Starting phenix.real_space_refine on Fri Jul 3 11:40:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qhh_13972/07_2026/7qhh_13972.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qhh_13972/07_2026/7qhh_13972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qhh_13972/07_2026/7qhh_13972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qhh_13972/07_2026/7qhh_13972.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qhh_13972/07_2026/7qhh_13972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qhh_13972/07_2026/7qhh_13972.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7qhh_13972/07_2026/7qhh_13972.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qhh_13972/07_2026/7qhh_13972.cif" } resolution = 3.6 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 8884 2.51 5 N 2202 2.21 5 O 2478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13626 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 2682 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 571 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 8, 'ASN:plan1': 6, 'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ARG:plan': 10, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 223 Chain: "B" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2691 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 581 Unresolved non-hydrogen dihedrals: 404 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLU:plan': 18, 'TYR:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 9, 'ASP:plan': 11, 'PHE:plan': 2, 'GLN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 222 Chain: "C" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 2682 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 571 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 8, 'ASN:plan1': 6, 'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ARG:plan': 10, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 223 Chain: "D" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2691 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 581 Unresolved non-hydrogen dihedrals: 404 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLU:plan': 18, 'TYR:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 9, 'ASP:plan': 11, 'PHE:plan': 2, 'GLN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 222 Chain: "J" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1282 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "I" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1282 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'OLC': 1, 'PAM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'79N': 1, 'PAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'OLC': 1, 'PAM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'79N': 1, 'PAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PAM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PAM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.84, per 1000 atoms: 0.21 Number of scatterers: 13626 At special positions: 0 Unit cell: (124.02, 109.18, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2478 8.00 N 2202 7.00 C 8884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.04 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.06 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.04 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.06 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=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 838.8 milliseconds 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 22 sheets defined 57.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.715A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 591 through 626 removed outlier: 3.512A pdb=" N VAL A 597 " --> pdb=" O SER A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 660 through 672 removed outlier: 3.562A pdb=" N LYS A 671 " --> pdb=" O TRP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 693 Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 738 through 753 removed outlier: 3.659A pdb=" N LEU A 747 " --> pdb=" O ASN A 743 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 767 Processing helix chain 'A' and resid 788 through 815 removed outlier: 3.711A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.792A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 488 removed outlier: 3.704A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.545A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 643 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.702A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 457 through 465 Processing helix chain 'C' and resid 478 through 484 removed outlier: 3.715A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 568 through 582 Processing helix chain 'C' and resid 591 through 626 removed outlier: 3.512A pdb=" N VAL C 597 " --> pdb=" O SER C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 649 through 658 Processing helix chain 'C' and resid 660 through 672 removed outlier: 3.561A pdb=" N LYS C 671 " --> pdb=" O TRP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 693 Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 738 through 753 removed outlier: 3.659A pdb=" N LEU C 747 " --> pdb=" O ASN C 743 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER C 750 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 767 Processing helix chain 'C' and resid 788 through 815 removed outlier: 3.710A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.792A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 488 removed outlier: 3.703A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.544A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 643 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.703A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 41 removed outlier: 3.554A pdb=" N VAL J 21 " --> pdb=" O LYS J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 128 Processing helix chain 'J' and resid 128 through 151 removed outlier: 3.652A pdb=" N ALA J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG J 149 " --> pdb=" O VAL J 145 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL J 150 " --> pdb=" O ALA J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 185 removed outlier: 3.579A pdb=" N LEU J 159 " --> pdb=" O ARG J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 234 removed outlier: 3.775A pdb=" N TYR J 206 " --> pdb=" O GLY J 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 41 removed outlier: 3.555A pdb=" N VAL I 21 " --> pdb=" O LYS I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 128 Processing helix chain 'I' and resid 128 through 151 removed outlier: 3.652A pdb=" N ALA I 146 " --> pdb=" O GLY I 142 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG I 149 " --> pdb=" O VAL I 145 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL I 150 " --> pdb=" O ALA I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 185 removed outlier: 3.579A pdb=" N LEU I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 234 removed outlier: 3.775A pdb=" N TYR I 206 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 394 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA4, first strand: chain 'A' and resid 642 through 645 removed outlier: 6.012A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 642 through 645 removed outlier: 6.012A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 395 through 398 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 removed outlier: 5.917A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 5.917A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 391 through 394 Processing sheet with id=AB3, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB4, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB5, first strand: chain 'C' and resid 642 through 645 removed outlier: 6.013A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 642 through 645 removed outlier: 6.013A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 395 through 398 Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 5.917A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 5.917A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 100 through 102 Processing sheet with id=AC4, first strand: chain 'I' and resid 100 through 102 936 hydrogen bonds defined for protein. 2766 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: 2.77 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2224 1.32 - 1.45: 3822 1.45 - 1.57: 7764 1.57 - 1.70: 0 1.70 - 1.83: 90 Bond restraints: 13900 Sorted by residual: bond pdb=" C LYS A 726 " pdb=" O LYS A 726 " ideal model delta sigma weight residual 1.234 1.282 -0.048 1.26e-02 6.30e+03 1.45e+01 bond pdb=" C LYS C 726 " pdb=" O LYS C 726 " ideal model delta sigma weight residual 1.234 1.282 -0.048 1.26e-02 6.30e+03 1.44e+01 bond pdb=" CA SER C 512 " pdb=" CB SER C 512 " ideal model delta sigma weight residual 1.532 1.472 0.060 1.65e-02 3.67e+03 1.33e+01 bond pdb=" N ILE A 485 " pdb=" CA ILE A 485 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.19e-02 7.06e+03 1.31e+01 bond pdb=" CA SER A 512 " pdb=" CB SER A 512 " ideal model delta sigma weight residual 1.532 1.472 0.060 1.65e-02 3.67e+03 1.31e+01 ... (remaining 13895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 9961 1.29 - 2.57: 5760 2.57 - 3.86: 2617 3.86 - 5.15: 579 5.15 - 6.43: 55 Bond angle restraints: 18972 Sorted by residual: angle pdb=" CA GLY B 465 " pdb=" C GLY B 465 " pdb=" O GLY B 465 " ideal model delta sigma weight residual 120.75 114.86 5.89 1.03e+00 9.43e-01 3.27e+01 angle pdb=" CA GLY D 465 " pdb=" C GLY D 465 " pdb=" O GLY D 465 " ideal model delta sigma weight residual 120.75 114.88 5.87 1.03e+00 9.43e-01 3.24e+01 angle pdb=" C VAL B 464 " pdb=" N GLY B 465 " pdb=" CA GLY B 465 " ideal model delta sigma weight residual 119.98 125.83 -5.85 1.11e+00 8.12e-01 2.78e+01 angle pdb=" C VAL D 464 " pdb=" N GLY D 465 " pdb=" CA GLY D 465 " ideal model delta sigma weight residual 119.98 125.82 -5.84 1.11e+00 8.12e-01 2.76e+01 angle pdb=" CA GLY C 495 " pdb=" C GLY C 495 " pdb=" O GLY C 495 " ideal model delta sigma weight residual 121.19 116.63 4.56 9.10e-01 1.21e+00 2.52e+01 ... (remaining 18967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.79: 7057 12.79 - 25.58: 601 25.58 - 38.37: 172 38.37 - 51.16: 52 51.16 - 63.95: 30 Dihedral angle restraints: 7912 sinusoidal: 2256 harmonic: 5656 Sorted by residual: dihedral pdb=" CB CYS D 718 " pdb=" SG CYS D 718 " pdb=" SG CYS D 773 " pdb=" CB CYS D 773 " ideal model delta sinusoidal sigma weight residual 93.00 156.95 -63.95 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 156.94 -63.94 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS A 714 " pdb=" SG CYS A 714 " pdb=" SG CYS A 769 " pdb=" CB CYS A 769 " ideal model delta sinusoidal sigma weight residual -86.00 -120.13 34.13 1 1.00e+01 1.00e-02 1.65e+01 ... (remaining 7909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 966 0.060 - 0.119: 858 0.119 - 0.178: 362 0.178 - 0.238: 50 0.238 - 0.297: 10 Chirality restraints: 2246 Sorted by residual: chirality pdb=" CA VAL D 626 " pdb=" N VAL D 626 " pdb=" C VAL D 626 " pdb=" CB VAL D 626 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA VAL B 626 " pdb=" N VAL B 626 " pdb=" C VAL B 626 " pdb=" CB VAL B 626 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ILE C 587 " pdb=" N ILE C 587 " pdb=" C ILE C 587 " pdb=" CB ILE C 587 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2243 not shown) Planarity restraints: 2414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 79N D 902 " 0.138 2.00e-02 2.50e+03 1.40e-01 1.95e+02 pdb=" C7 79N D 902 " 0.141 2.00e-02 2.50e+03 pdb=" C8 79N D 902 " -0.148 2.00e-02 2.50e+03 pdb=" C9 79N D 902 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 79N B 902 " -0.137 2.00e-02 2.50e+03 1.39e-01 1.94e+02 pdb=" C7 79N B 902 " -0.141 2.00e-02 2.50e+03 pdb=" C8 79N B 902 " 0.148 2.00e-02 2.50e+03 pdb=" C9 79N B 902 " 0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PAM I1502 " 0.143 2.00e-02 2.50e+03 1.09e-01 1.18e+02 pdb=" C11 PAM I1502 " -0.057 2.00e-02 2.50e+03 pdb=" C8 PAM I1502 " 0.057 2.00e-02 2.50e+03 pdb=" C9 PAM I1502 " -0.143 2.00e-02 2.50e+03 ... (remaining 2411 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 7267 3.02 - 3.49: 15140 3.49 - 3.96: 21572 3.96 - 4.43: 24524 4.43 - 4.90: 39208 Nonbonded interactions: 107711 Sorted by model distance: nonbonded pdb=" O TRP D 606 " pdb=" OG1 THR D 609 " model vdw 2.546 3.040 nonbonded pdb=" O TRP B 606 " pdb=" OG1 THR B 609 " model vdw 2.546 3.040 nonbonded pdb=" O GLN J 20 " pdb=" OG1 THR J 24 " model vdw 2.569 3.040 nonbonded pdb=" O GLN I 20 " pdb=" OG1 THR I 24 " model vdw 2.569 3.040 nonbonded pdb=" N ILE A 587 " pdb=" O ILE A 587 " model vdw 2.569 2.496 ... (remaining 107706 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'J' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.570 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 : 0.014 0.060 13908 Z= 1.066 Angle : 1.829 6.433 18988 Z= 1.428 Chirality : 0.090 0.297 2246 Planarity : 0.010 0.140 2414 Dihedral : 12.100 59.203 4276 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 0.31 % Favored : 99.59 % Rotamer: Outliers : 0.19 % Allowed : 2.64 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.83 (0.17), residues: 1942 helix: -0.13 (0.14), residues: 1094 sheet: -0.52 (0.39), residues: 168 loop : -1.05 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 694 TYR 0.046 0.006 TYR B 732 PHE 0.036 0.005 PHE A 537 TRP 0.040 0.008 TRP B 766 HIS 0.004 0.002 HIS J 198 Details of bonding type rmsd/Z covalent geometry : bond 0.01402 / 1.07 (13900) covalent geometry : angle 1.82936 / 1.43 (18972) SS BOND : bond 0.01315 / 0.99 ( 8) SS BOND : angle 1.95171 / 1.21 ( 16) hydrogen bonds : bond 0.18419 / 12.83 ( 920) hydrogen bonds : angle 7.05859 / 5.21 ( 2766) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 374 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 THR cc_start: 0.6900 (p) cc_final: 0.6577 (t) REVERT: A 581 MET cc_start: 0.8199 (mmt) cc_final: 0.7845 (mmt) REVERT: A 646 LEU cc_start: 0.8022 (tp) cc_final: 0.7560 (mt) REVERT: A 663 PHE cc_start: 0.8822 (m-80) cc_final: 0.8581 (m-80) REVERT: A 678 PHE cc_start: 0.7432 (m-80) cc_final: 0.7151 (m-80) REVERT: A 705 ASN cc_start: 0.7677 (t0) cc_final: 0.6990 (t0) REVERT: B 704 LEU cc_start: 0.8572 (pt) cc_final: 0.8111 (tp) REVERT: B 764 ASN cc_start: 0.7113 (m-40) cc_final: 0.6598 (m-40) REVERT: B 769 ASP cc_start: 0.8477 (m-30) cc_final: 0.7695 (m-30) REVERT: C 416 ARG cc_start: 0.6802 (ttp-170) cc_final: 0.5769 (tpt90) REVERT: C 478 THR cc_start: 0.6917 (p) cc_final: 0.6598 (t) REVERT: C 581 MET cc_start: 0.8198 (mmt) cc_final: 0.7857 (mmt) REVERT: C 646 LEU cc_start: 0.8087 (tp) cc_final: 0.7656 (mt) REVERT: C 663 PHE cc_start: 0.8806 (m-80) cc_final: 0.8558 (m-80) REVERT: C 678 PHE cc_start: 0.7512 (m-80) cc_final: 0.7199 (m-80) REVERT: C 705 ASN cc_start: 0.7573 (t0) cc_final: 0.6767 (t0) REVERT: D 658 PHE cc_start: 0.7386 (t80) cc_final: 0.7178 (t80) REVERT: D 661 ARG cc_start: 0.8645 (ptt180) cc_final: 0.8411 (ptt90) REVERT: D 704 LEU cc_start: 0.8567 (pt) cc_final: 0.8079 (tp) REVERT: D 764 ASN cc_start: 0.7028 (m-40) cc_final: 0.6542 (m-40) REVERT: D 769 ASP cc_start: 0.8467 (m-30) cc_final: 0.7707 (m-30) outliers start: 2 outliers final: 0 residues processed: 374 average time/residue: 0.1188 time to fit residues: 64.1212 Evaluate side-chains 243 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 HIS I 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.201944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.162589 restraints weight = 20329.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.150627 restraints weight = 26570.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.149903 restraints weight = 27697.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.150128 restraints weight = 22717.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.149234 restraints weight = 20146.053| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 13908 Z= 0.287 Angle : 0.612 7.481 18988 Z= 0.326 Chirality : 0.043 0.205 2246 Planarity : 0.004 0.040 2414 Dihedral : 8.746 59.925 2276 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.26 % Allowed : 12.83 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.54 (0.19), residues: 1942 helix: 2.26 (0.15), residues: 1136 sheet: -0.90 (0.36), residues: 196 loop : -0.70 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 125 TYR 0.019 0.002 TYR J 201 PHE 0.023 0.002 PHE A 527 TRP 0.033 0.003 TRP D 766 HIS 0.006 0.002 HIS J 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.29 (13900) covalent geometry : angle 0.61121 / 0.33 (18972) SS BOND : bond 0.00470 / 0.35 ( 8) SS BOND : angle 1.31026 / 0.82 ( 16) hydrogen bonds : bond 0.04477 / 3.13 ( 920) hydrogen bonds : angle 4.56916 / 3.41 ( 2766) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 ASN cc_start: 0.7794 (t0) cc_final: 0.7510 (t0) REVERT: A 646 LEU cc_start: 0.7652 (tp) cc_final: 0.7339 (mt) REVERT: A 663 PHE cc_start: 0.7444 (m-80) cc_final: 0.7229 (m-80) REVERT: B 813 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7548 (mm-30) REVERT: C 571 ASN cc_start: 0.7801 (t0) cc_final: 0.7561 (t0) REVERT: C 572 SER cc_start: 0.8883 (m) cc_final: 0.8536 (t) REVERT: C 646 LEU cc_start: 0.7671 (tp) cc_final: 0.7358 (mt) REVERT: D 694 ARG cc_start: 0.7528 (mtt90) cc_final: 0.7309 (ttm110) REVERT: D 813 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7569 (mm-30) outliers start: 24 outliers final: 16 residues processed: 276 average time/residue: 0.0989 time to fit residues: 41.1969 Evaluate side-chains 256 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain C residue 787 ASN Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 143 VAL Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 144 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 29 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 91 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 64 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.204792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.168526 restraints weight = 20544.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.159510 restraints weight = 26830.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.156567 restraints weight = 26551.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.156818 restraints weight = 24446.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.156892 restraints weight = 19430.863| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13908 Z= 0.118 Angle : 0.481 7.301 18988 Z= 0.255 Chirality : 0.039 0.136 2246 Planarity : 0.004 0.043 2414 Dihedral : 7.742 59.655 2276 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.79 % Allowed : 15.38 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 2.17 (0.19), residues: 1942 helix: 2.92 (0.15), residues: 1126 sheet: -0.90 (0.37), residues: 186 loop : -0.62 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 661 TYR 0.023 0.001 TYR I 226 PHE 0.012 0.001 PHE J 130 TRP 0.047 0.002 TRP D 766 HIS 0.003 0.001 HIS J 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (13900) covalent geometry : angle 0.48032 / 0.25 (18972) SS BOND : bond 0.00280 / 0.20 ( 8) SS BOND : angle 1.05035 / 0.67 ( 16) hydrogen bonds : bond 0.03531 / 2.45 ( 920) hydrogen bonds : angle 3.96403 / 2.94 ( 2766) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 265 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 541 PHE cc_start: 0.7581 (t80) cc_final: 0.7293 (t80) REVERT: B 813 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7517 (mm-30) REVERT: C 571 ASN cc_start: 0.7871 (t0) cc_final: 0.7653 (t0) REVERT: D 721 MET cc_start: 0.7387 (ptp) cc_final: 0.7069 (ptt) REVERT: D 813 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7506 (mm-30) outliers start: 19 outliers final: 10 residues processed: 278 average time/residue: 0.0992 time to fit residues: 42.3292 Evaluate side-chains 250 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 240 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain I residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 23 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 192 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 chunk 120 optimal weight: 20.0000 chunk 178 optimal weight: 0.8980 chunk 44 optimal weight: 30.0000 chunk 194 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 ASN ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 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 = 0.4490 r_free = 0.4490 target = 0.204118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.168092 restraints weight = 20473.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.157608 restraints weight = 26474.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.154540 restraints weight = 29226.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153613 restraints weight = 24801.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.150309 restraints weight = 25621.462| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13908 Z= 0.131 Angle : 0.489 7.448 18988 Z= 0.256 Chirality : 0.039 0.143 2246 Planarity : 0.003 0.045 2414 Dihedral : 7.239 59.022 2276 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 3.21 % Allowed : 15.09 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 2.12 (0.19), residues: 1942 helix: 2.87 (0.15), residues: 1126 sheet: -1.28 (0.38), residues: 182 loop : -0.52 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 661 TYR 0.027 0.001 TYR I 226 PHE 0.020 0.001 PHE I 165 TRP 0.020 0.001 TRP B 766 HIS 0.001 0.001 HIS J 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (13900) covalent geometry : angle 0.48883 / 0.26 (18972) SS BOND : bond 0.00280 / 0.21 ( 8) SS BOND : angle 0.94743 / 0.60 ( 16) hydrogen bonds : bond 0.03434 / 2.40 ( 920) hydrogen bonds : angle 3.87343 / 2.88 ( 2766) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 808 ILE cc_start: 0.8713 (mm) cc_final: 0.8465 (mt) REVERT: B 813 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7632 (mm-30) REVERT: C 663 PHE cc_start: 0.7368 (m-80) cc_final: 0.7114 (m-80) REVERT: C 808 ILE cc_start: 0.8807 (mm) cc_final: 0.8596 (mt) REVERT: D 721 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7099 (ptt) REVERT: D 813 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7614 (mm-30) outliers start: 34 outliers final: 23 residues processed: 274 average time/residue: 0.1019 time to fit residues: 42.2691 Evaluate side-chains 264 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 787 ASN Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 164 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 11 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 123 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 12 optimal weight: 0.0570 chunk 95 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.204947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.168741 restraints weight = 20682.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.158929 restraints weight = 28933.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.156182 restraints weight = 25071.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.154586 restraints weight = 22996.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.152593 restraints weight = 22169.023| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13908 Z= 0.116 Angle : 0.475 7.176 18988 Z= 0.251 Chirality : 0.039 0.130 2246 Planarity : 0.003 0.046 2414 Dihedral : 6.704 56.058 2276 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.55 % Allowed : 17.36 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 2.15 (0.19), residues: 1942 helix: 2.88 (0.15), residues: 1130 sheet: -1.30 (0.38), residues: 182 loop : -0.49 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 661 TYR 0.028 0.001 TYR J 226 PHE 0.021 0.001 PHE I 165 TRP 0.017 0.001 TRP C 762 HIS 0.002 0.001 HIS J 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (13900) covalent geometry : angle 0.47486 / 0.25 (18972) SS BOND : bond 0.00237 / 0.18 ( 8) SS BOND : angle 0.91696 / 0.59 ( 16) hydrogen bonds : bond 0.03252 / 2.27 ( 920) hydrogen bonds : angle 3.80526 / 2.83 ( 2766) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 808 ILE cc_start: 0.8768 (mm) cc_final: 0.8527 (mt) REVERT: B 408 MET cc_start: 0.6337 (mmp) cc_final: 0.6105 (mmp) REVERT: B 813 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7566 (mm-30) REVERT: C 663 PHE cc_start: 0.7299 (m-80) cc_final: 0.7032 (m-80) REVERT: C 808 ILE cc_start: 0.8819 (mm) cc_final: 0.8606 (mt) REVERT: D 721 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7078 (ptt) REVERT: D 813 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7577 (mm-30) outliers start: 27 outliers final: 15 residues processed: 263 average time/residue: 0.0930 time to fit residues: 37.8219 Evaluate side-chains 256 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 164 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 104 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 7 optimal weight: 0.0770 chunk 75 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.202752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.157875 restraints weight = 20271.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145002 restraints weight = 26730.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139705 restraints weight = 26382.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140748 restraints weight = 24358.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.141471 restraints weight = 18358.786| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13908 Z= 0.155 Angle : 0.506 8.380 18988 Z= 0.261 Chirality : 0.039 0.138 2246 Planarity : 0.003 0.047 2414 Dihedral : 6.723 55.739 2276 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.83 % Allowed : 17.45 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.99 (0.19), residues: 1942 helix: 2.74 (0.15), residues: 1132 sheet: -1.39 (0.37), residues: 182 loop : -0.50 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 661 TYR 0.031 0.001 TYR I 226 PHE 0.014 0.001 PHE I 165 TRP 0.019 0.001 TRP C 762 HIS 0.003 0.001 HIS I 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (13900) covalent geometry : angle 0.50521 / 0.26 (18972) SS BOND : bond 0.00250 / 0.18 ( 8) SS BOND : angle 0.88133 / 0.56 ( 16) hydrogen bonds : bond 0.03316 / 2.31 ( 920) hydrogen bonds : angle 3.83856 / 2.85 ( 2766) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 808 ILE cc_start: 0.8686 (mm) cc_final: 0.8482 (mt) REVERT: B 408 MET cc_start: 0.6749 (mmp) cc_final: 0.6549 (mmp) REVERT: B 813 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7694 (mm-30) REVERT: C 572 SER cc_start: 0.8812 (m) cc_final: 0.8487 (t) REVERT: D 460 TRP cc_start: 0.5918 (m-90) cc_final: 0.5713 (m-90) REVERT: D 721 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7255 (ptt) REVERT: D 813 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7700 (mm-30) outliers start: 30 outliers final: 24 residues processed: 273 average time/residue: 0.0997 time to fit residues: 42.2769 Evaluate side-chains 266 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 787 ASN Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 162 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 149 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 chunk 181 optimal weight: 6.9990 chunk 122 optimal weight: 30.0000 chunk 183 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 705 ASN C 705 ASN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.197964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.156019 restraints weight = 20510.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.145572 restraints weight = 24867.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142928 restraints weight = 25299.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.143825 restraints weight = 23264.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.142971 restraints weight = 20746.417| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 13908 Z= 0.380 Angle : 0.684 10.389 18988 Z= 0.355 Chirality : 0.045 0.195 2246 Planarity : 0.004 0.047 2414 Dihedral : 7.963 57.536 2276 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.15 % Allowed : 16.98 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.16 (0.19), residues: 1942 helix: 1.92 (0.15), residues: 1140 sheet: -1.05 (0.39), residues: 160 loop : -0.82 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 125 TYR 0.037 0.002 TYR I 226 PHE 0.029 0.003 PHE A 678 TRP 0.014 0.002 TRP I 44 HIS 0.010 0.003 HIS I 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00913 / 0.38 (13900) covalent geometry : angle 0.68380 / 0.36 (18972) SS BOND : bond 0.00441 / 0.31 ( 8) SS BOND : angle 1.16101 / 0.70 ( 16) hydrogen bonds : bond 0.04323 / 3.00 ( 920) hydrogen bonds : angle 4.55677 / 3.38 ( 2766) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8619 (t) REVERT: A 693 LYS cc_start: 0.6678 (mmmm) cc_final: 0.6396 (mmmm) REVERT: B 408 MET cc_start: 0.6425 (mmp) cc_final: 0.6167 (mmp) REVERT: B 767 TRP cc_start: 0.6634 (m-90) cc_final: 0.5815 (t-100) REVERT: C 693 LYS cc_start: 0.6640 (mmmm) cc_final: 0.6371 (mmmm) REVERT: D 408 MET cc_start: 0.6097 (mmp) cc_final: 0.5837 (mmp) REVERT: D 721 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7412 (ptt) REVERT: D 767 TRP cc_start: 0.6583 (m-90) cc_final: 0.5681 (t-100) REVERT: I 226 TYR cc_start: 0.8085 (t80) cc_final: 0.7868 (t80) outliers start: 44 outliers final: 33 residues processed: 270 average time/residue: 0.1036 time to fit residues: 43.3173 Evaluate side-chains 262 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 787 ASN Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 89 optimal weight: 30.0000 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 30.0000 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 178 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 ASN C 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.202181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.157816 restraints weight = 20241.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 79)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143256 restraints weight = 26004.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.141696 restraints weight = 27883.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.143115 restraints weight = 25526.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.143833 restraints weight = 19662.514| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13908 Z= 0.138 Angle : 0.543 8.869 18988 Z= 0.272 Chirality : 0.040 0.195 2246 Planarity : 0.003 0.047 2414 Dihedral : 7.273 57.737 2276 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.92 % Allowed : 19.81 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.62 (0.19), residues: 1942 helix: 2.42 (0.15), residues: 1128 sheet: -1.02 (0.40), residues: 160 loop : -0.80 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 661 TYR 0.032 0.001 TYR J 226 PHE 0.016 0.001 PHE J 165 TRP 0.034 0.002 TRP B 766 HIS 0.001 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (13900) covalent geometry : angle 0.54258 / 0.27 (18972) SS BOND : bond 0.00229 / 0.16 ( 8) SS BOND : angle 1.03742 / 0.67 ( 16) hydrogen bonds : bond 0.03357 / 2.32 ( 920) hydrogen bonds : angle 4.04852 / 3.00 ( 2766) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8493 (t) REVERT: A 808 ILE cc_start: 0.8783 (mm) cc_final: 0.8559 (mt) REVERT: B 767 TRP cc_start: 0.6708 (m-90) cc_final: 0.5837 (t-100) REVERT: B 813 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7758 (mm-30) REVERT: C 572 SER cc_start: 0.8752 (m) cc_final: 0.8455 (t) REVERT: D 408 MET cc_start: 0.6552 (mmp) cc_final: 0.6330 (mmp) REVERT: D 721 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7328 (ptt) REVERT: D 767 TRP cc_start: 0.6703 (m-90) cc_final: 0.5797 (t-100) REVERT: D 769 ASP cc_start: 0.6862 (m-30) cc_final: 0.6476 (m-30) outliers start: 31 outliers final: 22 residues processed: 256 average time/residue: 0.1008 time to fit residues: 39.7025 Evaluate side-chains 254 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 164 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 12 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 126 optimal weight: 30.0000 chunk 83 optimal weight: 10.0000 chunk 173 optimal weight: 0.5980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.200888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.155801 restraints weight = 20351.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.145504 restraints weight = 26162.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.143686 restraints weight = 23994.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.143675 restraints weight = 21022.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.143301 restraints weight = 18427.810| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13908 Z= 0.204 Angle : 0.581 8.822 18988 Z= 0.295 Chirality : 0.042 0.216 2246 Planarity : 0.004 0.047 2414 Dihedral : 7.021 59.398 2276 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.21 % Allowed : 20.09 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.51 (0.19), residues: 1942 helix: 2.33 (0.15), residues: 1128 sheet: -1.14 (0.40), residues: 160 loop : -0.82 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 661 TYR 0.035 0.002 TYR J 226 PHE 0.017 0.002 PHE J 165 TRP 0.043 0.002 TRP B 766 HIS 0.003 0.001 HIS I 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.20 (13900) covalent geometry : angle 0.58009 / 0.29 (18972) SS BOND : bond 0.00342 / 0.25 ( 8) SS BOND : angle 1.24554 / 0.80 ( 16) hydrogen bonds : bond 0.03554 / 2.46 ( 920) hydrogen bonds : angle 4.14028 / 3.06 ( 2766) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8887 (OUTLIER) cc_final: 0.8577 (t) REVERT: A 808 ILE cc_start: 0.8823 (mm) cc_final: 0.8596 (mt) REVERT: B 767 TRP cc_start: 0.6609 (m-90) cc_final: 0.5809 (t-100) REVERT: B 813 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 572 SER cc_start: 0.8820 (m) cc_final: 0.8556 (t) REVERT: D 408 MET cc_start: 0.6224 (mmp) cc_final: 0.5945 (mmp) REVERT: D 721 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7443 (ptt) REVERT: D 767 TRP cc_start: 0.6508 (m-90) cc_final: 0.5702 (t-100) REVERT: D 769 ASP cc_start: 0.6749 (m-30) cc_final: 0.6376 (m-30) REVERT: I 226 TYR cc_start: 0.8095 (t80) cc_final: 0.7880 (t80) outliers start: 34 outliers final: 27 residues processed: 254 average time/residue: 0.1000 time to fit residues: 39.0485 Evaluate side-chains 255 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 166 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 193 optimal weight: 0.9990 chunk 45 optimal weight: 0.0970 chunk 42 optimal weight: 4.9990 chunk 86 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 ASN C 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.200518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154664 restraints weight = 20332.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143106 restraints weight = 25559.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140849 restraints weight = 23009.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.140536 restraints weight = 18747.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.140142 restraints weight = 17379.165| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13908 Z= 0.216 Angle : 0.587 8.668 18988 Z= 0.299 Chirality : 0.042 0.203 2246 Planarity : 0.004 0.047 2414 Dihedral : 7.120 58.632 2276 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.92 % Allowed : 20.47 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.44 (0.19), residues: 1942 helix: 2.25 (0.15), residues: 1128 sheet: -1.23 (0.43), residues: 138 loop : -0.82 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 416 TYR 0.034 0.002 TYR J 226 PHE 0.015 0.002 PHE C 580 TRP 0.042 0.002 TRP D 766 HIS 0.003 0.001 HIS I 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (13900) covalent geometry : angle 0.58611 / 0.30 (18972) SS BOND : bond 0.00336 / 0.25 ( 8) SS BOND : angle 1.11618 / 0.71 ( 16) hydrogen bonds : bond 0.03590 / 2.48 ( 920) hydrogen bonds : angle 4.18399 / 3.10 ( 2766) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8594 (t) REVERT: A 808 ILE cc_start: 0.8828 (mm) cc_final: 0.8586 (mt) REVERT: B 767 TRP cc_start: 0.6543 (m-90) cc_final: 0.5654 (t-100) REVERT: B 813 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7811 (mm-30) REVERT: C 572 SER cc_start: 0.8823 (m) cc_final: 0.8570 (t) REVERT: D 408 MET cc_start: 0.6285 (mmp) cc_final: 0.5906 (mmp) REVERT: D 721 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7411 (ptt) REVERT: D 767 TRP cc_start: 0.6588 (m-90) cc_final: 0.5695 (t-100) REVERT: I 226 TYR cc_start: 0.8073 (t80) cc_final: 0.7864 (t80) outliers start: 31 outliers final: 29 residues processed: 251 average time/residue: 0.1036 time to fit residues: 40.1994 Evaluate side-chains 261 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 787 ASN Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 33 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 173 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 92 optimal weight: 0.3980 chunk 127 optimal weight: 7.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 ASN ** I 83 HIS ** 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 = 0.4447 r_free = 0.4447 target = 0.199737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.155972 restraints weight = 20390.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.144553 restraints weight = 25820.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.142670 restraints weight = 25163.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142636 restraints weight = 20605.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142045 restraints weight = 19244.566| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 13908 Z= 0.268 Angle : 0.623 9.130 18988 Z= 0.318 Chirality : 0.043 0.193 2246 Planarity : 0.004 0.047 2414 Dihedral : 7.445 59.560 2276 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.11 % Allowed : 20.66 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.30 (0.19), residues: 1942 helix: 2.11 (0.15), residues: 1126 sheet: -1.02 (0.47), residues: 118 loop : -0.91 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 661 TYR 0.045 0.002 TYR I 179 PHE 0.019 0.002 PHE J 165 TRP 0.044 0.002 TRP D 766 HIS 0.005 0.002 HIS I 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.27 (13900) covalent geometry : angle 0.62219 / 0.32 (18972) SS BOND : bond 0.00369 / 0.27 ( 8) SS BOND : angle 1.09162 / 0.68 ( 16) hydrogen bonds : bond 0.03797 / 2.63 ( 920) hydrogen bonds : angle 4.31344 / 3.19 ( 2766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.33 seconds wall clock time: 40 minutes 52.51 seconds (2452.51 seconds total)