdb=" O VAL D 202 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 279 through 281 removed outlier: 4.072A pdb=" N LEU D 366 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 405 through 409 removed outlier: 6.834A pdb=" N THR D 475 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE D 408 " --> pdb=" O THR D 475 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP D 477 " --> pdb=" O ILE D 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 488 through 490 Processing sheet with id= AA, first strand: chain 'D' and resid 530 through 532 Processing sheet with id= AB, first strand: chain 'D' and resid 534 through 537 766 hydrogen bonds defined for protein. 2049 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: 7.44 Time building geometry restraints manager: 10.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3918 1.31 - 1.44: 6372 1.44 - 1.57: 13338 1.57 - 1.70: 4 1.70 - 1.83: 240 Bond restraints: 23872 Sorted by residual: bond pdb=" C1 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.862 1.591 0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C1 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.862 1.591 0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C4 QGP B 901 " pdb=" O6 QGP B 901 " ideal model delta sigma weight residual 1.401 1.224 0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" C4 QGP D 901 " pdb=" O6 QGP D 901 " ideal model delta sigma weight residual 1.401 1.225 0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" C16 QGP B 901 " pdb=" C9 QGP B 901 " ideal model delta sigma weight residual 1.527 1.373 0.154 2.00e-02 2.50e+03 5.90e+01 ... (remaining 23867 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.53: 483 105.53 - 112.68: 13109 112.68 - 119.84: 7989 119.84 - 126.99: 10717 126.99 - 134.15: 292 Bond angle restraints: 32590 Sorted by residual: angle pdb=" N VAL C 225 " pdb=" CA VAL C 225 " pdb=" C VAL C 225 " ideal model delta sigma weight residual 113.20 108.26 4.94 9.60e-01 1.09e+00 2.65e+01 angle pdb=" N VAL A 225 " pdb=" CA VAL A 225 " pdb=" C VAL A 225 " ideal model delta sigma weight residual 113.20 108.28 4.92 9.60e-01 1.09e+00 2.62e+01 angle pdb=" N HIS B 802 " pdb=" CA HIS B 802 " pdb=" C HIS B 802 " ideal model delta sigma weight residual 113.88 108.32 5.56 1.23e+00 6.61e-01 2.04e+01 angle pdb=" N HIS D 802 " pdb=" CA HIS D 802 " pdb=" C HIS D 802 " ideal model delta sigma weight residual 113.88 108.41 5.47 1.23e+00 6.61e-01 1.98e+01 angle pdb=" C GLN C 378 " pdb=" N ASN C 379 " pdb=" CA ASN C 379 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 ... (remaining 32585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12380 17.92 - 35.84: 1225 35.84 - 53.76: 211 53.76 - 71.68: 44 71.68 - 89.60: 22 Dihedral angle restraints: 13882 sinusoidal: 4864 harmonic: 9018 Sorted by residual: dihedral pdb=" CB CYS D 746 " pdb=" SG CYS D 746 " pdb=" SG CYS D 801 " pdb=" CB CYS D 801 " ideal model delta sinusoidal sigma weight residual -86.00 -155.88 69.88 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" CB CYS B 746 " pdb=" SG CYS B 746 " pdb=" SG CYS B 801 " pdb=" CB CYS B 801 " ideal model delta sinusoidal sigma weight residual -86.00 -155.88 69.88 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" CB CYS A 441 " pdb=" SG CYS A 441 " pdb=" SG CYS A 475 " pdb=" CB CYS A 475 " ideal model delta sinusoidal sigma weight residual 93.00 33.79 59.21 1 1.00e+01 1.00e-02 4.69e+01 ... (remaining 13879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 3758 0.119 - 0.238: 98 0.238 - 0.357: 2 0.357 - 0.476: 2 0.476 - 0.595: 2 Chirality restraints: 3862 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" CG LEU A 119 " pdb=" CB LEU A 119 " pdb=" CD1 LEU A 119 " pdb=" CD2 LEU A 119 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.59 2.00e-01 2.50e+01 8.85e+00 ... (remaining 3859 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 128 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C GLY B 128 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY B 128 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 129 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 128 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C GLY D 128 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY D 128 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY D 129 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 700 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C ALA B 700 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA B 700 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU B 701 " -0.013 2.00e-02 2.50e+03 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 712 2.66 - 3.22: 25485 3.22 - 3.78: 34903 3.78 - 4.34: 44111 4.34 - 4.90: 68330 Nonbonded interactions: 173541 Sorted by model distance: nonbonded pdb=" NH2 ARG A 233 " pdb=" O MET A 258 " model vdw 2.095 2.520 nonbonded pdb=" NH2 ARG C 233 " pdb=" O MET C 258 " model vdw 2.105 2.520 nonbonded pdb=" O MET B 829 " pdb=" OG SER B 832 " model vdw 2.137 2.440 nonbonded pdb=" O MET D 829 " pdb=" OG SER D 832 " model vdw 2.138 2.440 nonbonded pdb=" O LYS B 380 " pdb=" OG SER B 383 " model vdw 2.166 2.440 ... (remaining 173536 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 6.090 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 59.630 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.150 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.009 0.271 23872 Z= 0.638 Angle : 0.944 12.115 32590 Z= 0.520 Chirality : 0.054 0.595 3862 Planarity : 0.005 0.049 4134 Dihedral : 15.072 89.604 8004 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 18.01 % Favored : 81.79 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.87 (0.12), residues: 3076 helix: -2.02 (0.12), residues: 1176 sheet: -3.78 (0.20), residues: 366 loop : -4.20 (0.12), residues: 1534 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 317 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 333 average time/residue: 0.3102 time to fit residues: 170.3401 Evaluate side-chains 221 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 216 time to evaluate : 2.808 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1987 time to fit residues: 5.6323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 158 optimal weight: 40.0000 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 0.0370 chunk 94 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 47 ASN A 146 HIS A 161 ASN A 291 GLN A 671 ASN A 707 GLN ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 745 ASN A 763 GLN B 184 ASN B 656 GLN B 767 GLN C 47 ASN C 146 HIS C 161 ASN C 291 GLN C 671 ASN C 707 GLN C 726 HIS C 730 HIS C 731 ASN C 745 ASN C 763 GLN D 184 ASN D 656 GLN D 767 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 23872 Z= 0.192 Angle : 0.689 15.202 32590 Z= 0.356 Chirality : 0.048 0.504 3862 Planarity : 0.004 0.052 4134 Dihedral : 6.474 46.363 3268 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.66 % Favored : 89.27 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.20 (0.14), residues: 3076 helix: -0.40 (0.14), residues: 1192 sheet: -2.54 (0.28), residues: 264 loop : -3.58 (0.13), residues: 1620 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 292 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 23 residues processed: 333 average time/residue: 0.2827 time to fit residues: 161.2543 Evaluate side-chains 262 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 239 time to evaluate : 2.813 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2280 time to fit residues: 13.5734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 282 optimal weight: 0.0670 chunk 304 optimal weight: 0.0370 chunk 251 optimal weight: 0.6980 chunk 279 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 23872 Z= 0.201 Angle : 0.652 11.081 32590 Z= 0.336 Chirality : 0.047 0.530 3862 Planarity : 0.004 0.054 4134 Dihedral : 6.055 44.910 3268 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.66 (0.15), residues: 3076 helix: 0.13 (0.15), residues: 1214 sheet: -2.34 (0.29), residues: 276 loop : -3.37 (0.14), residues: 1586 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 262 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 31 residues processed: 309 average time/residue: 0.2784 time to fit residues: 146.9848 Evaluate side-chains 263 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 232 time to evaluate : 2.918 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2153 time to fit residues: 16.2867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 0.5980 chunk 212 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 134 optimal weight: 0.6980 chunk 189 optimal weight: 8.9990 chunk 283 optimal weight: 0.8980 chunk 299 optimal weight: 3.9990 chunk 147 optimal weight: 0.1980 chunk 268 optimal weight: 4.9990 chunk 80 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 23872 Z= 0.158 Angle : 0.626 11.753 32590 Z= 0.318 Chirality : 0.046 0.547 3862 Planarity : 0.004 0.055 4134 Dihedral : 5.698 44.981 3268 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.27 (0.15), residues: 3076 helix: 0.42 (0.15), residues: 1212 sheet: -2.10 (0.29), residues: 278 loop : -3.11 (0.14), residues: 1586 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 275 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 20 residues processed: 308 average time/residue: 0.2880 time to fit residues: 152.2172 Evaluate side-chains 266 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 246 time to evaluate : 2.790 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2235 time to fit residues: 12.0840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 223 optimal weight: 0.7980 chunk 123 optimal weight: 0.3980 chunk 255 optimal weight: 7.9990 chunk 207 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS D 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 23872 Z= 0.199 Angle : 0.636 11.364 32590 Z= 0.321 Chirality : 0.047 0.758 3862 Planarity : 0.004 0.057 4134 Dihedral : 5.576 44.809 3268 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.08 (0.15), residues: 3076 helix: 0.55 (0.15), residues: 1208 sheet: -2.15 (0.30), residues: 262 loop : -2.94 (0.14), residues: 1606 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 259 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 21 residues processed: 287 average time/residue: 0.2906 time to fit residues: 143.6042 Evaluate side-chains 263 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 242 time to evaluate : 2.773 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2446 time to fit residues: 12.9455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 0.0050 chunk 269 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 138 optimal weight: 0.0270 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 0.0370 chunk 157 optimal weight: 20.0000 overall best weight: 0.8134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 23872 Z= 0.160 Angle : 0.627 12.517 32590 Z= 0.312 Chirality : 0.048 0.986 3862 Planarity : 0.004 0.056 4134 Dihedral : 5.386 45.159 3268 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 3076 helix: 0.69 (0.15), residues: 1190 sheet: -2.01 (0.30), residues: 278 loop : -2.76 (0.15), residues: 1608 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 264 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 283 average time/residue: 0.2880 time to fit residues: 139.6644 Evaluate side-chains 262 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 255 time to evaluate : 2.802 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2179 time to fit residues: 6.6152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 219 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 252 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 298 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 182 optimal weight: 0.0870 chunk 137 optimal weight: 9.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN C 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 23872 Z= 0.222 Angle : 0.656 17.358 32590 Z= 0.326 Chirality : 0.047 0.752 3862 Planarity : 0.004 0.055 4134 Dihedral : 5.398 45.180 3268 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.15), residues: 3076 helix: 0.85 (0.16), residues: 1180 sheet: -1.94 (0.27), residues: 310 loop : -2.76 (0.15), residues: 1586 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 253 time to evaluate : 2.843 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 280 average time/residue: 0.2959 time to fit residues: 141.7534 Evaluate side-chains 267 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 246 time to evaluate : 2.982 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2083 time to fit residues: 11.8680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 0.0570 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 147 optimal weight: 0.4980 chunk 27 optimal weight: 8.9990 chunk 234 optimal weight: 2.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 HIS ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 23872 Z= 0.166 Angle : 0.645 17.320 32590 Z= 0.318 Chirality : 0.048 1.001 3862 Planarity : 0.004 0.055 4134 Dihedral : 5.268 45.797 3268 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.15), residues: 3076 helix: 0.86 (0.15), residues: 1188 sheet: -1.77 (0.28), residues: 310 loop : -2.70 (0.15), residues: 1578 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 266 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 275 average time/residue: 0.2880 time to fit residues: 136.5992 Evaluate side-chains 258 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 251 time to evaluate : 2.701 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2301 time to fit residues: 6.4095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 3.9990 chunk 286 optimal weight: 0.9980 chunk 261 optimal weight: 20.0000 chunk 278 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 251 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 817 GLN D 385 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 23872 Z= 0.248 Angle : 0.687 16.857 32590 Z= 0.339 Chirality : 0.049 1.024 3862 Planarity : 0.004 0.055 4134 Dihedral : 5.389 45.762 3268 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.15), residues: 3076 helix: 0.90 (0.16), residues: 1182 sheet: -1.85 (0.27), residues: 326 loop : -2.69 (0.15), residues: 1568 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 249 time to evaluate : 3.078 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 258 average time/residue: 0.2911 time to fit residues: 129.3283 Evaluate side-chains 252 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 238 time to evaluate : 2.630 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2334 time to fit residues: 9.4052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 7.9990 chunk 294 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 23872 Z= 0.211 Angle : 0.671 17.337 32590 Z= 0.331 Chirality : 0.048 0.933 3862 Planarity : 0.004 0.055 4134 Dihedral : 5.352 46.107 3268 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.15), residues: 3076 helix: 0.94 (0.16), residues: 1182 sheet: -1.71 (0.28), residues: 298 loop : -2.63 (0.15), residues: 1596 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 247 time to evaluate : 3.126 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 252 average time/residue: 0.2910 time to fit residues: 126.9603 Evaluate side-chains 245 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 241 time to evaluate : 2.830 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2670 time to fit residues: 5.6861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 75 optimal weight: 0.4980 chunk 226 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 246 optimal weight: 0.3980 chunk 103 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN C 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.105612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.088083 restraints weight = 70179.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.089666 restraints weight = 42925.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090411 restraints weight = 34457.267| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 23872 Z= 0.261 Angle : 0.693 17.086 32590 Z= 0.343 Chirality : 0.048 0.892 3862 Planarity : 0.004 0.054 4134 Dihedral : 5.444 46.108 3268 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.15), residues: 3076 helix: 0.93 (0.16), residues: 1182 sheet: -1.92 (0.27), residues: 308 loop : -2.63 (0.15), residues: 1586 =============================================================================== Job complete usr+sys time: 3812.87 seconds wall clock time: 70 minutes 47.57 seconds (4247.57 seconds total)