Starting phenix.real_space_refine on Fri Mar 6 07:57:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wi0_21681/03_2026/6wi0_21681.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wi0_21681/03_2026/6wi0_21681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wi0_21681/03_2026/6wi0_21681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wi0_21681/03_2026/6wi0_21681.map" model { file = "/net/cci-nas-00/data/ceres_data/6wi0_21681/03_2026/6wi0_21681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wi0_21681/03_2026/6wi0_21681.cif" } resolution = 4.27 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 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= 0.014 sd= 0.788 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9484 atoms to isotropic. 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 S 106 5.16 5 Cl 4 4.86 5 C 14200 2.51 5 N 3586 2.21 5 O 4068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21964 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 5545 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 32, 'TRANS': 759} Chain breaks: 4 Unresolved non-hydrogen bonds: 732 Unresolved non-hydrogen angles: 880 Unresolved non-hydrogen dihedrals: 616 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 25, 'TRP:plan': 1, 'GLN:plan1': 12, 'GLU:plan': 38, 'HIS:plan': 9, 'PHE:plan': 2, 'ASP:plan': 18, 'ASN:plan1': 11, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 484 Chain: "B" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 5356 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 26, 'TRANS': 737} Chain breaks: 4 Unresolved non-hydrogen bonds: 715 Unresolved non-hydrogen angles: 868 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 20, 'GLU:plan': 30, 'HIS:plan': 7, 'PHE:plan': 8, 'ARG:plan': 18, 'GLN:plan1': 11, 'TYR:plan': 9, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 479 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: C, D, F Time building chain proxies: 8.20, per 1000 atoms: 0.37 Number of scatterers: 21964 At special positions: 0 Unit cell: (138.37, 154.81, 183.58, 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) Cl 4 17.00 S 106 16.00 O 4068 8.00 N 3586 7.00 C 14200 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=2.04 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.05 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 901 " - " ASN B 542 " " NAG D 901 " - " ASN D 542 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN D 688 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 978.5 milliseconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 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: 5816 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 30 sheets defined 42.4% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 36 through 53 removed outlier: 3.534A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 3.704A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.692A pdb=" N GLY A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.614A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 150 through 158 removed outlier: 3.573A pdb=" N MET A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.959A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 235 removed outlier: 3.651A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 removed outlier: 4.074A pdb=" N VAL A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 277 through 283 removed outlier: 4.087A pdb=" N ARG A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.506A pdb=" N GLN A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 removed outlier: 4.180A pdb=" N SER A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 489 removed outlier: 3.988A pdb=" N ARG A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 529 removed outlier: 3.507A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.648A pdb=" N ILE A 548 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 604 removed outlier: 3.840A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 635 removed outlier: 3.757A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 678 removed outlier: 4.453A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 709 through 717 removed outlier: 4.098A pdb=" N TYR A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 728 Processing helix chain 'A' and resid 734 through 744 removed outlier: 4.328A pdb=" N ILE A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 761 removed outlier: 4.533A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 804 removed outlier: 3.514A pdb=" N VAL A 793 " --> pdb=" O TRP A 789 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER A 796 " --> pdb=" O GLN A 792 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN A 803 " --> pdb=" O LYS A 799 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 812 Processing helix chain 'A' and resid 830 through 835 Processing helix chain 'A' and resid 835 through 861 removed outlier: 3.635A pdb=" N MET A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 233 through 248 removed outlier: 4.147A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.890A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 removed outlier: 3.574A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 501 Processing helix chain 'B' and resid 517 through 523 removed outlier: 3.679A pdb=" N GLU B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 523 " --> pdb=" O ARG B 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 517 through 523' Processing helix chain 'B' and resid 555 through 575 removed outlier: 4.236A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.930A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 654 removed outlier: 3.605A pdb=" N ILE B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 707 removed outlier: 7.144A pdb=" N GLU B 701 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N MET B 702 " --> pdb=" O ASN B 698 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 723 removed outlier: 3.731A pdb=" N LEU B 718 " --> pdb=" O VAL B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 4.784A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 785 removed outlier: 4.348A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.660A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 842 removed outlier: 4.013A pdb=" N TYR B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 845 No H-bonds generated for 'chain 'B' and resid 843 through 845' Processing helix chain 'C' and resid 36 through 53 removed outlier: 3.535A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 removed outlier: 3.704A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 86 Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.692A pdb=" N GLY C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.614A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 150 through 158 removed outlier: 3.573A pdb=" N MET C 155 " --> pdb=" O TRP C 151 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.958A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 235 removed outlier: 3.651A pdb=" N GLU C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 257 removed outlier: 4.074A pdb=" N VAL C 252 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA C 257 " --> pdb=" O TYR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 277 through 283 removed outlier: 4.087A pdb=" N ARG C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 315 removed outlier: 3.506A pdb=" N GLN C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 removed outlier: 4.179A pdb=" N SER C 348 " --> pdb=" O ARG C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 489 removed outlier: 3.989A pdb=" N ARG C 489 " --> pdb=" O ILE C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 529 removed outlier: 3.508A pdb=" N GLY C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 548 removed outlier: 3.648A pdb=" N ILE C 548 " --> pdb=" O ALA C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 604 removed outlier: 3.839A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 635 removed outlier: 3.757A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 678 removed outlier: 4.452A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 663 " --> pdb=" O GLY C 659 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 694 Processing helix chain 'C' and resid 709 through 717 removed outlier: 4.097A pdb=" N TYR C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 728 Processing helix chain 'C' and resid 734 through 744 removed outlier: 4.329A pdb=" N ILE C 739 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN C 740 " --> pdb=" O ALA C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 761 removed outlier: 4.533A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 804 removed outlier: 3.513A pdb=" N VAL C 793 " --> pdb=" O TRP C 789 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER C 796 " --> pdb=" O GLN C 792 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 803 " --> pdb=" O LYS C 799 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY C 804 " --> pdb=" O SER C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 812 Processing helix chain 'C' and resid 830 through 835 Processing helix chain 'C' and resid 835 through 861 removed outlier: 3.635A pdb=" N MET C 839 " --> pdb=" O ALA C 835 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE C 854 " --> pdb=" O PHE C 850 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 855 " --> pdb=" O LEU C 851 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 856 " --> pdb=" O ILE C 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 214 through 221 Processing helix chain 'D' and resid 233 through 248 removed outlier: 4.147A pdb=" N THR D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.890A pdb=" N ILE D 340 " --> pdb=" O ASN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 removed outlier: 3.573A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 501 Processing helix chain 'D' and resid 517 through 523 removed outlier: 3.679A pdb=" N GLU D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL D 523 " --> pdb=" O ARG D 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 517 through 523' Processing helix chain 'D' and resid 555 through 575 removed outlier: 4.235A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA D 571 " --> pdb=" O LEU D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.931A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 654 removed outlier: 3.605A pdb=" N ILE D 641 " --> pdb=" O PHE D 637 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 653 " --> pdb=" O ASN D 649 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 707 removed outlier: 7.143A pdb=" N GLU D 701 " --> pdb=" O ASN D 697 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N MET D 702 " --> pdb=" O ASN D 698 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TYR D 705 " --> pdb=" O GLU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 714 through 723 removed outlier: 3.731A pdb=" N LEU D 718 " --> pdb=" O VAL D 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 4.784A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 785 removed outlier: 4.350A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 778 " --> pdb=" O ARG D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.659A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 842 removed outlier: 4.012A pdb=" N TYR D 823 " --> pdb=" O ALA D 819 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU D 825 " --> pdb=" O VAL D 821 " (cutoff:3.500A) Processing helix chain 'D' and resid 843 through 845 No H-bonds generated for 'chain 'D' and resid 843 through 845' Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 216 removed outlier: 7.717A pdb=" N ILE A 163 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 215 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 165 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 292 removed outlier: 5.998A pdb=" N TYR A 372 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE A 387 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A 374 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.475A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 422 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 535 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 536 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY A 780 " --> pdb=" O ALA A 536 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 431 through 433 Processing sheet with id=AA6, first strand: chain 'A' and resid 510 through 511 removed outlier: 3.651A pdb=" N VAL A 511 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AA8, first strand: chain 'A' and resid 749 through 753 Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 73 removed outlier: 6.038A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 124 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 198 through 204 removed outlier: 7.739A pdb=" N PHE B 169 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 202 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE B 171 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU B 204 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR B 173 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 372 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB3, first strand: chain 'B' and resid 417 through 420 removed outlier: 3.599A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 524 through 525 removed outlier: 3.684A pdb=" N ILE B 766 " --> pdb=" O ASP B 524 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 530 through 532 removed outlier: 4.078A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 729 through 732 Processing sheet with id=AB7, first strand: chain 'C' and resid 59 through 65 Processing sheet with id=AB8, first strand: chain 'C' and resid 211 through 216 removed outlier: 7.718A pdb=" N ILE C 163 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL C 215 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU C 165 " --> pdb=" O VAL C 215 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 288 through 292 removed outlier: 5.998A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 497 through 498 removed outlier: 6.475A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL C 535 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA C 536 " --> pdb=" O GLY C 780 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY C 780 " --> pdb=" O ALA C 536 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 431 through 433 Processing sheet with id=AC3, first strand: chain 'C' and resid 510 through 511 removed outlier: 3.651A pdb=" N VAL C 511 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 556 through 557 Processing sheet with id=AC5, first strand: chain 'C' and resid 749 through 753 Processing sheet with id=AC6, first strand: chain 'D' and resid 69 through 73 removed outlier: 6.038A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 124 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 198 through 204 removed outlier: 7.739A pdb=" N PHE D 169 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL D 202 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE D 171 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU D 204 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR D 173 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AC9, first strand: chain 'D' and resid 417 through 420 removed outlier: 3.600A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 524 through 525 removed outlier: 3.683A pdb=" N ILE D 766 " --> pdb=" O ASP D 524 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.077A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 729 through 732 926 hydrogen bonds defined for protein. 2598 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: 4.69 Time building geometry restraints manager: 2.56 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: 3564 1.31 - 1.44: 6012 1.44 - 1.57: 12684 1.57 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 22434 Sorted by residual: bond pdb=" N QGM A1001 " pdb=" CAV QGM A1001 " ideal model delta sigma weight residual 1.347 1.473 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" N QGM C1001 " pdb=" CAV QGM C1001 " ideal model delta sigma weight residual 1.347 1.473 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" ND2 QGM C1001 " pdb=" CAR QGM C1001 " ideal model delta sigma weight residual 1.354 1.448 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" ND2 QGM A1001 " pdb=" CAR QGM A1001 " ideal model delta sigma weight residual 1.354 1.448 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAR QGM A1001 " pdb=" NAN QGM A1001 " ideal model delta sigma weight residual 1.376 1.454 -0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 22429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 30535 2.98 - 5.97: 234 5.97 - 8.95: 27 8.95 - 11.94: 2 11.94 - 14.92: 2 Bond angle restraints: 30800 Sorted by residual: angle pdb=" N VAL D 576 " pdb=" CA VAL D 576 " pdb=" C VAL D 576 " ideal model delta sigma weight residual 113.39 105.61 7.78 1.47e+00 4.63e-01 2.80e+01 angle pdb=" N VAL B 576 " pdb=" CA VAL B 576 " pdb=" C VAL B 576 " ideal model delta sigma weight residual 113.39 105.61 7.78 1.47e+00 4.63e-01 2.80e+01 angle pdb=" CA QGM A1001 " pdb=" N QGM A1001 " pdb=" CAV QGM A1001 " ideal model delta sigma weight residual 123.80 108.88 14.92 3.00e+00 1.11e-01 2.47e+01 angle pdb=" CA QGM C1001 " pdb=" N QGM C1001 " pdb=" CAV QGM C1001 " ideal model delta sigma weight residual 123.80 108.88 14.92 3.00e+00 1.11e-01 2.47e+01 angle pdb=" C ILE B 85 " pdb=" N CYS B 86 " pdb=" CA CYS B 86 " ideal model delta sigma weight residual 121.14 114.38 6.76 1.75e+00 3.27e-01 1.49e+01 ... (remaining 30795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.80: 12192 19.80 - 39.60: 771 39.60 - 59.41: 137 59.41 - 79.21: 20 79.21 - 99.01: 12 Dihedral angle restraints: 13132 sinusoidal: 4132 harmonic: 9000 Sorted by residual: dihedral pdb=" CB CYS A 831 " pdb=" SG CYS A 831 " pdb=" SG CYS D 557 " pdb=" CB CYS D 557 " ideal model delta sinusoidal sigma weight residual 93.00 6.42 86.58 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CB CYS B 557 " pdb=" SG CYS B 557 " pdb=" SG CYS C 831 " pdb=" CB CYS C 831 " ideal model delta sinusoidal sigma weight residual 93.00 6.79 86.21 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CA GLU D 412 " pdb=" C GLU D 412 " pdb=" N GLU D 413 " pdb=" CA GLU D 413 " ideal model delta harmonic sigma weight residual 180.00 135.06 44.94 0 5.00e+00 4.00e-02 8.08e+01 ... (remaining 13129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.307: 3806 0.307 - 0.613: 2 0.613 - 0.920: 0 0.920 - 1.227: 0 1.227 - 1.533: 2 Chirality restraints: 3810 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 -0.87 -1.53 2.00e-02 2.50e+03 5.88e+03 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 -0.87 -1.53 2.00e-02 2.50e+03 5.87e+03 chirality pdb=" CG QGM A1001 " pdb=" CB QGM A1001 " pdb=" CD1 QGM A1001 " pdb=" ND2 QGM A1001 " both_signs ideal model delta sigma weight residual False -2.43 -2.85 0.42 2.00e-01 2.50e+01 4.41e+00 ... (remaining 3807 not shown) Planarity restraints: 3886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 103 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO C 104 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 103 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO A 104 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 258 " -0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 259 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " -0.026 5.00e-02 4.00e+02 ... (remaining 3883 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 770 2.69 - 3.24: 24547 3.24 - 3.79: 33931 3.79 - 4.35: 41571 4.35 - 4.90: 63324 Nonbonded interactions: 164143 Sorted by model distance: nonbonded pdb=" O MET B 829 " pdb=" OG SER B 832 " model vdw 2.134 3.040 nonbonded pdb=" O MET D 829 " pdb=" OG SER D 832 " model vdw 2.134 3.040 nonbonded pdb=" OG SER C 93 " pdb=" OG1 THR C 122 " model vdw 2.151 3.040 nonbonded pdb=" OG SER A 93 " pdb=" OG1 THR A 122 " model vdw 2.152 3.040 nonbonded pdb=" OG SER C 762 " pdb=" O TYR C 816 " model vdw 2.167 3.040 ... (remaining 164138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 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=0.50 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.500 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 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 : 0.005 0.126 22460 Z= 0.265 Angle : 0.876 36.446 30854 Z= 0.457 Chirality : 0.058 1.533 3810 Planarity : 0.004 0.054 3882 Dihedral : 13.977 99.011 7262 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.19 % Favored : 89.62 % Rotamer: Outliers : 0.60 % Allowed : 7.54 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.12), residues: 3072 helix: -2.57 (0.12), residues: 1112 sheet: -3.00 (0.23), residues: 350 loop : -3.43 (0.13), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 124 TYR 0.013 0.002 TYR A 713 PHE 0.012 0.002 PHE B 784 TRP 0.014 0.002 TRP B 796 HIS 0.005 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00524 (22434) covalent geometry : angle 0.77365 (30800) SS BOND : bond 0.00887 ( 18) SS BOND : angle 1.97253 ( 36) hydrogen bonds : bond 0.17544 ( 926) hydrogen bonds : angle 7.18338 ( 2598) Misc. bond : bond 0.00059 ( 2) link_BETA1-4 : bond 0.06533 ( 2) link_BETA1-4 : angle 25.19395 ( 6) link_NAG-ASN : bond 0.01353 ( 4) link_NAG-ASN : angle 10.43264 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 259 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6010 (mtp) cc_final: 0.5590 (mtm) REVERT: B 176 PHE cc_start: 0.6067 (t80) cc_final: 0.5644 (t80) REVERT: B 515 ILE cc_start: 0.8929 (mt) cc_final: 0.8690 (tt) REVERT: C 154 MET cc_start: 0.6230 (mtp) cc_final: 0.5757 (mtm) REVERT: D 300 ILE cc_start: 0.6747 (tt) cc_final: 0.6540 (mt) outliers start: 12 outliers final: 4 residues processed: 267 average time/residue: 0.1248 time to fit residues: 56.6078 Evaluate side-chains 190 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 186 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.0270 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.7980 overall best weight: 2.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN A 147 GLN A 425 HIS A 426 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS B 153 GLN B 192 ASN B 341 ASN B 359 HIS B 817 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN C 147 GLN C 414 GLN C 425 HIS C 426 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 ASN D 341 ASN D 359 HIS D 817 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.070219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.055750 restraints weight = 129330.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.057278 restraints weight = 77190.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.058328 restraints weight = 54713.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.059029 restraints weight = 43270.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.059507 restraints weight = 36864.374| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22460 Z= 0.149 Angle : 0.677 17.259 30854 Z= 0.339 Chirality : 0.045 0.193 3810 Planarity : 0.004 0.061 3882 Dihedral : 8.325 91.917 3432 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.69 % Favored : 91.18 % Rotamer: Outliers : 0.15 % Allowed : 6.59 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.14), residues: 3072 helix: -0.80 (0.14), residues: 1178 sheet: -2.57 (0.23), residues: 400 loop : -2.81 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 124 TYR 0.015 0.001 TYR B 287 PHE 0.013 0.001 PHE C 505 TRP 0.022 0.001 TRP B 796 HIS 0.003 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00322 (22434) covalent geometry : angle 0.64993 (30800) SS BOND : bond 0.00787 ( 18) SS BOND : angle 1.81561 ( 36) hydrogen bonds : bond 0.04554 ( 926) hydrogen bonds : angle 5.30859 ( 2598) Misc. bond : bond 0.00278 ( 2) link_BETA1-4 : bond 0.01627 ( 2) link_BETA1-4 : angle 3.35317 ( 6) link_NAG-ASN : bond 0.01431 ( 4) link_NAG-ASN : angle 8.90150 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 244 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8204 (mmm) cc_final: 0.7513 (mmt) REVERT: A 493 PHE cc_start: 0.8585 (m-80) cc_final: 0.8134 (m-80) REVERT: A 628 MET cc_start: 0.8554 (tmm) cc_final: 0.8118 (tmm) REVERT: A 723 MET cc_start: 0.8085 (mmm) cc_final: 0.7718 (mmm) REVERT: B 132 MET cc_start: 0.8916 (mmp) cc_final: 0.8090 (mmm) REVERT: B 133 ILE cc_start: 0.8799 (pt) cc_final: 0.8423 (pt) REVERT: B 134 MET cc_start: 0.8823 (pmm) cc_final: 0.8377 (pmm) REVERT: B 157 MET cc_start: 0.9369 (mmm) cc_final: 0.9003 (tmm) REVERT: B 321 CYS cc_start: 0.1918 (p) cc_final: 0.1534 (p) REVERT: B 503 MET cc_start: 0.8615 (mpp) cc_final: 0.8290 (mpp) REVERT: B 646 TYR cc_start: 0.9180 (t80) cc_final: 0.8859 (t80) REVERT: B 698 ASN cc_start: 0.8111 (t0) cc_final: 0.7689 (t0) REVERT: C 240 ILE cc_start: 0.9043 (mt) cc_final: 0.8787 (tt) REVERT: C 261 MET cc_start: 0.8262 (mmm) cc_final: 0.7797 (mmt) REVERT: D 132 MET cc_start: 0.9136 (mmp) cc_final: 0.8252 (mmm) REVERT: D 134 MET cc_start: 0.8887 (pmm) cc_final: 0.8685 (pmm) REVERT: D 136 ASP cc_start: 0.8516 (t70) cc_final: 0.8209 (t0) REVERT: D 321 CYS cc_start: 0.1324 (p) cc_final: 0.1056 (p) REVERT: D 457 CYS cc_start: 0.7595 (m) cc_final: 0.7367 (m) REVERT: D 503 MET cc_start: 0.8750 (ptp) cc_final: 0.8269 (ptt) REVERT: D 698 ASN cc_start: 0.8518 (t0) cc_final: 0.8068 (t0) outliers start: 3 outliers final: 2 residues processed: 247 average time/residue: 0.1178 time to fit residues: 50.3023 Evaluate side-chains 193 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 59 optimal weight: 2.9990 chunk 118 optimal weight: 0.0770 chunk 114 optimal weight: 0.0970 chunk 17 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 200 optimal weight: 40.0000 chunk 150 optimal weight: 0.1980 chunk 156 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 overall best weight: 1.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 341 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.072008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.057567 restraints weight = 130190.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.059124 restraints weight = 78600.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.060165 restraints weight = 55932.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060873 restraints weight = 44418.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061356 restraints weight = 37829.416| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22460 Z= 0.117 Angle : 0.609 16.316 30854 Z= 0.304 Chirality : 0.043 0.160 3810 Planarity : 0.004 0.067 3882 Dihedral : 7.846 89.927 3432 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.15), residues: 3072 helix: 0.11 (0.15), residues: 1168 sheet: -2.20 (0.23), residues: 410 loop : -2.33 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 187 TYR 0.014 0.001 TYR D 287 PHE 0.036 0.001 PHE B 241 TRP 0.021 0.001 TRP D 796 HIS 0.003 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00258 (22434) covalent geometry : angle 0.58284 (30800) SS BOND : bond 0.00390 ( 18) SS BOND : angle 1.63199 ( 36) hydrogen bonds : bond 0.03851 ( 926) hydrogen bonds : angle 4.80841 ( 2598) Misc. bond : bond 0.00307 ( 2) link_BETA1-4 : bond 0.00652 ( 2) link_BETA1-4 : angle 3.03435 ( 6) link_NAG-ASN : bond 0.01363 ( 4) link_NAG-ASN : angle 8.39732 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 230 MET cc_start: 0.8842 (mmm) cc_final: 0.8200 (mmm) REVERT: A 261 MET cc_start: 0.8334 (mmm) cc_final: 0.7511 (mmt) REVERT: A 493 PHE cc_start: 0.8521 (m-80) cc_final: 0.8014 (m-80) REVERT: A 628 MET cc_start: 0.8487 (tmm) cc_final: 0.8125 (tmm) REVERT: B 132 MET cc_start: 0.9095 (mmp) cc_final: 0.8304 (mmm) REVERT: B 133 ILE cc_start: 0.8831 (pt) cc_final: 0.8430 (pt) REVERT: B 134 MET cc_start: 0.9020 (pmm) cc_final: 0.8485 (pmm) REVERT: B 136 ASP cc_start: 0.8558 (t70) cc_final: 0.8249 (t0) REVERT: B 321 CYS cc_start: 0.1404 (p) cc_final: 0.1042 (p) REVERT: B 503 MET cc_start: 0.8611 (mpp) cc_final: 0.8322 (mpp) REVERT: B 646 TYR cc_start: 0.9090 (t80) cc_final: 0.8783 (t80) REVERT: B 698 ASN cc_start: 0.8153 (t0) cc_final: 0.7751 (t0) REVERT: C 240 ILE cc_start: 0.9056 (mt) cc_final: 0.8811 (tt) REVERT: C 261 MET cc_start: 0.8311 (mmm) cc_final: 0.7992 (mmt) REVERT: C 723 MET cc_start: 0.7310 (mmp) cc_final: 0.6689 (mmt) REVERT: D 132 MET cc_start: 0.9232 (mmp) cc_final: 0.8461 (mmm) REVERT: D 133 ILE cc_start: 0.8581 (pt) cc_final: 0.8157 (pt) REVERT: D 134 MET cc_start: 0.8905 (pmm) cc_final: 0.8429 (pmm) REVERT: D 136 ASP cc_start: 0.8551 (t70) cc_final: 0.8255 (t0) REVERT: D 142 MET cc_start: 0.8027 (mmt) cc_final: 0.7611 (mmm) REVERT: D 321 CYS cc_start: 0.0980 (p) cc_final: 0.0749 (p) REVERT: D 457 CYS cc_start: 0.7464 (m) cc_final: 0.7236 (m) REVERT: D 497 MET cc_start: 0.8880 (tpp) cc_final: 0.8634 (tpt) REVERT: D 503 MET cc_start: 0.8871 (ptp) cc_final: 0.8664 (ptp) REVERT: D 646 TYR cc_start: 0.9125 (t80) cc_final: 0.8809 (t80) REVERT: D 698 ASN cc_start: 0.8417 (t0) cc_final: 0.7946 (t0) REVERT: D 706 MET cc_start: 0.9133 (mmm) cc_final: 0.8798 (mmt) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1158 time to fit residues: 52.5989 Evaluate side-chains 197 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 10.0000 chunk 35 optimal weight: 0.0010 chunk 234 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 237 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 181 optimal weight: 0.2980 chunk 201 optimal weight: 20.0000 chunk 214 optimal weight: 0.8980 chunk 226 optimal weight: 6.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.072504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057878 restraints weight = 128058.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.059472 restraints weight = 76868.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060545 restraints weight = 54495.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.061275 restraints weight = 43078.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.061718 restraints weight = 36679.111| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22460 Z= 0.113 Angle : 0.596 15.555 30854 Z= 0.297 Chirality : 0.043 0.161 3810 Planarity : 0.004 0.065 3882 Dihedral : 7.574 87.814 3432 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.36 % Favored : 92.51 % Rotamer: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.15), residues: 3072 helix: 0.34 (0.15), residues: 1172 sheet: -1.90 (0.24), residues: 406 loop : -2.12 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 36 TYR 0.014 0.001 TYR D 287 PHE 0.025 0.001 PHE D 842 TRP 0.019 0.001 TRP B 610 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00253 (22434) covalent geometry : angle 0.57154 (30800) SS BOND : bond 0.00347 ( 18) SS BOND : angle 1.53706 ( 36) hydrogen bonds : bond 0.03560 ( 926) hydrogen bonds : angle 4.62142 ( 2598) Misc. bond : bond 0.00286 ( 2) link_BETA1-4 : bond 0.00731 ( 2) link_BETA1-4 : angle 2.65112 ( 6) link_NAG-ASN : bond 0.01287 ( 4) link_NAG-ASN : angle 8.02074 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8666 (t0) cc_final: 0.8423 (t0) REVERT: A 230 MET cc_start: 0.8820 (mmm) cc_final: 0.8175 (mmm) REVERT: A 261 MET cc_start: 0.8338 (mmm) cc_final: 0.7702 (mmt) REVERT: A 493 PHE cc_start: 0.8471 (m-80) cc_final: 0.7979 (m-80) REVERT: A 628 MET cc_start: 0.8460 (tmm) cc_final: 0.7996 (tmm) REVERT: B 132 MET cc_start: 0.9156 (mmp) cc_final: 0.8313 (mmm) REVERT: B 134 MET cc_start: 0.9131 (pmm) cc_final: 0.8512 (pmm) REVERT: B 321 CYS cc_start: 0.1012 (p) cc_final: 0.0749 (p) REVERT: B 503 MET cc_start: 0.8576 (mpp) cc_final: 0.8280 (mpp) REVERT: B 609 LEU cc_start: 0.9200 (mm) cc_final: 0.8755 (pp) REVERT: B 646 TYR cc_start: 0.9063 (t80) cc_final: 0.8759 (t80) REVERT: B 698 ASN cc_start: 0.8049 (t0) cc_final: 0.7622 (t0) REVERT: C 153 GLU cc_start: 0.9269 (mp0) cc_final: 0.9051 (mp0) REVERT: C 240 ILE cc_start: 0.9097 (mt) cc_final: 0.8893 (tt) REVERT: C 261 MET cc_start: 0.8329 (mmm) cc_final: 0.8119 (mmt) REVERT: C 628 MET cc_start: 0.8185 (tmm) cc_final: 0.7682 (tmm) REVERT: C 723 MET cc_start: 0.7636 (mmp) cc_final: 0.7242 (mmt) REVERT: D 132 MET cc_start: 0.9090 (mmp) cc_final: 0.8431 (mmm) REVERT: D 134 MET cc_start: 0.9028 (pmm) cc_final: 0.8458 (pmm) REVERT: D 136 ASP cc_start: 0.8597 (t70) cc_final: 0.8281 (t0) REVERT: D 142 MET cc_start: 0.7809 (mmt) cc_final: 0.7483 (mmm) REVERT: D 321 CYS cc_start: 0.0848 (p) cc_final: 0.0590 (p) REVERT: D 646 TYR cc_start: 0.9112 (t80) cc_final: 0.8710 (t80) REVERT: D 698 ASN cc_start: 0.8358 (t0) cc_final: 0.7890 (t0) REVERT: D 706 MET cc_start: 0.9066 (mmm) cc_final: 0.8783 (mmt) outliers start: 2 outliers final: 0 residues processed: 254 average time/residue: 0.1213 time to fit residues: 53.5275 Evaluate side-chains 202 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 60 optimal weight: 0.8980 chunk 250 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 106 optimal weight: 30.0000 chunk 162 optimal weight: 6.9990 chunk 276 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 153 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.070306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.055923 restraints weight = 130777.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.057449 restraints weight = 78605.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.058443 restraints weight = 55821.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.059142 restraints weight = 44428.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.059608 restraints weight = 38002.349| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 22460 Z= 0.193 Angle : 0.665 14.951 30854 Z= 0.337 Chirality : 0.045 0.168 3810 Planarity : 0.004 0.065 3882 Dihedral : 7.742 90.199 3432 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.05 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.15), residues: 3072 helix: 0.28 (0.15), residues: 1160 sheet: -2.15 (0.22), residues: 444 loop : -2.07 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 36 TYR 0.017 0.002 TYR C 713 PHE 0.026 0.002 PHE B 241 TRP 0.020 0.002 TRP D 796 HIS 0.005 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00419 (22434) covalent geometry : angle 0.64281 (30800) SS BOND : bond 0.00702 ( 18) SS BOND : angle 1.77401 ( 36) hydrogen bonds : bond 0.03956 ( 926) hydrogen bonds : angle 4.83089 ( 2598) Misc. bond : bond 0.00156 ( 2) link_BETA1-4 : bond 0.01071 ( 2) link_BETA1-4 : angle 2.54931 ( 6) link_NAG-ASN : bond 0.01139 ( 4) link_NAG-ASN : angle 7.91130 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8659 (t0) cc_final: 0.8449 (t70) REVERT: A 261 MET cc_start: 0.8624 (mmm) cc_final: 0.8381 (mmp) REVERT: A 493 PHE cc_start: 0.8449 (m-80) cc_final: 0.7976 (m-80) REVERT: A 597 MET cc_start: 0.9341 (tmm) cc_final: 0.8981 (tmm) REVERT: A 628 MET cc_start: 0.8450 (tmm) cc_final: 0.8038 (tmm) REVERT: A 723 MET cc_start: 0.7649 (mmm) cc_final: 0.7434 (mmt) REVERT: B 73 MET cc_start: 0.8497 (tpt) cc_final: 0.8215 (tpp) REVERT: B 132 MET cc_start: 0.9211 (mmp) cc_final: 0.8387 (mmm) REVERT: B 134 MET cc_start: 0.9166 (pmm) cc_final: 0.8413 (pmm) REVERT: B 321 CYS cc_start: 0.1243 (p) cc_final: 0.0895 (p) REVERT: B 503 MET cc_start: 0.8674 (mpp) cc_final: 0.8323 (mpp) REVERT: B 646 TYR cc_start: 0.9095 (t80) cc_final: 0.8809 (t80) REVERT: B 698 ASN cc_start: 0.8017 (t0) cc_final: 0.7596 (t0) REVERT: C 130 ASP cc_start: 0.8319 (t0) cc_final: 0.8086 (t0) REVERT: C 240 ILE cc_start: 0.9121 (mt) cc_final: 0.8896 (tt) REVERT: C 655 MET cc_start: 0.9046 (tpt) cc_final: 0.8433 (mmm) REVERT: D 132 MET cc_start: 0.9257 (mmp) cc_final: 0.8529 (mmm) REVERT: D 134 MET cc_start: 0.9056 (pmm) cc_final: 0.8383 (pmm) REVERT: D 136 ASP cc_start: 0.8618 (t70) cc_final: 0.8304 (t0) REVERT: D 321 CYS cc_start: 0.1046 (p) cc_final: 0.0616 (p) REVERT: D 646 TYR cc_start: 0.9136 (t80) cc_final: 0.8797 (t80) REVERT: D 698 ASN cc_start: 0.8330 (t0) cc_final: 0.7916 (t0) REVERT: D 706 MET cc_start: 0.9176 (mmm) cc_final: 0.8851 (mmt) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1214 time to fit residues: 49.9169 Evaluate side-chains 192 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 258 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 105 optimal weight: 30.0000 chunk 157 optimal weight: 7.9990 chunk 219 optimal weight: 0.0170 chunk 240 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 300 optimal weight: 0.0770 chunk 273 optimal weight: 9.9990 overall best weight: 1.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS C 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.072715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.058127 restraints weight = 127361.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059708 restraints weight = 76923.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.060783 restraints weight = 54549.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061512 restraints weight = 43162.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.061951 restraints weight = 36743.201| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22460 Z= 0.105 Angle : 0.597 14.132 30854 Z= 0.296 Chirality : 0.043 0.154 3810 Planarity : 0.004 0.061 3882 Dihedral : 7.272 82.532 3432 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.58 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.15), residues: 3072 helix: 0.61 (0.16), residues: 1164 sheet: -1.45 (0.24), residues: 420 loop : -1.93 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 36 TYR 0.020 0.001 TYR C 266 PHE 0.032 0.001 PHE D 241 TRP 0.014 0.001 TRP D 796 HIS 0.008 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00234 (22434) covalent geometry : angle 0.57648 (30800) SS BOND : bond 0.00519 ( 18) SS BOND : angle 1.65148 ( 36) hydrogen bonds : bond 0.03406 ( 926) hydrogen bonds : angle 4.48446 ( 2598) Misc. bond : bond 0.00311 ( 2) link_BETA1-4 : bond 0.00737 ( 2) link_BETA1-4 : angle 2.44527 ( 6) link_NAG-ASN : bond 0.01127 ( 4) link_NAG-ASN : angle 7.23757 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8526 (t0) cc_final: 0.8286 (t0) REVERT: A 230 MET cc_start: 0.8866 (mmm) cc_final: 0.8182 (mmm) REVERT: A 261 MET cc_start: 0.8608 (mmm) cc_final: 0.8376 (mmt) REVERT: A 493 PHE cc_start: 0.8449 (m-80) cc_final: 0.7972 (m-80) REVERT: A 597 MET cc_start: 0.9343 (tmm) cc_final: 0.9057 (tmm) REVERT: A 628 MET cc_start: 0.8413 (tmm) cc_final: 0.7997 (tmm) REVERT: A 719 GLU cc_start: 0.7704 (tp30) cc_final: 0.7375 (tm-30) REVERT: B 73 MET cc_start: 0.8389 (tpt) cc_final: 0.8087 (tpp) REVERT: B 132 MET cc_start: 0.9180 (mmp) cc_final: 0.8357 (mmm) REVERT: B 134 MET cc_start: 0.9155 (pmm) cc_final: 0.8355 (pmm) REVERT: B 136 ASP cc_start: 0.8530 (t70) cc_final: 0.8227 (t0) REVERT: B 321 CYS cc_start: 0.1010 (p) cc_final: 0.0532 (p) REVERT: B 508 MET cc_start: 0.8626 (ptp) cc_final: 0.8389 (mtm) REVERT: B 612 LEU cc_start: 0.9436 (tp) cc_final: 0.9020 (tp) REVERT: B 646 TYR cc_start: 0.9017 (t80) cc_final: 0.8674 (t80) REVERT: B 698 ASN cc_start: 0.7859 (t0) cc_final: 0.7496 (t0) REVERT: C 153 GLU cc_start: 0.9281 (mp0) cc_final: 0.9028 (mp0) REVERT: C 493 PHE cc_start: 0.8549 (m-80) cc_final: 0.8003 (m-80) REVERT: D 132 MET cc_start: 0.9092 (mmp) cc_final: 0.8484 (mmm) REVERT: D 134 MET cc_start: 0.9034 (pmm) cc_final: 0.8299 (pmm) REVERT: D 136 ASP cc_start: 0.8538 (t70) cc_final: 0.8238 (t0) REVERT: D 142 MET cc_start: 0.7718 (mmt) cc_final: 0.7367 (mmm) REVERT: D 646 TYR cc_start: 0.9078 (t80) cc_final: 0.8722 (t80) REVERT: D 698 ASN cc_start: 0.8282 (t0) cc_final: 0.7893 (t0) REVERT: D 706 MET cc_start: 0.9085 (mmm) cc_final: 0.8803 (mmt) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1185 time to fit residues: 52.3141 Evaluate side-chains 209 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 196 optimal weight: 7.9990 chunk 256 optimal weight: 8.9990 chunk 227 optimal weight: 0.0980 chunk 79 optimal weight: 0.0060 chunk 281 optimal weight: 10.0000 chunk 249 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 overall best weight: 3.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 127 HIS D 152 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.071197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.056769 restraints weight = 128847.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.058233 restraints weight = 79207.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.059207 restraints weight = 57227.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.059882 restraints weight = 45935.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.060302 restraints weight = 39477.922| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22460 Z= 0.158 Angle : 0.634 13.353 30854 Z= 0.318 Chirality : 0.044 0.172 3810 Planarity : 0.004 0.061 3882 Dihedral : 7.315 84.229 3432 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.43 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.15), residues: 3072 helix: 0.59 (0.16), residues: 1162 sheet: -1.88 (0.23), residues: 438 loop : -1.81 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 36 TYR 0.014 0.001 TYR C 713 PHE 0.026 0.002 PHE A 714 TRP 0.019 0.001 TRP B 796 HIS 0.004 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00348 (22434) covalent geometry : angle 0.61453 (30800) SS BOND : bond 0.00669 ( 18) SS BOND : angle 1.85268 ( 36) hydrogen bonds : bond 0.03566 ( 926) hydrogen bonds : angle 4.62048 ( 2598) Misc. bond : bond 0.00197 ( 2) link_BETA1-4 : bond 0.00767 ( 2) link_BETA1-4 : angle 2.37517 ( 6) link_NAG-ASN : bond 0.00993 ( 4) link_NAG-ASN : angle 7.07809 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8519 (t0) cc_final: 0.8306 (t70) REVERT: A 426 GLN cc_start: 0.9144 (tp40) cc_final: 0.8591 (tm-30) REVERT: A 493 PHE cc_start: 0.8417 (m-80) cc_final: 0.7975 (m-80) REVERT: A 597 MET cc_start: 0.9333 (tmm) cc_final: 0.9113 (tmm) REVERT: A 628 MET cc_start: 0.8361 (tmm) cc_final: 0.7997 (tmm) REVERT: B 73 MET cc_start: 0.8254 (tpt) cc_final: 0.8027 (tpp) REVERT: B 132 MET cc_start: 0.9268 (mmp) cc_final: 0.8360 (mmm) REVERT: B 134 MET cc_start: 0.8999 (pmm) cc_final: 0.8174 (pmm) REVERT: B 142 MET cc_start: 0.8026 (mmt) cc_final: 0.7645 (mmp) REVERT: B 646 TYR cc_start: 0.9085 (t80) cc_final: 0.8793 (t80) REVERT: B 698 ASN cc_start: 0.7889 (t0) cc_final: 0.7564 (t0) REVERT: C 493 PHE cc_start: 0.8453 (m-80) cc_final: 0.7830 (m-80) REVERT: D 132 MET cc_start: 0.9277 (mmp) cc_final: 0.8556 (mmm) REVERT: D 134 MET cc_start: 0.8307 (pmm) cc_final: 0.7990 (pmm) REVERT: D 136 ASP cc_start: 0.8487 (t70) cc_final: 0.8227 (t0) REVERT: D 142 MET cc_start: 0.7691 (mmt) cc_final: 0.7419 (mmp) REVERT: D 646 TYR cc_start: 0.9109 (t80) cc_final: 0.8744 (t80) REVERT: D 698 ASN cc_start: 0.8083 (t0) cc_final: 0.7712 (t0) REVERT: D 706 MET cc_start: 0.9064 (mmm) cc_final: 0.8800 (mmt) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1142 time to fit residues: 48.5340 Evaluate side-chains 201 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 95 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 109 optimal weight: 0.2980 chunk 296 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 252 optimal weight: 8.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.070248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.055764 restraints weight = 129272.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.057206 restraints weight = 79938.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.058171 restraints weight = 58058.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.058842 restraints weight = 46691.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.059307 restraints weight = 40122.954| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22460 Z= 0.202 Angle : 0.682 13.024 30854 Z= 0.343 Chirality : 0.045 0.184 3810 Planarity : 0.004 0.061 3882 Dihedral : 7.638 89.280 3432 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.05 % Favored : 90.85 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.15), residues: 3072 helix: 0.40 (0.15), residues: 1162 sheet: -1.86 (0.23), residues: 446 loop : -1.89 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 36 TYR 0.015 0.002 TYR C 713 PHE 0.025 0.002 PHE C 660 TRP 0.042 0.002 TRP D 796 HIS 0.005 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00437 (22434) covalent geometry : angle 0.66390 (30800) SS BOND : bond 0.00401 ( 18) SS BOND : angle 1.93751 ( 36) hydrogen bonds : bond 0.03844 ( 926) hydrogen bonds : angle 4.84828 ( 2598) Misc. bond : bond 0.00228 ( 2) link_BETA1-4 : bond 0.01068 ( 2) link_BETA1-4 : angle 2.30289 ( 6) link_NAG-ASN : bond 0.00904 ( 4) link_NAG-ASN : angle 7.04447 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8559 (t0) cc_final: 0.8340 (t0) REVERT: A 493 PHE cc_start: 0.8453 (m-80) cc_final: 0.8015 (m-80) REVERT: A 628 MET cc_start: 0.8317 (tmm) cc_final: 0.8083 (tmm) REVERT: B 73 MET cc_start: 0.8340 (tpt) cc_final: 0.8102 (tpp) REVERT: B 132 MET cc_start: 0.9238 (mmp) cc_final: 0.8487 (mmm) REVERT: B 134 MET cc_start: 0.8582 (pmm) cc_final: 0.8231 (pmm) REVERT: B 136 ASP cc_start: 0.8497 (t70) cc_final: 0.8205 (t0) REVERT: B 142 MET cc_start: 0.8201 (mmt) cc_final: 0.7813 (mmp) REVERT: B 508 MET cc_start: 0.8665 (ptp) cc_final: 0.8323 (mtm) REVERT: C 493 PHE cc_start: 0.8465 (m-80) cc_final: 0.7857 (m-80) REVERT: D 132 MET cc_start: 0.9292 (mmp) cc_final: 0.8607 (mmm) REVERT: D 134 MET cc_start: 0.8471 (pmm) cc_final: 0.8031 (pmm) REVERT: D 136 ASP cc_start: 0.8540 (t70) cc_final: 0.8268 (t0) REVERT: D 142 MET cc_start: 0.7742 (mmt) cc_final: 0.7443 (mmp) REVERT: D 698 ASN cc_start: 0.8134 (t0) cc_final: 0.7724 (t0) REVERT: D 706 MET cc_start: 0.9173 (mmm) cc_final: 0.8871 (mmt) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1155 time to fit residues: 47.1303 Evaluate side-chains 186 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 247 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 263 optimal weight: 0.0570 chunk 145 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 chunk 240 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 chunk 193 optimal weight: 0.9980 chunk 211 optimal weight: 10.0000 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.071443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.056850 restraints weight = 127657.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.058323 restraints weight = 78317.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059309 restraints weight = 56695.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.060001 restraints weight = 45504.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.060482 restraints weight = 39086.946| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22460 Z= 0.136 Angle : 0.638 12.866 30854 Z= 0.317 Chirality : 0.044 0.225 3810 Planarity : 0.004 0.060 3882 Dihedral : 7.488 88.910 3432 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.78 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.15), residues: 3072 helix: 0.66 (0.16), residues: 1148 sheet: -1.74 (0.23), residues: 442 loop : -1.79 (0.17), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 36 TYR 0.014 0.001 TYR D 646 PHE 0.025 0.002 PHE A 714 TRP 0.033 0.002 TRP D 796 HIS 0.003 0.001 HIS C 53 Details of bonding type rmsd covalent geometry : bond 0.00302 (22434) covalent geometry : angle 0.62025 (30800) SS BOND : bond 0.00421 ( 18) SS BOND : angle 1.95333 ( 36) hydrogen bonds : bond 0.03614 ( 926) hydrogen bonds : angle 4.64292 ( 2598) Misc. bond : bond 0.00240 ( 2) link_BETA1-4 : bond 0.00917 ( 2) link_BETA1-4 : angle 2.29637 ( 6) link_NAG-ASN : bond 0.00957 ( 4) link_NAG-ASN : angle 6.79172 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8493 (t0) cc_final: 0.8291 (t70) REVERT: A 493 PHE cc_start: 0.8402 (m-80) cc_final: 0.8012 (m-80) REVERT: A 628 MET cc_start: 0.8276 (tmm) cc_final: 0.8063 (tmm) REVERT: B 73 MET cc_start: 0.8311 (tpt) cc_final: 0.7980 (tpp) REVERT: B 132 MET cc_start: 0.9254 (mmp) cc_final: 0.8552 (mmm) REVERT: B 134 MET cc_start: 0.8590 (pmm) cc_final: 0.8211 (pmm) REVERT: B 136 ASP cc_start: 0.8462 (t70) cc_final: 0.8182 (t0) REVERT: B 142 MET cc_start: 0.7980 (mmt) cc_final: 0.7672 (mmt) REVERT: B 503 MET cc_start: 0.8950 (ptp) cc_final: 0.8372 (ptt) REVERT: B 508 MET cc_start: 0.8619 (ptp) cc_final: 0.8283 (mtm) REVERT: B 646 TYR cc_start: 0.9148 (t80) cc_final: 0.8815 (t80) REVERT: B 698 ASN cc_start: 0.7895 (t0) cc_final: 0.7564 (t0) REVERT: C 153 GLU cc_start: 0.9244 (mp0) cc_final: 0.9042 (mp0) REVERT: C 493 PHE cc_start: 0.8419 (m-80) cc_final: 0.7798 (m-80) REVERT: D 73 MET cc_start: 0.8102 (tpt) cc_final: 0.7825 (tpp) REVERT: D 132 MET cc_start: 0.9287 (mmp) cc_final: 0.8601 (mmm) REVERT: D 134 MET cc_start: 0.8427 (pmm) cc_final: 0.7950 (pmm) REVERT: D 136 ASP cc_start: 0.8519 (t70) cc_final: 0.8264 (t0) REVERT: D 142 MET cc_start: 0.7743 (mmt) cc_final: 0.7434 (mmp) REVERT: D 698 ASN cc_start: 0.8067 (t0) cc_final: 0.7717 (t0) REVERT: D 706 MET cc_start: 0.9148 (mmm) cc_final: 0.8848 (mmt) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1197 time to fit residues: 50.3748 Evaluate side-chains 193 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 114 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 260 optimal weight: 20.0000 chunk 289 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 280 optimal weight: 0.5980 chunk 189 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.071015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.056450 restraints weight = 128846.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.057918 restraints weight = 79494.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.058899 restraints weight = 57536.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059584 restraints weight = 46185.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.060036 restraints weight = 39677.763| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22460 Z= 0.155 Angle : 0.662 13.831 30854 Z= 0.329 Chirality : 0.045 0.347 3810 Planarity : 0.004 0.062 3882 Dihedral : 7.497 89.932 3432 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.56 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.16), residues: 3072 helix: 0.69 (0.16), residues: 1136 sheet: -1.82 (0.23), residues: 452 loop : -1.76 (0.17), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 36 TYR 0.013 0.001 TYR D 287 PHE 0.023 0.002 PHE C 660 TRP 0.033 0.002 TRP D 796 HIS 0.004 0.001 HIS C 53 Details of bonding type rmsd covalent geometry : bond 0.00344 (22434) covalent geometry : angle 0.64335 (30800) SS BOND : bond 0.00477 ( 18) SS BOND : angle 2.35907 ( 36) hydrogen bonds : bond 0.03703 ( 926) hydrogen bonds : angle 4.70425 ( 2598) Misc. bond : bond 0.00230 ( 2) link_BETA1-4 : bond 0.00798 ( 2) link_BETA1-4 : angle 2.28321 ( 6) link_NAG-ASN : bond 0.00900 ( 4) link_NAG-ASN : angle 6.72289 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8511 (t0) cc_final: 0.8305 (t70) REVERT: A 493 PHE cc_start: 0.8415 (m-80) cc_final: 0.7988 (m-80) REVERT: A 523 MET cc_start: 0.8817 (mmt) cc_final: 0.8493 (mmt) REVERT: A 628 MET cc_start: 0.8351 (tmm) cc_final: 0.8090 (tmm) REVERT: B 73 MET cc_start: 0.8319 (tpt) cc_final: 0.7984 (tpp) REVERT: B 132 MET cc_start: 0.9278 (mmp) cc_final: 0.8619 (mmm) REVERT: B 134 MET cc_start: 0.8629 (pmm) cc_final: 0.8226 (pmm) REVERT: B 136 ASP cc_start: 0.8597 (t70) cc_final: 0.8277 (t0) REVERT: B 142 MET cc_start: 0.8146 (mmt) cc_final: 0.7844 (mmt) REVERT: B 503 MET cc_start: 0.8997 (ptp) cc_final: 0.8414 (ptt) REVERT: B 508 MET cc_start: 0.8684 (ptp) cc_final: 0.8282 (mtm) REVERT: B 646 TYR cc_start: 0.9152 (t80) cc_final: 0.8753 (t80) REVERT: B 698 ASN cc_start: 0.7910 (t0) cc_final: 0.7600 (t0) REVERT: C 153 GLU cc_start: 0.9270 (mp0) cc_final: 0.9063 (mp0) REVERT: C 493 PHE cc_start: 0.8426 (m-80) cc_final: 0.7797 (m-80) REVERT: D 73 MET cc_start: 0.8149 (tpt) cc_final: 0.7831 (tpp) REVERT: D 132 MET cc_start: 0.9274 (mmp) cc_final: 0.8589 (mmm) REVERT: D 134 MET cc_start: 0.8465 (pmm) cc_final: 0.7957 (pmm) REVERT: D 136 ASP cc_start: 0.8526 (t70) cc_final: 0.8265 (t0) REVERT: D 142 MET cc_start: 0.7795 (mmt) cc_final: 0.7493 (mmp) REVERT: D 698 ASN cc_start: 0.8075 (t0) cc_final: 0.7730 (t0) REVERT: D 706 MET cc_start: 0.9171 (mmm) cc_final: 0.8865 (mmt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1182 time to fit residues: 47.7277 Evaluate side-chains 193 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 308 optimal weight: 1.9990 chunk 282 optimal weight: 10.0000 chunk 272 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 164 optimal weight: 30.0000 chunk 256 optimal weight: 1.9990 chunk 262 optimal weight: 50.0000 chunk 87 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 231 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.071758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.057162 restraints weight = 127466.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.058643 restraints weight = 78951.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059636 restraints weight = 57191.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.060322 restraints weight = 45948.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060736 restraints weight = 39447.858| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22460 Z= 0.124 Angle : 0.630 13.490 30854 Z= 0.311 Chirality : 0.044 0.271 3810 Planarity : 0.004 0.063 3882 Dihedral : 7.241 84.905 3432 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.36 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.16), residues: 3072 helix: 0.84 (0.16), residues: 1130 sheet: -1.75 (0.22), residues: 476 loop : -1.66 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 692 TYR 0.013 0.001 TYR D 287 PHE 0.023 0.001 PHE C 660 TRP 0.032 0.001 TRP D 796 HIS 0.003 0.001 HIS C 53 Details of bonding type rmsd covalent geometry : bond 0.00280 (22434) covalent geometry : angle 0.61259 (30800) SS BOND : bond 0.00557 ( 18) SS BOND : angle 2.22782 ( 36) hydrogen bonds : bond 0.03484 ( 926) hydrogen bonds : angle 4.54013 ( 2598) Misc. bond : bond 0.00267 ( 2) link_BETA1-4 : bond 0.00772 ( 2) link_BETA1-4 : angle 2.22506 ( 6) link_NAG-ASN : bond 0.00897 ( 4) link_NAG-ASN : angle 6.42965 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3484.36 seconds wall clock time: 61 minutes 4.07 seconds (3664.07 seconds total)