Starting phenix.real_space_refine on Wed Mar 4 13:30:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qhh_13972/03_2026/7qhh_13972.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qhh_13972/03_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_13972/03_2026/7qhh_13972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qhh_13972/03_2026/7qhh_13972.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qhh_13972/03_2026/7qhh_13972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qhh_13972/03_2026/7qhh_13972.map" } 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-5986/lib/python3.9/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: 3.07, per 1000 atoms: 0.23 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: 1.31 Conformation dependent library (CDL) restraints added in 537.3 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: 0.40 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: 2.39 Time building geometry restraints manager: 1.68 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 - 25.86: 7674 25.86 - 51.72: 228 51.72 - 77.58: 26 77.58 - 103.45: 4 103.45 - 129.31: 4 Dihedral angle restraints: 7936 sinusoidal: 2280 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=" C24 OLC A 903 " pdb=" C21 OLC A 903 " pdb=" C22 OLC A 903 " pdb=" O20 OLC A 903 " ideal model delta sinusoidal sigma weight residual 182.78 53.47 129.31 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 7933 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: 0.02 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.500 Find NCS groups from input model: 0.100 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 : 13.085 129.307 4300 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 covalent geometry : bond 0.01402 (13900) covalent geometry : angle 1.82936 (18972) SS BOND : bond 0.01315 ( 8) SS BOND : angle 1.95171 ( 16) hydrogen bonds : bond 0.18419 ( 920) hydrogen bonds : angle 7.05859 ( 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 : 0.396 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: 0.1185 time to fit residues: 63.2650 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 : 0.490 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4464 r_free = 0.4464 target = 0.201805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.162692 restraints weight = 20360.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.155022 restraints weight = 25784.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.153100 restraints weight = 22611.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.152081 restraints weight = 20968.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.151604 restraints weight = 20731.856| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 13908 Z= 0.290 Angle : 0.622 7.475 18988 Z= 0.329 Chirality : 0.043 0.206 2246 Planarity : 0.004 0.039 2414 Dihedral : 9.517 60.800 2300 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.36 % Allowed : 12.83 % Favored : 84.81 % 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: 1.50 (0.19), residues: 1942 helix: 2.24 (0.15), residues: 1136 sheet: -0.94 (0.36), residues: 196 loop : -0.71 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 125 TYR 0.020 0.002 TYR J 201 PHE 0.025 0.002 PHE C 527 TRP 0.032 0.003 TRP D 766 HIS 0.006 0.002 HIS J 105 Details of bonding type rmsd covalent geometry : bond 0.00697 (13900) covalent geometry : angle 0.62134 (18972) SS BOND : bond 0.00457 ( 8) SS BOND : angle 1.34411 ( 16) hydrogen bonds : bond 0.04424 ( 920) hydrogen bonds : angle 4.54816 ( 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 279 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 254 time to evaluate : 0.382 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: 0.7890 (t0) cc_final: 0.7626 (t0) REVERT: A 572 SER cc_start: 0.8915 (m) cc_final: 0.8628 (t) REVERT: A 646 LEU cc_start: 0.7529 (tp) cc_final: 0.7263 (mt) REVERT: B 813 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7567 (mm-30) REVERT: C 571 ASN cc_start: 0.7884 (t0) cc_final: 0.7616 (t0) REVERT: C 572 SER cc_start: 0.8922 (m) cc_final: 0.8628 (t) REVERT: C 646 LEU cc_start: 0.7557 (tp) cc_final: 0.7282 (mt) REVERT: D 813 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7589 (mm-30) outliers start: 25 outliers final: 18 residues processed: 271 average time/residue: 0.1018 time to fit residues: 41.3149 Evaluate side-chains 257 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 239 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 431 GLU 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 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: 10.0000 chunk 171 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 0.0270 chunk 42 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4500 r_free = 0.4500 target = 0.205246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.166654 restraints weight = 20623.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.154673 restraints weight = 26864.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.153880 restraints weight = 25049.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.153502 restraints weight = 22342.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.152962 restraints weight = 20184.911| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13908 Z= 0.112 Angle : 0.482 7.510 18988 Z= 0.255 Chirality : 0.039 0.137 2246 Planarity : 0.004 0.043 2414 Dihedral : 8.376 59.559 2300 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.60 % Allowed : 15.66 % Favored : 82.74 % 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: 2.20 (0.19), residues: 1942 helix: 2.95 (0.15), residues: 1126 sheet: -0.90 (0.38), residues: 186 loop : -0.61 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 661 TYR 0.025 0.001 TYR J 226 PHE 0.013 0.001 PHE J 130 TRP 0.044 0.002 TRP D 766 HIS 0.003 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00237 (13900) covalent geometry : angle 0.48121 (18972) SS BOND : bond 0.00278 ( 8) SS BOND : angle 1.03769 ( 16) hydrogen bonds : bond 0.03523 ( 920) hydrogen bonds : angle 3.92117 ( 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: 17 poor density : 267 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 ASN cc_start: 0.7843 (t0) cc_final: 0.7624 (t0) REVERT: B 541 PHE cc_start: 0.7619 (t80) cc_final: 0.7313 (t80) REVERT: B 813 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7585 (mm-30) REVERT: C 571 ASN cc_start: 0.7840 (t0) cc_final: 0.7622 (t0) REVERT: D 721 MET cc_start: 0.7404 (ptp) cc_final: 0.7027 (ptt) REVERT: D 813 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7568 (mm-30) outliers start: 17 outliers final: 10 residues processed: 278 average time/residue: 0.0973 time to fit residues: 41.0671 Evaluate side-chains 249 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 239 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 658 PHE Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 586 ASP 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: 4.9990 chunk 96 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 44 optimal weight: 30.0000 chunk 194 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN C 705 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.199291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.156450 restraints weight = 20428.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146170 restraints weight = 26971.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.143795 restraints weight = 26594.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.144153 restraints weight = 23520.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.143490 restraints weight = 22183.997| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 13908 Z= 0.321 Angle : 0.618 7.696 18988 Z= 0.322 Chirality : 0.043 0.189 2246 Planarity : 0.004 0.045 2414 Dihedral : 8.925 57.886 2300 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 4.34 % Allowed : 15.47 % Favored : 80.19 % 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: 1.50 (0.19), residues: 1942 helix: 2.26 (0.15), residues: 1140 sheet: -1.31 (0.36), residues: 196 loop : -0.66 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 661 TYR 0.030 0.002 TYR I 226 PHE 0.024 0.002 PHE J 165 TRP 0.018 0.002 TRP B 766 HIS 0.005 0.002 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00773 (13900) covalent geometry : angle 0.61722 (18972) SS BOND : bond 0.00422 ( 8) SS BOND : angle 1.12134 ( 16) hydrogen bonds : bond 0.04112 ( 920) hydrogen bonds : angle 4.38046 ( 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 301 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8886 (m) cc_final: 0.8612 (t) REVERT: B 408 MET cc_start: 0.6806 (OUTLIER) cc_final: 0.6530 (mmp) REVERT: B 813 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7763 (mm-30) REVERT: C 572 SER cc_start: 0.8851 (m) cc_final: 0.8572 (t) REVERT: D 721 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7379 (ptt) REVERT: D 813 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7761 (mm-30) outliers start: 46 outliers final: 33 residues processed: 279 average time/residue: 0.0990 time to fit residues: 42.3727 Evaluate side-chains 271 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 533 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 A residue 787 ASN Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 708 MET 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 684 GLU Chi-restraints excluded: chain C residue 787 ASN Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 484 VAL 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 24 THR 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 24 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 11 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 103 optimal weight: 0.0050 chunk 60 optimal weight: 0.5980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4481 r_free = 0.4481 target = 0.203069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.156743 restraints weight = 20493.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143174 restraints weight = 26869.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136931 restraints weight = 23540.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.138645 restraints weight = 18849.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.139073 restraints weight = 15555.695| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13908 Z= 0.114 Angle : 0.501 7.638 18988 Z= 0.257 Chirality : 0.039 0.150 2246 Planarity : 0.003 0.048 2414 Dihedral : 7.690 58.004 2300 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.83 % Allowed : 18.21 % Favored : 78.96 % 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: 1.90 (0.19), residues: 1942 helix: 2.68 (0.15), residues: 1128 sheet: -1.43 (0.37), residues: 182 loop : -0.55 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 661 TYR 0.028 0.001 TYR J 226 PHE 0.019 0.001 PHE I 165 TRP 0.016 0.001 TRP D 460 HIS 0.001 0.001 HIS J 105 Details of bonding type rmsd covalent geometry : bond 0.00254 (13900) covalent geometry : angle 0.50069 (18972) SS BOND : bond 0.00246 ( 8) SS BOND : angle 0.95652 ( 16) hydrogen bonds : bond 0.03301 ( 920) hydrogen bonds : angle 3.94628 ( 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 267 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 808 ILE cc_start: 0.8655 (mm) cc_final: 0.8451 (mt) REVERT: B 408 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6746 (mmp) REVERT: B 721 MET cc_start: 0.7674 (ptt) cc_final: 0.7396 (ptt) REVERT: B 813 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7750 (mm-30) REVERT: D 408 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6495 (mmp) REVERT: D 661 ARG cc_start: 0.8022 (ptt90) cc_final: 0.7780 (ppt170) REVERT: D 721 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7515 (ptt) REVERT: D 813 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7752 (mm-30) REVERT: D 901 GLU cc_start: 0.5246 (pt0) cc_final: 0.4036 (mm-30) outliers start: 30 outliers final: 17 residues processed: 253 average time/residue: 0.0913 time to fit residues: 36.0963 Evaluate side-chains 247 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 655 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain D residue 408 MET 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 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 84 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 104 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 7 optimal weight: 0.0670 chunk 75 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 105 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.201341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.157822 restraints weight = 20288.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.149274 restraints weight = 25999.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146572 restraints weight = 23945.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.147171 restraints weight = 23670.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.146000 restraints weight = 18269.978| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13908 Z= 0.165 Angle : 0.510 7.712 18988 Z= 0.267 Chirality : 0.040 0.148 2246 Planarity : 0.004 0.069 2414 Dihedral : 7.440 58.603 2300 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.55 % Allowed : 18.96 % Favored : 78.49 % 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: 1.78 (0.19), residues: 1942 helix: 2.56 (0.15), residues: 1128 sheet: -1.12 (0.40), residues: 164 loop : -0.70 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 661 TYR 0.032 0.002 TYR I 226 PHE 0.037 0.002 PHE I 165 TRP 0.019 0.001 TRP A 762 HIS 0.003 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00390 (13900) covalent geometry : angle 0.50933 (18972) SS BOND : bond 0.00275 ( 8) SS BOND : angle 0.94982 ( 16) hydrogen bonds : bond 0.03418 ( 920) hydrogen bonds : angle 4.00058 ( 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 270 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8798 (m) cc_final: 0.8507 (t) REVERT: A 808 ILE cc_start: 0.8820 (mm) cc_final: 0.8602 (mt) REVERT: B 408 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6416 (mmp) REVERT: B 721 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7173 (ptt) REVERT: B 813 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7723 (mm-30) REVERT: C 572 SER cc_start: 0.8779 (m) cc_final: 0.8493 (t) REVERT: C 808 ILE cc_start: 0.8823 (mm) cc_final: 0.8614 (mt) REVERT: D 408 MET cc_start: 0.6377 (mmp) cc_final: 0.6042 (mmp) REVERT: D 721 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7323 (ptt) REVERT: D 813 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7727 (mm-30) outliers start: 27 outliers final: 16 residues processed: 260 average time/residue: 0.0899 time to fit residues: 36.7382 Evaluate side-chains 256 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 237 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 684 GLU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 162 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 122 optimal weight: 30.0000 chunk 183 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.199168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.152938 restraints weight = 20370.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140725 restraints weight = 24889.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.138935 restraints weight = 25569.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.138982 restraints weight = 21865.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.137703 restraints weight = 19828.503| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13908 Z= 0.260 Angle : 0.578 7.141 18988 Z= 0.303 Chirality : 0.042 0.173 2246 Planarity : 0.004 0.048 2414 Dihedral : 7.847 59.270 2300 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.30 % Allowed : 19.43 % 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: 1.49 (0.19), residues: 1942 helix: 2.27 (0.15), residues: 1140 sheet: -0.85 (0.43), residues: 140 loop : -0.92 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 125 TYR 0.037 0.002 TYR J 226 PHE 0.036 0.002 PHE I 165 TRP 0.020 0.002 TRP C 762 HIS 0.005 0.002 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00628 (13900) covalent geometry : angle 0.57755 (18972) SS BOND : bond 0.00394 ( 8) SS BOND : angle 1.03278 ( 16) hydrogen bonds : bond 0.03779 ( 920) hydrogen bonds : angle 4.25913 ( 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 274 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8855 (m) cc_final: 0.8642 (t) REVERT: A 693 LYS cc_start: 0.6643 (mmmm) cc_final: 0.6379 (mmmm) REVERT: B 408 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.5926 (mmp) REVERT: B 721 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7512 (ptt) REVERT: B 767 TRP cc_start: 0.6702 (m-90) cc_final: 0.5847 (t-100) REVERT: B 813 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7805 (mm-30) REVERT: C 572 SER cc_start: 0.8849 (m) cc_final: 0.8633 (t) REVERT: C 693 LYS cc_start: 0.6641 (mmmm) cc_final: 0.6394 (mmmm) REVERT: D 408 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.6002 (mmp) REVERT: D 721 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7449 (ptt) REVERT: D 767 TRP cc_start: 0.6704 (m-90) cc_final: 0.5755 (t-100) outliers start: 35 outliers final: 27 residues processed: 257 average time/residue: 0.0981 time to fit residues: 39.0332 Evaluate side-chains 256 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 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 408 MET Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 721 MET 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 684 GLU Chi-restraints excluded: chain D residue 408 MET 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 24 THR 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 24 THR 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 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: 8.9990 chunk 14 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.198502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.155990 restraints weight = 20110.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.151895 restraints weight = 25809.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.149874 restraints weight = 23631.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.142452 restraints weight = 20923.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.139689 restraints weight = 22090.712| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 13908 Z= 0.343 Angle : 0.648 8.484 18988 Z= 0.340 Chirality : 0.044 0.208 2246 Planarity : 0.004 0.047 2414 Dihedral : 8.552 59.767 2300 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.77 % Allowed : 19.91 % Favored : 76.32 % 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: 1.13 (0.19), residues: 1942 helix: 1.96 (0.15), residues: 1124 sheet: -1.35 (0.44), residues: 136 loop : -0.87 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 416 TYR 0.036 0.002 TYR I 226 PHE 0.034 0.002 PHE I 165 TRP 0.018 0.002 TRP B 766 HIS 0.007 0.002 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00826 (13900) covalent geometry : angle 0.64770 (18972) SS BOND : bond 0.00408 ( 8) SS BOND : angle 1.11488 ( 16) hydrogen bonds : bond 0.04112 ( 920) hydrogen bonds : angle 4.55765 ( 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 268 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8851 (m) cc_final: 0.8623 (t) REVERT: A 693 LYS cc_start: 0.6629 (mmmm) cc_final: 0.6410 (mmmm) REVERT: B 408 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.5672 (mmp) REVERT: B 721 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7581 (ptt) REVERT: B 767 TRP cc_start: 0.6771 (m-90) cc_final: 0.5950 (t-100) REVERT: B 769 ASP cc_start: 0.6531 (m-30) cc_final: 0.6263 (m-30) REVERT: C 572 SER cc_start: 0.8863 (m) cc_final: 0.8633 (t) REVERT: C 693 LYS cc_start: 0.6649 (mmmm) cc_final: 0.6447 (mmmm) REVERT: C 762 TRP cc_start: 0.5646 (m-10) cc_final: 0.5412 (m-10) REVERT: D 408 MET cc_start: 0.6335 (OUTLIER) cc_final: 0.5993 (mmp) REVERT: D 721 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7478 (ptt) REVERT: D 767 TRP cc_start: 0.6712 (m-90) cc_final: 0.5876 (t-100) REVERT: J 179 TYR cc_start: 0.8875 (t80) cc_final: 0.8654 (t80) REVERT: I 179 TYR cc_start: 0.8886 (t80) cc_final: 0.8671 (t80) outliers start: 40 outliers final: 30 residues processed: 247 average time/residue: 0.0906 time to fit residues: 35.1748 Evaluate side-chains 258 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 533 SER Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 408 MET 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 B residue 721 MET Chi-restraints excluded: chain C residue 483 GLU 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 684 GLU Chi-restraints excluded: chain C residue 787 ASN Chi-restraints excluded: chain D residue 408 MET 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 24 THR 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 I residue 24 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 12 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 126 optimal weight: 0.2980 chunk 83 optimal weight: 0.0040 chunk 173 optimal weight: 0.6980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.203350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.163572 restraints weight = 20155.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.152096 restraints weight = 25285.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.151061 restraints weight = 23595.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150774 restraints weight = 19499.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.150525 restraints weight = 17709.700| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13908 Z= 0.113 Angle : 0.532 8.891 18988 Z= 0.272 Chirality : 0.039 0.134 2246 Planarity : 0.003 0.048 2414 Dihedral : 7.408 58.908 2300 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.08 % Allowed : 21.89 % Favored : 76.04 % 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: 1.64 (0.19), residues: 1942 helix: 2.46 (0.16), residues: 1126 sheet: -1.66 (0.44), residues: 134 loop : -0.69 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 688 TYR 0.031 0.001 TYR I 226 PHE 0.033 0.001 PHE I 165 TRP 0.041 0.002 TRP B 766 HIS 0.001 0.001 HIS J 105 Details of bonding type rmsd covalent geometry : bond 0.00255 (13900) covalent geometry : angle 0.53097 (18972) SS BOND : bond 0.00179 ( 8) SS BOND : angle 1.06414 ( 16) hydrogen bonds : bond 0.03252 ( 920) hydrogen bonds : angle 4.01864 ( 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 263 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 241 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: 0.8340 (mmt) cc_final: 0.7937 (mmt) REVERT: A 808 ILE cc_start: 0.8823 (mm) cc_final: 0.8594 (mt) REVERT: B 408 MET cc_start: 0.6104 (OUTLIER) cc_final: 0.5589 (mmp) REVERT: B 721 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7248 (ptt) REVERT: B 767 TRP cc_start: 0.6443 (m-90) cc_final: 0.5587 (t-100) REVERT: B 769 ASP cc_start: 0.6417 (m-30) cc_final: 0.6041 (m-30) REVERT: B 813 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7739 (mm-30) REVERT: C 581 MET cc_start: 0.8349 (mmt) cc_final: 0.7963 (mmt) REVERT: C 663 PHE cc_start: 0.7495 (m-80) cc_final: 0.7279 (m-80) REVERT: C 762 TRP cc_start: 0.5317 (m-10) cc_final: 0.5107 (m-10) REVERT: D 408 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5978 (mmp) REVERT: D 431 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.4916 (pp20) REVERT: D 721 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7225 (ptt) REVERT: D 767 TRP cc_start: 0.6461 (m-90) cc_final: 0.5678 (t-100) outliers start: 22 outliers final: 15 residues processed: 251 average time/residue: 0.0903 time to fit residues: 35.4640 Evaluate side-chains 242 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain D residue 408 MET 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 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 137 LEU Chi-restraints excluded: chain I residue 164 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 166 optimal weight: 4.9990 chunk 44 optimal weight: 30.0000 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 193 optimal weight: 0.1980 chunk 45 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 86 optimal weight: 40.0000 chunk 36 optimal weight: 4.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.200374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.156214 restraints weight = 20349.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.144762 restraints weight = 25593.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.143772 restraints weight = 22394.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143225 restraints weight = 19609.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.143004 restraints weight = 18349.938| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13908 Z= 0.186 Angle : 0.560 8.544 18988 Z= 0.286 Chirality : 0.041 0.164 2246 Planarity : 0.004 0.048 2414 Dihedral : 7.424 58.965 2300 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.89 % Allowed : 21.60 % Favored : 76.51 % 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: 1.59 (0.19), residues: 1942 helix: 2.40 (0.16), residues: 1128 sheet: -1.45 (0.48), residues: 112 loop : -0.78 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 661 TYR 0.036 0.002 TYR J 226 PHE 0.014 0.002 PHE C 580 TRP 0.054 0.002 TRP D 766 HIS 0.002 0.001 HIS J 105 Details of bonding type rmsd covalent geometry : bond 0.00447 (13900) covalent geometry : angle 0.55935 (18972) SS BOND : bond 0.00297 ( 8) SS BOND : angle 0.91986 ( 16) hydrogen bonds : bond 0.03431 ( 920) hydrogen bonds : angle 4.10158 ( 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 247 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8837 (m) cc_final: 0.8570 (t) REVERT: A 808 ILE cc_start: 0.8821 (mm) cc_final: 0.8586 (mt) REVERT: B 408 MET cc_start: 0.6107 (mmp) cc_final: 0.5588 (mmp) REVERT: B 721 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7437 (ptt) REVERT: B 767 TRP cc_start: 0.6559 (m-90) cc_final: 0.5729 (t-100) REVERT: B 813 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7782 (mm-30) REVERT: C 572 SER cc_start: 0.8835 (m) cc_final: 0.8570 (t) REVERT: C 663 PHE cc_start: 0.7489 (m-80) cc_final: 0.7261 (m-80) REVERT: C 762 TRP cc_start: 0.5395 (m-10) cc_final: 0.5167 (m-10) REVERT: D 408 MET cc_start: 0.6130 (mmp) cc_final: 0.5840 (mmp) REVERT: D 721 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7322 (ptt) REVERT: D 767 TRP cc_start: 0.6517 (m-90) cc_final: 0.5738 (t-100) REVERT: J 179 TYR cc_start: 0.8849 (t80) cc_final: 0.8614 (t80) REVERT: I 179 TYR cc_start: 0.8851 (t80) cc_final: 0.8614 (t80) outliers start: 20 outliers final: 18 residues processed: 240 average time/residue: 0.0898 time to fit residues: 33.8775 Evaluate side-chains 244 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 626 VAL 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 B residue 721 MET 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 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 214 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 137 LEU 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: 0.0040 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 173 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 92 optimal weight: 0.1980 chunk 127 optimal weight: 7.9990 overall best weight: 1.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.201007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.156564 restraints weight = 20438.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 85)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139135 restraints weight = 26320.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135209 restraints weight = 27670.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135355 restraints weight = 21984.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136477 restraints weight = 18567.734| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13908 Z= 0.153 Angle : 0.541 8.300 18988 Z= 0.275 Chirality : 0.041 0.212 2246 Planarity : 0.003 0.048 2414 Dihedral : 7.151 59.361 2300 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.17 % Allowed : 21.70 % Favored : 76.13 % 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: 1.63 (0.20), residues: 1942 helix: 2.42 (0.16), residues: 1134 sheet: -1.54 (0.47), residues: 112 loop : -0.76 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 688 TYR 0.031 0.002 TYR J 226 PHE 0.044 0.001 PHE I 165 TRP 0.041 0.002 TRP D 766 HIS 0.002 0.001 HIS J 105 Details of bonding type rmsd covalent geometry : bond 0.00364 (13900) covalent geometry : angle 0.54013 (18972) SS BOND : bond 0.00273 ( 8) SS BOND : angle 1.05440 ( 16) hydrogen bonds : bond 0.03303 ( 920) hydrogen bonds : angle 4.01674 ( 2766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2188.73 seconds wall clock time: 38 minutes 21.00 seconds (2301.00 seconds total)