Starting phenix.real_space_refine on Thu Feb 5 16:48:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rn4_54080/02_2026/9rn4_54080.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rn4_54080/02_2026/9rn4_54080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rn4_54080/02_2026/9rn4_54080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rn4_54080/02_2026/9rn4_54080.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rn4_54080/02_2026/9rn4_54080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rn4_54080/02_2026/9rn4_54080.map" } resolution = 3.4 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= 0.005 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 123 5.16 5 C 12143 2.51 5 N 2984 2.21 5 O 3295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18546 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3223 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3215 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 410, 3215 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 3280 Chain: "B" Number of atoms: 3188 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 407, 3180 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 407, 3180 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3244 Chain: "C" Number of atoms: 3221 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3213 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 410, 3213 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3278 Chain: "D" Number of atoms: 3215 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3207 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 410, 3207 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3272 Chain: "E" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1382 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 179} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1356 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 3 Chain: "G" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1391 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 179} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1401 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 180} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' CA': 1, 'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 7.14, per 1000 atoms: 0.38 Number of scatterers: 18546 At special positions: 0 Unit cell: (119.451, 115.332, 142.517, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 123 16.00 O 3295 8.00 N 2984 7.00 C 12143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 795 " distance=2.04 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 795 " distance=2.04 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 795 " distance=2.04 Simple disulfide: pdb=" SG CYS D 740 " - pdb=" SG CYS D 795 " distance=2.04 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.04 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.02 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.02 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 1.2 seconds 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4334 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 25 sheets defined 59.0% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 438 through 441 Processing helix chain 'A' and resid 445 through 459 Processing helix chain 'A' and resid 483 through 491 Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 544 through 568 removed outlier: 3.785A pdb=" N VAL A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 removed outlier: 3.579A pdb=" N LEU A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 649 removed outlier: 3.617A pdb=" N VAL A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 624 " --> pdb=" O GLY A 620 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TRP A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 652 No H-bonds generated for 'chain 'A' and resid 650 through 652' Processing helix chain 'A' and resid 657 through 663 Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 686 through 699 removed outlier: 3.788A pdb=" N SER A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.625A pdb=" N GLN A 736 " --> pdb=" O GLU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 778 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 815 through 832 removed outlier: 3.636A pdb=" N LEU A 821 " --> pdb=" O VAL A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 846 Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 438 through 441 Processing helix chain 'B' and resid 445 through 459 Processing helix chain 'B' and resid 483 through 491 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 537 through 541 removed outlier: 3.865A pdb=" N LEU B 540 " --> pdb=" O PHE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 568 removed outlier: 3.861A pdb=" N VAL B 552 " --> pdb=" O TRP B 548 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 607 Processing helix chain 'B' and resid 619 through 649 removed outlier: 3.508A pdb=" N VAL B 623 " --> pdb=" O SER B 619 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 625 " --> pdb=" O ARG B 621 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 631 " --> pdb=" O TRP B 627 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 663 Processing helix chain 'B' and resid 675 through 684 Processing helix chain 'B' and resid 686 through 699 removed outlier: 3.788A pdb=" N SER B 698 " --> pdb=" O THR B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 718 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.627A pdb=" N GLN B 736 " --> pdb=" O GLU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 778 Processing helix chain 'B' and resid 779 through 790 Processing helix chain 'B' and resid 814 through 844 removed outlier: 3.599A pdb=" N PHE B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 826 " --> pdb=" O VAL B 822 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU B 835 " --> pdb=" O VAL B 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 437 Processing helix chain 'C' and resid 438 through 441 Processing helix chain 'C' and resid 445 through 459 Processing helix chain 'C' and resid 483 through 491 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 537 through 541 removed outlier: 3.664A pdb=" N ASP C 541 " --> pdb=" O SER C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 548 Processing helix chain 'C' and resid 550 through 568 removed outlier: 3.584A pdb=" N ILE C 556 " --> pdb=" O VAL C 552 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 564 " --> pdb=" O VAL C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 606 removed outlier: 3.708A pdb=" N LEU C 599 " --> pdb=" O ILE C 595 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 627 removed outlier: 4.040A pdb=" N VAL C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 648 removed outlier: 3.533A pdb=" N THR C 639 " --> pdb=" O ILE C 635 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 663 Processing helix chain 'C' and resid 675 through 684 Processing helix chain 'C' and resid 686 through 699 removed outlier: 3.787A pdb=" N SER C 698 " --> pdb=" O THR C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 718 Processing helix chain 'C' and resid 728 through 736 removed outlier: 3.625A pdb=" N GLN C 736 " --> pdb=" O GLU C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 778 Processing helix chain 'C' and resid 779 through 790 Processing helix chain 'C' and resid 815 through 820 Processing helix chain 'C' and resid 820 through 845 removed outlier: 3.609A pdb=" N GLY C 826 " --> pdb=" O VAL C 822 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET C 829 " --> pdb=" O LEU C 825 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 834 " --> pdb=" O LEU C 830 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 835 " --> pdb=" O VAL C 831 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 437 Processing helix chain 'D' and resid 438 through 441 Processing helix chain 'D' and resid 445 through 459 Processing helix chain 'D' and resid 483 through 491 Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 544 through 550 removed outlier: 3.673A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 568 removed outlier: 3.525A pdb=" N VAL D 560 " --> pdb=" O ILE D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 607 removed outlier: 3.508A pdb=" N TRP D 600 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE D 606 " --> pdb=" O SER D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 648 removed outlier: 3.508A pdb=" N VAL D 623 " --> pdb=" O SER D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 663 Processing helix chain 'D' and resid 675 through 684 Processing helix chain 'D' and resid 686 through 699 removed outlier: 3.787A pdb=" N SER D 698 " --> pdb=" O THR D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 718 Processing helix chain 'D' and resid 728 through 736 removed outlier: 3.627A pdb=" N GLN D 736 " --> pdb=" O GLU D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 778 Processing helix chain 'D' and resid 779 through 790 Processing helix chain 'D' and resid 810 through 815 removed outlier: 3.776A pdb=" N VAL D 814 " --> pdb=" O SER D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 846 removed outlier: 3.581A pdb=" N GLU D 843 " --> pdb=" O LYS D 839 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 30 Processing helix chain 'E' and resid 94 through 105 Processing helix chain 'E' and resid 105 through 127 removed outlier: 3.599A pdb=" N VAL E 112 " --> pdb=" O PRO E 108 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU E 126 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 163 removed outlier: 3.557A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 212 removed outlier: 3.600A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 30 removed outlier: 3.683A pdb=" N GLY F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY F 29 " --> pdb=" O THR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 105 through 128 removed outlier: 3.507A pdb=" N PHE F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 153 removed outlier: 3.665A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 159 removed outlier: 3.507A pdb=" N ALA F 159 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 212 removed outlier: 3.732A pdb=" N ALA F 212 " --> pdb=" O LEU F 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 30 removed outlier: 3.695A pdb=" N ALA G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL G 28 " --> pdb=" O MET G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 105 Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.596A pdb=" N VAL G 112 " --> pdb=" O PRO G 108 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.512A pdb=" N SER G 137 " --> pdb=" O ASN G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 212 removed outlier: 3.994A pdb=" N ILE G 188 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA G 212 " --> pdb=" O LEU G 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 30 removed outlier: 3.511A pdb=" N THR H 13 " --> pdb=" O GLN H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 100 removed outlier: 3.635A pdb=" N ARG H 99 " --> pdb=" O GLU H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 129 removed outlier: 3.742A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 163 removed outlier: 3.503A pdb=" N ALA H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP H 163 " --> pdb=" O ALA H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 212 Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 466 Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AA3, first strand: chain 'A' and resid 511 through 513 Processing sheet with id=AA4, first strand: chain 'A' and resid 518 through 520 removed outlier: 3.933A pdb=" N MET A 518 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 668 through 670 removed outlier: 6.410A pdb=" N ALA A 668 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU A 725 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY A 670 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N GLU A 727 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 524 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 462 through 466 Processing sheet with id=AA7, first strand: chain 'B' and resid 429 through 430 Processing sheet with id=AA8, first strand: chain 'B' and resid 511 through 513 Processing sheet with id=AA9, first strand: chain 'B' and resid 518 through 520 removed outlier: 3.932A pdb=" N MET B 518 " --> pdb=" O TYR B 754 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 668 through 670 removed outlier: 6.412A pdb=" N ALA B 668 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU B 725 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY B 670 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N GLU B 727 " --> pdb=" O GLY B 670 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N PHE B 722 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS B 527 " --> pdb=" O PHE B 722 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 524 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 462 through 466 Processing sheet with id=AB3, first strand: chain 'C' and resid 429 through 430 Processing sheet with id=AB4, first strand: chain 'C' and resid 511 through 513 Processing sheet with id=AB5, first strand: chain 'C' and resid 518 through 520 removed outlier: 3.934A pdb=" N MET C 518 " --> pdb=" O TYR C 754 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 668 through 670 removed outlier: 6.411A pdb=" N ALA C 668 " --> pdb=" O ALA C 723 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU C 725 " --> pdb=" O ALA C 668 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY C 670 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N GLU C 727 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N PHE C 722 " --> pdb=" O LYS C 527 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS C 527 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE C 524 " --> pdb=" O VAL C 745 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 462 through 466 removed outlier: 6.502A pdb=" N VAL D 417 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA D 465 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL D 419 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 429 through 430 Processing sheet with id=AB9, first strand: chain 'D' and resid 511 through 513 Processing sheet with id=AC1, first strand: chain 'D' and resid 518 through 520 removed outlier: 3.934A pdb=" N MET D 518 " --> pdb=" O TYR D 754 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 668 through 670 removed outlier: 6.410A pdb=" N ALA D 668 " --> pdb=" O ALA D 723 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU D 725 " --> pdb=" O ALA D 668 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY D 670 " --> pdb=" O LEU D 725 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N GLU D 727 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N PHE D 722 " --> pdb=" O LYS D 527 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS D 527 " --> pdb=" O PHE D 722 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE D 524 " --> pdb=" O VAL D 745 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 57 through 61 Processing sheet with id=AC4, first strand: chain 'E' and resid 65 through 67 Processing sheet with id=AC5, first strand: chain 'F' and resid 35 through 38 removed outlier: 3.737A pdb=" N CYS F 67 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AC7, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.522A pdb=" N VAL H 57 " --> pdb=" O GLY H 38 " (cutoff:3.500A) 1067 hydrogen bonds defined for protein. 3090 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: 3.50 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4169 1.33 - 1.46: 5633 1.46 - 1.59: 8962 1.59 - 1.72: 0 1.72 - 1.85: 202 Bond restraints: 18966 Sorted by residual: bond pdb=" C LYS C 527 " pdb=" O LYS C 527 " ideal model delta sigma weight residual 1.234 1.299 -0.065 1.35e-02 5.49e+03 2.29e+01 bond pdb=" C LYS B 527 " pdb=" O LYS B 527 " ideal model delta sigma weight residual 1.232 1.295 -0.063 1.37e-02 5.33e+03 2.13e+01 bond pdb=" C LYS D 527 " pdb=" O LYS D 527 " ideal model delta sigma weight residual 1.234 1.294 -0.060 1.33e-02 5.65e+03 2.03e+01 bond pdb=" N PRO D 468 " pdb=" CD PRO D 468 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.93e+01 bond pdb=" N PRO B 468 " pdb=" CD PRO B 468 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.91e+01 ... (remaining 18961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 24698 2.54 - 5.08: 801 5.08 - 7.61: 54 7.61 - 10.15: 16 10.15 - 12.69: 8 Bond angle restraints: 25577 Sorted by residual: angle pdb=" CA PRO B 468 " pdb=" N PRO B 468 " pdb=" CD PRO B 468 " ideal model delta sigma weight residual 112.00 99.31 12.69 1.40e+00 5.10e-01 8.22e+01 angle pdb=" CA PRO D 468 " pdb=" N PRO D 468 " pdb=" CD PRO D 468 " ideal model delta sigma weight residual 112.00 99.31 12.69 1.40e+00 5.10e-01 8.21e+01 angle pdb=" CA PRO C 468 " pdb=" N PRO C 468 " pdb=" CD PRO C 468 " ideal model delta sigma weight residual 112.00 99.37 12.63 1.40e+00 5.10e-01 8.14e+01 angle pdb=" CA PRO A 468 " pdb=" N PRO A 468 " pdb=" CD PRO A 468 " ideal model delta sigma weight residual 112.00 99.37 12.63 1.40e+00 5.10e-01 8.13e+01 angle pdb=" CA PRO D 767 " pdb=" N PRO D 767 " pdb=" CD PRO D 767 " ideal model delta sigma weight residual 112.00 99.82 12.18 1.40e+00 5.10e-01 7.56e+01 ... (remaining 25572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.59: 10857 26.59 - 53.19: 240 53.19 - 79.78: 64 79.78 - 106.38: 1 106.38 - 132.97: 5 Dihedral angle restraints: 11167 sinusoidal: 4387 harmonic: 6780 Sorted by residual: dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual -86.00 -30.80 -55.20 1 1.00e+01 1.00e-02 4.12e+01 dihedral pdb=" CA TYR F 176 " pdb=" C TYR F 176 " pdb=" N GLY F 177 " pdb=" CA GLY F 177 " ideal model delta harmonic sigma weight residual -180.00 -152.52 -27.48 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA LYS B 527 " pdb=" C LYS B 527 " pdb=" N LYS B 528 " pdb=" CA LYS B 528 " ideal model delta harmonic sigma weight residual 180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 11164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2279 0.078 - 0.155: 484 0.155 - 0.233: 78 0.233 - 0.310: 12 0.310 - 0.388: 2 Chirality restraints: 2855 Sorted by residual: chirality pdb=" CA LYS D 527 " pdb=" N LYS D 527 " pdb=" C LYS D 527 " pdb=" CB LYS D 527 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA LYS B 527 " pdb=" N LYS B 527 " pdb=" C LYS B 527 " pdb=" CB LYS B 527 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA LYS C 527 " pdb=" N LYS C 527 " pdb=" C LYS C 527 " pdb=" CB LYS C 527 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 2852 not shown) Planarity restraints: 3135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLC A1003 " 0.066 2.00e-02 2.50e+03 7.66e-02 5.87e+01 pdb=" C11 OLC A1003 " -0.074 2.00e-02 2.50e+03 pdb=" C8 OLC A1003 " -0.078 2.00e-02 2.50e+03 pdb=" C9 OLC A1003 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC D1002 " -0.059 2.00e-02 2.50e+03 6.82e-02 4.65e+01 pdb=" C11 OLC D1002 " 0.066 2.00e-02 2.50e+03 pdb=" C8 OLC D1002 " 0.070 2.00e-02 2.50e+03 pdb=" C9 OLC D1002 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 467 " -0.119 5.00e-02 4.00e+02 1.67e-01 4.46e+01 pdb=" N PRO D 468 " 0.288 5.00e-02 4.00e+02 pdb=" CA PRO D 468 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO D 468 " -0.077 5.00e-02 4.00e+02 ... (remaining 3132 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.65: 20 1.65 - 2.46: 113 2.46 - 3.27: 20702 3.27 - 4.09: 46619 4.09 - 4.90: 87047 Warning: very small nonbonded interaction distances. Nonbonded interactions: 154501 Sorted by model distance: nonbonded pdb=" OD2 ASP D 512 " pdb=" NH1 ARG D 765 " model vdw 0.836 3.120 nonbonded pdb=" OD2 ASP B 512 " pdb=" NH1 ARG B 765 " model vdw 0.837 3.120 nonbonded pdb=" OD2 ASP C 512 " pdb=" NH1 ARG C 765 " model vdw 0.838 3.120 nonbonded pdb=" OD2 ASP A 512 " pdb=" NH1 ARG A 765 " model vdw 0.838 3.120 nonbonded pdb=" CG ASP A 512 " pdb=" NH1 ARG A 765 " model vdw 1.056 3.350 ... (remaining 154496 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 415 through 573 or (resid 574 through 588 and (name N or n \ ame CA or name C or name O or name CB )) or resid 589 through 595 or resid 597 t \ hrough 649 or (resid 650 through 653 and (name N or name CA or name C or name O \ or name CB )) or resid 654 or (resid 655 and (name N or name CA or name C or nam \ e O or name CB )) or resid 656 through 796 or resid 807 through 844)) selection = (chain 'B' and (resid 415 through 530 or (resid 531 and (name N or name CA or na \ me C or name O or name CB )) or resid 532 through 595 or resid 597 through 649 o \ r (resid 650 through 653 and (name N or name CA or name C or name O or name CB ) \ ) or resid 654 through 844)) selection = (chain 'C' and (resid 415 through 530 or (resid 531 and (name N or name CA or na \ me C or name O or name CB )) or resid 532 through 573 or (resid 574 through 588 \ and (name N or name CA or name C or name O or name CB )) or resid 589 through 59 \ 5 or resid 597 through 649 or (resid 650 through 653 and (name N or name CA or n \ ame C or name O or name CB )) or resid 654 or (resid 655 and (name N or name CA \ or name C or name O or name CB )) or resid 656 through 796 or resid 807 through \ 844)) selection = (chain 'D' and (resid 415 through 530 or (resid 531 and (name N or name CA or na \ me C or name O or name CB )) or resid 532 or (resid 533 and (name N or name CA o \ r name C or name O or name CB )) or resid 534 through 573 or (resid 574 through \ 588 and (name N or name CA or name C or name O or name CB )) or resid 589 throug \ h 595 or resid 597 through 654 or (resid 655 and (name N or name CA or name C or \ name O or name CB )) or resid 656 through 796 or resid 807 through 844)) } ncs_group { reference = (chain 'E' and (resid 7 through 40 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 through 161 or resid 173 through 212)) selection = (chain 'F' and (resid 7 through 40 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 through 83 or resid 93 through 161 or resid \ 173 through 212)) selection = (chain 'G' and (resid 7 through 40 or resid 56 through 83 or resid 93 through 16 \ 1 or resid 173 through 212)) selection = (chain 'H' and (resid 7 through 40 or resid 56 through 83 or resid 93 through 16 \ 1 or resid 173 through 212)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.210 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 27.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 18982 Z= 0.511 Angle : 1.064 12.690 25601 Z= 0.645 Chirality : 0.066 0.388 2855 Planarity : 0.012 0.167 3135 Dihedral : 12.621 132.969 6797 Min Nonbonded Distance : 0.836 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.13 % Favored : 96.48 % Rotamer: Outliers : 0.36 % Allowed : 1.96 % Favored : 97.68 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 17.14 % 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: -2.67 (0.16), residues: 2306 helix: -1.47 (0.13), residues: 1330 sheet: -2.00 (0.32), residues: 222 loop : -1.91 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.004 ARG B 621 TYR 0.057 0.005 TYR A 491 PHE 0.044 0.004 PHE G 182 TRP 0.062 0.004 TRP C 573 HIS 0.013 0.003 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00950 (18966) covalent geometry : angle 1.06131 (25577) SS BOND : bond 0.00760 ( 12) SS BOND : angle 2.58470 ( 24) hydrogen bonds : bond 0.21468 ( 1067) hydrogen bonds : angle 8.09932 ( 3090) Misc. bond : bond 0.00653 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 295 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 302 average time/residue: 0.1758 time to fit residues: 76.0913 Evaluate side-chains 152 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 520 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN B 736 GLN C 736 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS H 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.102197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.059868 restraints weight = 123409.808| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 5.82 r_work: 0.3005 rms_B_bonded: 5.33 restraints_weight: 2.0000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18982 Z= 0.224 Angle : 0.683 9.356 25601 Z= 0.364 Chirality : 0.045 0.217 2855 Planarity : 0.007 0.106 3135 Dihedral : 6.906 102.020 2687 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.35 % Favored : 98.57 % Rotamer: Outliers : 1.50 % Allowed : 8.41 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.42 (0.17), residues: 2306 helix: 0.55 (0.14), residues: 1345 sheet: -1.97 (0.35), residues: 183 loop : -1.19 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 765 TYR 0.020 0.002 TYR E 174 PHE 0.023 0.002 PHE G 107 TRP 0.025 0.002 TRP D 789 HIS 0.009 0.002 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00494 (18966) covalent geometry : angle 0.68290 (25577) SS BOND : bond 0.00293 ( 12) SS BOND : angle 0.75191 ( 24) hydrogen bonds : bond 0.04660 ( 1067) hydrogen bonds : angle 4.55649 ( 3090) Misc. bond : bond 0.00058 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.9573 (mmm) cc_final: 0.9367 (mmm) REVERT: C 423 MET cc_start: 0.6454 (mmt) cc_final: 0.6181 (mmt) REVERT: C 429 MET cc_start: 0.7858 (mtm) cc_final: 0.7270 (mpp) REVERT: D 436 MET cc_start: 0.7415 (ppp) cc_final: 0.6787 (pmm) REVERT: F 58 MET cc_start: 0.8247 (mmm) cc_final: 0.7549 (mmm) REVERT: G 174 TYR cc_start: 0.9156 (p90) cc_final: 0.8851 (p90) outliers start: 29 outliers final: 14 residues processed: 184 average time/residue: 0.1419 time to fit residues: 39.2315 Evaluate side-chains 149 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 683 ARG Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 59 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 228 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 641 ASN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN H 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.102057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.059503 restraints weight = 137691.351| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 6.26 r_work: 0.3000 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18982 Z= 0.169 Angle : 0.605 9.968 25601 Z= 0.315 Chirality : 0.042 0.231 2855 Planarity : 0.005 0.066 3135 Dihedral : 6.403 94.343 2687 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.52 % Favored : 98.39 % Rotamer: Outliers : 1.55 % Allowed : 9.29 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: 0.77 (0.18), residues: 2306 helix: 1.68 (0.14), residues: 1346 sheet: -1.95 (0.34), residues: 170 loop : -0.93 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 682 TYR 0.019 0.001 TYR E 174 PHE 0.026 0.001 PHE H 116 TRP 0.020 0.001 TRP C 693 HIS 0.007 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00378 (18966) covalent geometry : angle 0.60522 (25577) SS BOND : bond 0.00162 ( 12) SS BOND : angle 0.38594 ( 24) hydrogen bonds : bond 0.04082 ( 1067) hydrogen bonds : angle 4.19854 ( 3090) Misc. bond : bond 0.00021 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.9127 (mtm) cc_final: 0.8920 (mpp) REVERT: A 730 MET cc_start: 0.9256 (ptt) cc_final: 0.8609 (mpp) REVERT: B 485 MET cc_start: 0.8110 (mpp) cc_final: 0.7552 (mmp) REVERT: B 651 MET cc_start: 0.8030 (ptp) cc_final: 0.7715 (ptp) REVERT: B 683 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7157 (ptt90) REVERT: B 730 MET cc_start: 0.8380 (mpp) cc_final: 0.8131 (mpp) REVERT: C 423 MET cc_start: 0.6815 (mmt) cc_final: 0.6615 (mmt) REVERT: C 429 MET cc_start: 0.7908 (mtm) cc_final: 0.7495 (mpp) REVERT: D 436 MET cc_start: 0.7463 (ppp) cc_final: 0.6641 (pmm) REVERT: D 485 MET cc_start: 0.7093 (mpp) cc_final: 0.6321 (mpp) REVERT: D 518 MET cc_start: 0.8496 (tpp) cc_final: 0.7678 (ptm) REVERT: D 525 MET cc_start: 0.8463 (tmm) cc_final: 0.8218 (tmm) REVERT: F 58 MET cc_start: 0.8187 (mmm) cc_final: 0.7848 (mmm) REVERT: F 149 ASN cc_start: 0.9397 (t0) cc_final: 0.9126 (t0) REVERT: G 174 TYR cc_start: 0.9188 (p90) cc_final: 0.8968 (p90) outliers start: 30 outliers final: 18 residues processed: 168 average time/residue: 0.1229 time to fit residues: 32.4613 Evaluate side-chains 151 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 683 ARG Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 192 MET Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 34 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 0 optimal weight: 70.0000 chunk 123 optimal weight: 30.0000 chunk 15 optimal weight: 0.7980 chunk 127 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 434 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.101169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.060018 restraints weight = 114713.856| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 5.66 r_work: 0.2978 rms_B_bonded: 5.30 restraints_weight: 2.0000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18982 Z= 0.196 Angle : 0.613 9.748 25601 Z= 0.315 Chirality : 0.042 0.212 2855 Planarity : 0.004 0.047 3135 Dihedral : 6.336 88.592 2687 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.56 % Favored : 98.35 % Rotamer: Outliers : 1.60 % Allowed : 10.47 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.18), residues: 2306 helix: 2.11 (0.14), residues: 1357 sheet: -1.90 (0.32), residues: 190 loop : -0.67 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 765 TYR 0.017 0.001 TYR E 174 PHE 0.021 0.001 PHE H 116 TRP 0.024 0.001 TRP C 693 HIS 0.005 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00437 (18966) covalent geometry : angle 0.61321 (25577) SS BOND : bond 0.00186 ( 12) SS BOND : angle 0.40740 ( 24) hydrogen bonds : bond 0.04013 ( 1067) hydrogen bonds : angle 4.17350 ( 3090) Misc. bond : bond 0.00015 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 MET cc_start: 0.8644 (tpp) cc_final: 0.8329 (tpp) REVERT: A 692 MET cc_start: 0.9541 (mmm) cc_final: 0.9108 (mmm) REVERT: A 730 MET cc_start: 0.9313 (ptt) cc_final: 0.8528 (mpp) REVERT: B 692 MET cc_start: 0.9266 (mtt) cc_final: 0.9031 (mtm) REVERT: C 423 MET cc_start: 0.6233 (mmt) cc_final: 0.5925 (mmt) REVERT: C 429 MET cc_start: 0.7837 (mtm) cc_final: 0.7289 (mpp) REVERT: C 436 MET cc_start: 0.5471 (tpp) cc_final: 0.5114 (tmm) REVERT: D 485 MET cc_start: 0.7006 (mpp) cc_final: 0.6343 (mpp) REVERT: D 525 MET cc_start: 0.8482 (tmm) cc_final: 0.8227 (tmm) REVERT: F 58 MET cc_start: 0.8269 (mmm) cc_final: 0.7964 (mmm) REVERT: F 149 ASN cc_start: 0.9398 (t0) cc_final: 0.9149 (t0) REVERT: G 81 ASP cc_start: 0.8926 (t0) cc_final: 0.8693 (t0) outliers start: 31 outliers final: 23 residues processed: 160 average time/residue: 0.1352 time to fit residues: 33.8750 Evaluate side-chains 154 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 192 MET Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 205 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 434 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.102627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.061351 restraints weight = 150124.448| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 6.49 r_work: 0.3008 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18982 Z= 0.120 Angle : 0.577 11.798 25601 Z= 0.292 Chirality : 0.041 0.227 2855 Planarity : 0.004 0.051 3135 Dihedral : 6.014 85.342 2687 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.22 % Favored : 98.70 % Rotamer: Outliers : 1.34 % Allowed : 11.20 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: 1.67 (0.18), residues: 2306 helix: 2.45 (0.14), residues: 1353 sheet: -1.85 (0.37), residues: 151 loop : -0.66 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 683 TYR 0.016 0.001 TYR E 174 PHE 0.022 0.001 PHE H 116 TRP 0.015 0.001 TRP D 789 HIS 0.005 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00268 (18966) covalent geometry : angle 0.57724 (25577) SS BOND : bond 0.00089 ( 12) SS BOND : angle 0.31614 ( 24) hydrogen bonds : bond 0.03606 ( 1067) hydrogen bonds : angle 3.96017 ( 3090) Misc. bond : bond 0.00012 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 MET cc_start: 0.8701 (tpp) cc_final: 0.8386 (tpp) REVERT: A 730 MET cc_start: 0.9305 (ptt) cc_final: 0.8579 (mpp) REVERT: B 683 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7213 (pmt170) REVERT: B 730 MET cc_start: 0.8379 (mpp) cc_final: 0.8075 (mpp) REVERT: C 423 MET cc_start: 0.6292 (mmt) cc_final: 0.5974 (mmt) REVERT: C 429 MET cc_start: 0.7852 (mtm) cc_final: 0.7307 (mpp) REVERT: C 436 MET cc_start: 0.5702 (tpp) cc_final: 0.5431 (tmm) REVERT: D 436 MET cc_start: 0.7448 (ppp) cc_final: 0.7064 (pmm) REVERT: D 485 MET cc_start: 0.6975 (mpp) cc_final: 0.6311 (mpp) REVERT: D 525 MET cc_start: 0.8535 (tmm) cc_final: 0.8300 (tmm) REVERT: D 696 MET cc_start: 0.7641 (ptm) cc_final: 0.7316 (ptm) REVERT: F 58 MET cc_start: 0.8259 (mmm) cc_final: 0.7968 (mmm) REVERT: F 149 ASN cc_start: 0.9399 (t0) cc_final: 0.9154 (t0) outliers start: 26 outliers final: 19 residues processed: 162 average time/residue: 0.1297 time to fit residues: 33.3415 Evaluate side-chains 151 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 683 ARG Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 549 MET Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 67 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.099762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.057742 restraints weight = 128052.413| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 5.91 r_work: 0.2909 rms_B_bonded: 5.36 restraints_weight: 2.0000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 18982 Z= 0.265 Angle : 0.679 11.542 25601 Z= 0.344 Chirality : 0.043 0.235 2855 Planarity : 0.004 0.039 3135 Dihedral : 6.531 78.769 2687 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.82 % Favored : 98.09 % Rotamer: Outliers : 1.65 % Allowed : 11.71 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.18), residues: 2306 helix: 2.37 (0.14), residues: 1355 sheet: -1.68 (0.35), residues: 174 loop : -0.59 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 765 TYR 0.016 0.001 TYR A 819 PHE 0.022 0.002 PHE F 116 TRP 0.014 0.002 TRP C 693 HIS 0.006 0.001 HIS G 205 Details of bonding type rmsd covalent geometry : bond 0.00593 (18966) covalent geometry : angle 0.67908 (25577) SS BOND : bond 0.00309 ( 12) SS BOND : angle 0.61982 ( 24) hydrogen bonds : bond 0.04296 ( 1067) hydrogen bonds : angle 4.30282 ( 3090) Misc. bond : bond 0.00026 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 MET cc_start: 0.9467 (tpp) cc_final: 0.9193 (mmm) REVERT: A 730 MET cc_start: 0.9386 (ptt) cc_final: 0.8741 (mpp) REVERT: C 423 MET cc_start: 0.6519 (mmt) cc_final: 0.6299 (mmt) REVERT: C 429 MET cc_start: 0.7932 (mtm) cc_final: 0.7372 (mpp) REVERT: C 436 MET cc_start: 0.5882 (tpp) cc_final: 0.5678 (tmm) REVERT: D 436 MET cc_start: 0.7517 (ppp) cc_final: 0.6717 (pmm) REVERT: D 485 MET cc_start: 0.7102 (mpp) cc_final: 0.6559 (mpp) REVERT: D 525 MET cc_start: 0.8574 (tmm) cc_final: 0.8342 (tmm) REVERT: F 58 MET cc_start: 0.8269 (mmm) cc_final: 0.8040 (mmm) REVERT: F 149 ASN cc_start: 0.9447 (t0) cc_final: 0.9238 (t0) REVERT: H 174 TYR cc_start: 0.8671 (p90) cc_final: 0.8420 (p90) outliers start: 32 outliers final: 27 residues processed: 158 average time/residue: 0.1366 time to fit residues: 33.7160 Evaluate side-chains 154 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 683 ARG Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 14 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 25 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.101783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.060448 restraints weight = 130484.578| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 6.10 r_work: 0.2975 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18982 Z= 0.120 Angle : 0.580 10.260 25601 Z= 0.290 Chirality : 0.041 0.237 2855 Planarity : 0.003 0.036 3135 Dihedral : 5.997 76.299 2687 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.26 % Favored : 98.65 % Rotamer: Outliers : 1.34 % Allowed : 11.71 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: 2.01 (0.18), residues: 2306 helix: 2.71 (0.14), residues: 1353 sheet: -1.76 (0.37), residues: 158 loop : -0.45 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 683 TYR 0.013 0.001 TYR E 174 PHE 0.017 0.001 PHE H 116 TRP 0.012 0.001 TRP D 789 HIS 0.004 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00270 (18966) covalent geometry : angle 0.58029 (25577) SS BOND : bond 0.00102 ( 12) SS BOND : angle 0.29316 ( 24) hydrogen bonds : bond 0.03614 ( 1067) hydrogen bonds : angle 3.91686 ( 3090) Misc. bond : bond 0.00013 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 MET cc_start: 0.9407 (tpp) cc_final: 0.9142 (mmm) REVERT: A 730 MET cc_start: 0.9370 (ptt) cc_final: 0.8834 (mpp) REVERT: C 423 MET cc_start: 0.6327 (mmt) cc_final: 0.6087 (mmt) REVERT: C 429 MET cc_start: 0.7934 (mtm) cc_final: 0.7423 (mpp) REVERT: D 485 MET cc_start: 0.6962 (mpp) cc_final: 0.6351 (mpp) REVERT: D 525 MET cc_start: 0.8556 (tmm) cc_final: 0.8339 (tmm) REVERT: F 58 MET cc_start: 0.8208 (mmm) cc_final: 0.7955 (mmm) REVERT: F 149 ASN cc_start: 0.9372 (t0) cc_final: 0.9108 (t0) REVERT: H 174 TYR cc_start: 0.8614 (p90) cc_final: 0.8372 (p90) outliers start: 26 outliers final: 21 residues processed: 158 average time/residue: 0.1127 time to fit residues: 28.2970 Evaluate side-chains 159 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 683 ARG Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 549 MET Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 221 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 194 optimal weight: 0.0050 chunk 199 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 146 optimal weight: 50.0000 chunk 156 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 641 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.101775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.060287 restraints weight = 137573.632| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 6.24 r_work: 0.2971 rms_B_bonded: 5.68 restraints_weight: 2.0000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18982 Z= 0.127 Angle : 0.596 9.975 25601 Z= 0.295 Chirality : 0.040 0.237 2855 Planarity : 0.003 0.037 3135 Dihedral : 5.737 70.972 2687 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.39 % Favored : 98.52 % Rotamer: Outliers : 1.24 % Allowed : 12.44 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: 2.06 (0.18), residues: 2306 helix: 2.77 (0.14), residues: 1355 sheet: -1.71 (0.35), residues: 177 loop : -0.45 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 683 TYR 0.013 0.001 TYR E 174 PHE 0.014 0.001 PHE F 116 TRP 0.015 0.001 TRP C 693 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00288 (18966) covalent geometry : angle 0.59610 (25577) SS BOND : bond 0.00141 ( 12) SS BOND : angle 0.33346 ( 24) hydrogen bonds : bond 0.03527 ( 1067) hydrogen bonds : angle 3.85939 ( 3090) Misc. bond : bond 0.00015 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 MET cc_start: 0.8677 (tpp) cc_final: 0.8123 (tpp) REVERT: A 607 MET cc_start: 0.9418 (tpp) cc_final: 0.9115 (mmm) REVERT: C 423 MET cc_start: 0.6308 (mmt) cc_final: 0.6060 (mmt) REVERT: C 429 MET cc_start: 0.7911 (mtm) cc_final: 0.7341 (mpp) REVERT: D 485 MET cc_start: 0.6954 (mpp) cc_final: 0.6378 (mpp) REVERT: D 525 MET cc_start: 0.8567 (tmm) cc_final: 0.8356 (tmm) REVERT: F 58 MET cc_start: 0.8217 (mmm) cc_final: 0.7970 (mmm) REVERT: F 149 ASN cc_start: 0.9382 (t0) cc_final: 0.9142 (t0) REVERT: H 174 TYR cc_start: 0.8670 (p90) cc_final: 0.8367 (p90) outliers start: 24 outliers final: 23 residues processed: 158 average time/residue: 0.1236 time to fit residues: 31.0245 Evaluate side-chains 159 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 683 ARG Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 549 MET Chi-restraints excluded: chain D residue 607 MET Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 143 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 227 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 127 optimal weight: 30.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.100965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.059623 restraints weight = 115381.644| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 5.63 r_work: 0.2968 rms_B_bonded: 5.29 restraints_weight: 2.0000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18982 Z= 0.171 Angle : 0.624 12.201 25601 Z= 0.309 Chirality : 0.041 0.239 2855 Planarity : 0.003 0.038 3135 Dihedral : 5.799 66.444 2687 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.61 % Favored : 98.31 % Rotamer: Outliers : 1.44 % Allowed : 12.49 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: 2.05 (0.18), residues: 2306 helix: 2.74 (0.14), residues: 1356 sheet: -1.68 (0.35), residues: 186 loop : -0.41 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 683 TYR 0.013 0.001 TYR B 689 PHE 0.014 0.001 PHE A 563 TRP 0.017 0.001 TRP C 693 HIS 0.004 0.001 HIS G 205 Details of bonding type rmsd covalent geometry : bond 0.00385 (18966) covalent geometry : angle 0.62379 (25577) SS BOND : bond 0.00200 ( 12) SS BOND : angle 0.38965 ( 24) hydrogen bonds : bond 0.03711 ( 1067) hydrogen bonds : angle 3.99011 ( 3090) Misc. bond : bond 0.00017 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 MET cc_start: 0.8768 (tpp) cc_final: 0.8137 (tpp) REVERT: A 607 MET cc_start: 0.9442 (tpp) cc_final: 0.9085 (mmm) REVERT: A 730 MET cc_start: 0.9264 (ptt) cc_final: 0.8472 (mtm) REVERT: C 423 MET cc_start: 0.6327 (mmt) cc_final: 0.6074 (mmt) REVERT: C 429 MET cc_start: 0.7942 (mtm) cc_final: 0.7369 (mpp) REVERT: D 485 MET cc_start: 0.6981 (mpp) cc_final: 0.6428 (mpp) REVERT: D 525 MET cc_start: 0.8566 (tmm) cc_final: 0.8345 (tmm) REVERT: F 58 MET cc_start: 0.8185 (mmm) cc_final: 0.7956 (mmm) REVERT: F 149 ASN cc_start: 0.9392 (t0) cc_final: 0.9129 (t0) REVERT: H 174 TYR cc_start: 0.8729 (p90) cc_final: 0.8234 (p90) outliers start: 28 outliers final: 24 residues processed: 155 average time/residue: 0.1286 time to fit residues: 31.5172 Evaluate side-chains 158 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 683 ARG Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 549 MET Chi-restraints excluded: chain D residue 607 MET Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 228 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.101342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.059955 restraints weight = 112687.450| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 5.65 r_work: 0.2979 rms_B_bonded: 5.30 restraints_weight: 2.0000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18982 Z= 0.150 Angle : 0.626 12.662 25601 Z= 0.308 Chirality : 0.041 0.242 2855 Planarity : 0.003 0.037 3135 Dihedral : 5.757 61.932 2687 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.78 % Favored : 98.13 % Rotamer: Outliers : 1.19 % Allowed : 12.49 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: 2.09 (0.18), residues: 2306 helix: 2.78 (0.14), residues: 1356 sheet: -1.73 (0.34), residues: 186 loop : -0.38 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 683 TYR 0.012 0.001 TYR E 174 PHE 0.013 0.001 PHE C 517 TRP 0.022 0.001 TRP C 693 HIS 0.004 0.001 HIS G 205 Details of bonding type rmsd covalent geometry : bond 0.00339 (18966) covalent geometry : angle 0.62659 (25577) SS BOND : bond 0.00149 ( 12) SS BOND : angle 0.36110 ( 24) hydrogen bonds : bond 0.03641 ( 1067) hydrogen bonds : angle 3.93557 ( 3090) Misc. bond : bond 0.00016 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 MET cc_start: 0.8755 (tpp) cc_final: 0.8176 (tpp) REVERT: A 607 MET cc_start: 0.9410 (tpp) cc_final: 0.9073 (mmm) REVERT: A 730 MET cc_start: 0.9261 (ptt) cc_final: 0.8533 (mtm) REVERT: B 485 MET cc_start: 0.8427 (mpp) cc_final: 0.7578 (mmp) REVERT: C 423 MET cc_start: 0.6399 (mmt) cc_final: 0.6135 (mmt) REVERT: C 429 MET cc_start: 0.7941 (mtm) cc_final: 0.7360 (mpp) REVERT: D 485 MET cc_start: 0.6937 (mpp) cc_final: 0.6393 (mpp) REVERT: D 525 MET cc_start: 0.8596 (tmm) cc_final: 0.8385 (tmm) REVERT: F 149 ASN cc_start: 0.9371 (t0) cc_final: 0.9125 (t0) REVERT: H 174 TYR cc_start: 0.8696 (p90) cc_final: 0.8233 (p90) outliers start: 23 outliers final: 23 residues processed: 153 average time/residue: 0.1361 time to fit residues: 32.9596 Evaluate side-chains 156 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 683 ARG Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 549 MET Chi-restraints excluded: chain D residue 607 MET Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 182 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.4160 r_free = 0.4160 target = 0.100341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.059239 restraints weight = 97118.301| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 5.16 r_work: 0.2969 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18982 Z= 0.197 Angle : 0.648 11.692 25601 Z= 0.321 Chirality : 0.042 0.243 2855 Planarity : 0.003 0.043 3135 Dihedral : 5.907 57.133 2687 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 1.44 % Allowed : 12.49 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: 2.06 (0.18), residues: 2306 helix: 2.74 (0.14), residues: 1355 sheet: -1.78 (0.34), residues: 187 loop : -0.35 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 697 TYR 0.013 0.001 TYR A 819 PHE 0.015 0.001 PHE A 563 TRP 0.022 0.001 TRP C 693 HIS 0.005 0.001 HIS G 205 Details of bonding type rmsd covalent geometry : bond 0.00444 (18966) covalent geometry : angle 0.64773 (25577) SS BOND : bond 0.00229 ( 12) SS BOND : angle 0.48182 ( 24) hydrogen bonds : bond 0.03833 ( 1067) hydrogen bonds : angle 4.05069 ( 3090) Misc. bond : bond 0.00020 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6148.68 seconds wall clock time: 105 minutes 34.77 seconds (6334.77 seconds total)