Starting phenix.real_space_refine on Sat Jul 4 06:37:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rn4_54080/07_2026/9rn4_54080.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rn4_54080/07_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_54080/07_2026/9rn4_54080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rn4_54080/07_2026/9rn4_54080.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rn4_54080/07_2026/9rn4_54080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rn4_54080/07_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-dev-6108/lib/python3.11/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, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Chain breaks: 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: "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: 6.06, per 1000 atoms: 0.33 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: 1.17 Conformation dependent library (CDL) restraints added in 974.0 milliseconds 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: 0.35 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: 2.93 Time building geometry restraints manager: 1.67 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: 6.890 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: 0.030 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.510 Find NCS groups from input model: 0.720 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 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/Z covalent geometry : bond 0.00950 / 0.51 (18966) covalent geometry : angle 1.06131 / 0.64 (25577) SS BOND : bond 0.00760 / 0.47 ( 12) SS BOND : angle 2.58470 / 1.84 ( 24) hydrogen bonds : bond 0.21468 / 13.96 ( 1067) hydrogen bonds : angle 8.09932 / 5.55 ( 3090) Misc. bond : bond 0.00653 / 0.33 ( 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 : 0.710 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: 0.1546 time to fit residues: 67.4432 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 : 0.711 ------------------------------------------------------------------------------- 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... 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 = 0.4190 r_free = 0.4190 target = 0.102224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.059830 restraints weight = 123549.774| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 5.85 r_work: 0.3007 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 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 = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18982 Z= 0.224 Angle : 0.684 9.324 25601 Z= 0.365 Chirality : 0.045 0.221 2855 Planarity : 0.007 0.103 3135 Dihedral : 6.891 101.821 2687 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.30 % Favored : 98.61 % Rotamer: Outliers : 1.39 % Allowed : 8.41 % Favored : 90.20 % 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: -0.41 (0.17), residues: 2306 helix: 0.55 (0.14), residues: 1345 sheet: -1.92 (0.36), residues: 171 loop : -1.19 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 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 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (18966) covalent geometry : angle 0.68416 / 0.37 (25577) SS BOND : bond 0.00296 / 0.19 ( 12) SS BOND : angle 0.76794 / 0.55 ( 24) hydrogen bonds : bond 0.04709 / 3.05 ( 1067) hydrogen bonds : angle 4.55831 / 3.14 ( 3090) Misc. bond : bond 0.00071 / 0.04 ( 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 189 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.704 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: symmetry clash REVERT: C 423 MET cc_start: 0.6472 (mmt) cc_final: 0.6202 (mmt) REVERT: C 429 MET cc_start: 0.7861 (mtm) cc_final: 0.7289 (mpp) REVERT: D 436 MET cc_start: 0.7423 (ppp) cc_final: 0.6794 (pmm) REVERT: F 58 MET cc_start: 0.8233 (mmm) cc_final: 0.7528 (mmm) REVERT: G 174 TYR cc_start: 0.9153 (p90) cc_final: 0.8848 (p90) REVERT: H 58 MET cc_start: 0.8776 (tpp) cc_final: 0.8541 (mpp) outliers start: 27 outliers final: 14 residues processed: 184 average time/residue: 0.1358 time to fit residues: 37.8801 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 : 0.534 ------------------------------------------------------------------------------- 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: 0.5980 chunk 7 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 179 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 228 optimal weight: 0.5980 chunk 173 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.103409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062227 restraints weight = 137241.193| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 6.38 r_work: 0.3017 rms_B_bonded: 5.74 restraints_weight: 2.0000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3651 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= 0.131 Angle : 0.586 9.474 25601 Z= 0.304 Chirality : 0.042 0.219 2855 Planarity : 0.005 0.069 3135 Dihedral : 6.303 95.799 2687 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.43 % Favored : 98.48 % Rotamer: Outliers : 1.39 % Allowed : 9.34 % Favored : 89.27 % 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: 0.72 (0.18), residues: 2306 helix: 1.65 (0.14), residues: 1349 sheet: -1.87 (0.33), residues: 189 loop : -0.98 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 37 TYR 0.019 0.001 TYR E 174 PHE 0.026 0.001 PHE H 116 TRP 0.017 0.001 TRP D 789 HIS 0.007 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (18966) covalent geometry : angle 0.58595 / 0.30 (25577) SS BOND : bond 0.00119 / 0.09 ( 12) SS BOND : angle 0.33291 / 0.25 ( 24) hydrogen bonds : bond 0.03937 / 2.55 ( 1067) hydrogen bonds : angle 4.11104 / 2.83 ( 3090) Misc. bond : bond 0.00019 / 0.01 ( 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 180 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.492 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: A 429 MET cc_start: 0.9099 (mtm) cc_final: 0.8852 (mpp) REVERT: B 485 MET cc_start: 0.7969 (mpp) cc_final: 0.7504 (mmt) REVERT: B 651 MET cc_start: 0.7998 (ptp) cc_final: 0.7671 (ptp) REVERT: C 423 MET cc_start: 0.6313 (mmt) cc_final: 0.6034 (mmt) REVERT: C 429 MET cc_start: 0.7815 (mtm) cc_final: 0.7292 (mpp) REVERT: C 518 MET cc_start: -0.2070 (mtm) cc_final: -0.2277 (mtm) REVERT: D 436 MET cc_start: 0.7463 (ppp) cc_final: 0.6717 (pmm) REVERT: D 485 MET cc_start: 0.7004 (mpp) cc_final: 0.6322 (mpp) REVERT: D 518 MET cc_start: 0.8436 (tpp) cc_final: 0.7749 (ptp) REVERT: D 525 MET cc_start: 0.8405 (tmm) cc_final: 0.8149 (tmm) REVERT: F 58 MET cc_start: 0.8185 (mmm) cc_final: 0.7895 (mmm) REVERT: F 149 ASN cc_start: 0.9366 (t0) cc_final: 0.9070 (t0) REVERT: G 174 TYR cc_start: 0.9181 (p90) cc_final: 0.8957 (p90) REVERT: H 58 MET cc_start: 0.8762 (tpp) cc_final: 0.8501 (mpp) outliers start: 27 outliers final: 17 residues processed: 173 average time/residue: 0.1198 time to fit residues: 32.5376 Evaluate side-chains 154 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 549 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 520 LEU 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 149 ASN Chi-restraints excluded: chain G residue 150 ILE 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: 0.8980 chunk 28 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 0 optimal weight: 70.0000 chunk 123 optimal weight: 30.0000 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN H 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.100620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059645 restraints weight = 115980.421| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 6.20 r_work: 0.2933 rms_B_bonded: 5.57 restraints_weight: 2.0000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18982 Z= 0.246 Angle : 0.650 9.957 25601 Z= 0.337 Chirality : 0.043 0.209 2855 Planarity : 0.004 0.073 3135 Dihedral : 6.474 87.285 2687 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.74 % Favored : 98.18 % Rotamer: Outliers : 1.81 % Allowed : 10.42 % Favored : 87.77 % 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: 1.22 (0.18), residues: 2306 helix: 2.03 (0.14), residues: 1353 sheet: -1.96 (0.34), residues: 173 loop : -0.69 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 683 TYR 0.016 0.001 TYR E 174 PHE 0.024 0.002 PHE B 681 TRP 0.014 0.001 TRP D 789 HIS 0.006 0.001 HIS G 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 (18966) covalent geometry : angle 0.65045 / 0.34 (25577) SS BOND : bond 0.00265 / 0.21 ( 12) SS BOND : angle 0.55310 / 0.32 ( 24) hydrogen bonds : bond 0.04274 / 2.76 ( 1067) hydrogen bonds : angle 4.31695 / 2.98 ( 3090) Misc. bond : bond 0.00023 / 0.01 ( 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 167 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.839 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 429 MET cc_start: 0.9101 (mtm) cc_final: 0.8889 (mpp) REVERT: A 525 MET cc_start: 0.8734 (tpp) cc_final: 0.8438 (tpp) REVERT: A 692 MET cc_start: 0.9563 (mmm) cc_final: 0.9033 (mmm) REVERT: B 692 MET cc_start: 0.9243 (mtt) cc_final: 0.9025 (mtm) REVERT: C 423 MET cc_start: 0.6400 (mmt) cc_final: 0.6111 (mmt) REVERT: C 429 MET cc_start: 0.7872 (mtm) cc_final: 0.7349 (mpp) REVERT: C 436 MET cc_start: 0.5589 (tpp) cc_final: 0.5251 (tmm) REVERT: D 485 MET cc_start: 0.7058 (mpp) cc_final: 0.6483 (mpp) REVERT: D 525 MET cc_start: 0.8477 (tmm) cc_final: 0.8230 (tmm) REVERT: F 58 MET cc_start: 0.8290 (mmm) cc_final: 0.7998 (mmm) REVERT: F 149 ASN cc_start: 0.9423 (t0) cc_final: 0.9193 (t0) outliers start: 35 outliers final: 28 residues processed: 155 average time/residue: 0.1335 time to fit residues: 32.7806 Evaluate side-chains 157 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 683 ARG Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 820 ILE 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 E residue 192 MET 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 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 66 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 205 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 HIS H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.102632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.061404 restraints weight = 151322.876| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 6.65 r_work: 0.3004 rms_B_bonded: 5.96 restraints_weight: 2.0000 r_work (final): 0.3004 ------------------------------------------------------------------------------- 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 = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18982 Z= 0.114 Angle : 0.579 11.615 25601 Z= 0.293 Chirality : 0.041 0.226 2855 Planarity : 0.004 0.059 3135 Dihedral : 6.029 84.786 2687 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.09 % Favored : 98.83 % Rotamer: Outliers : 1.34 % Allowed : 11.25 % Favored : 87.41 % 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: 2.47 (0.14), residues: 1348 sheet: -1.90 (0.35), residues: 172 loop : -0.61 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 683 TYR 0.015 0.001 TYR E 174 PHE 0.022 0.001 PHE H 116 TRP 0.018 0.001 TRP D 789 HIS 0.006 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (18966) covalent geometry : angle 0.57899 / 0.29 (25577) SS BOND : bond 0.00082 / 0.06 ( 12) SS BOND : angle 0.28550 / 0.19 ( 24) hydrogen bonds : bond 0.03595 / 2.33 ( 1067) hydrogen bonds : angle 3.95062 / 2.72 ( 3090) Misc. bond : bond 0.00010 / 0.01 ( 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 171 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.773 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: 0.8787 (tpp) cc_final: 0.8473 (tpp) REVERT: A 607 MET cc_start: 0.9449 (tpp) cc_final: 0.9188 (mmm) REVERT: B 730 MET cc_start: 0.8374 (mpp) cc_final: 0.8109 (mpp) REVERT: C 423 MET cc_start: 0.6264 (mmt) cc_final: 0.5935 (mmt) REVERT: C 429 MET cc_start: 0.7845 (mtm) cc_final: 0.7275 (mpp) REVERT: C 436 MET cc_start: 0.5851 (tpp) cc_final: 0.5599 (tmm) REVERT: D 436 MET cc_start: 0.7371 (ppp) cc_final: 0.6958 (pmm) REVERT: D 485 MET cc_start: 0.6929 (mpp) cc_final: 0.6133 (mpp) REVERT: D 525 MET cc_start: 0.8538 (tmm) cc_final: 0.8303 (tmm) REVERT: E 174 TYR cc_start: 0.8967 (p90) cc_final: 0.8678 (p90) REVERT: F 58 MET cc_start: 0.8342 (mmm) cc_final: 0.8039 (mmm) REVERT: F 149 ASN cc_start: 0.9388 (t0) cc_final: 0.9148 (t0) outliers start: 26 outliers final: 20 residues processed: 165 average time/residue: 0.1256 time to fit residues: 32.9154 Evaluate side-chains 152 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 171 optimal weight: 3.9990 chunk 159 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 117 optimal weight: 30.0000 chunk 55 optimal weight: 6.9990 chunk 231 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 107 optimal weight: 30.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.101777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.060125 restraints weight = 132469.223| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 6.06 r_work: 0.2966 rms_B_bonded: 5.60 restraints_weight: 2.0000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 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 = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.4586 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= 0.160 Angle : 0.601 10.654 25601 Z= 0.303 Chirality : 0.041 0.238 2855 Planarity : 0.004 0.041 3135 Dihedral : 6.040 79.618 2687 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.52 % Favored : 98.39 % Rotamer: Outliers : 1.44 % Allowed : 11.40 % Favored : 87.15 % 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: 1.86 (0.18), residues: 2306 helix: 2.61 (0.14), residues: 1352 sheet: -1.85 (0.33), residues: 184 loop : -0.48 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 697 TYR 0.023 0.001 TYR D 754 PHE 0.020 0.001 PHE H 116 TRP 0.014 0.001 TRP C 627 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (18966) covalent geometry : angle 0.60151 / 0.30 (25577) SS BOND : bond 0.00169 / 0.13 ( 12) SS BOND : angle 0.39818 / 0.24 ( 24) hydrogen bonds : bond 0.03710 / 2.39 ( 1067) hydrogen bonds : angle 4.02538 / 2.78 ( 3090) Misc. bond : bond 0.00016 / 0.01 ( 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 162 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.560 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: 0.8800 (tpp) cc_final: 0.8449 (tpp) REVERT: A 607 MET cc_start: 0.9521 (tpp) cc_final: 0.9135 (mmm) REVERT: C 423 MET cc_start: 0.6316 (mmt) cc_final: 0.6061 (mmt) REVERT: C 429 MET cc_start: 0.7891 (mtm) cc_final: 0.7359 (mpp) REVERT: C 696 MET cc_start: 0.4273 (ppp) cc_final: 0.4066 (ppp) REVERT: D 485 MET cc_start: 0.7002 (mpp) cc_final: 0.6252 (mpp) REVERT: D 525 MET cc_start: 0.8537 (tmm) cc_final: 0.8294 (tmm) REVERT: E 174 TYR cc_start: 0.9005 (p90) cc_final: 0.8759 (p90) REVERT: F 58 MET cc_start: 0.8290 (mmm) cc_final: 0.8037 (mmm) REVERT: F 149 ASN cc_start: 0.9400 (t0) cc_final: 0.9124 (t0) REVERT: H 191 GLU cc_start: 0.9432 (mm-30) cc_final: 0.9148 (mm-30) outliers start: 28 outliers final: 22 residues processed: 156 average time/residue: 0.1172 time to fit residues: 28.9336 Evaluate side-chains 156 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 683 ARG 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 0.0030 chunk 56 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.100342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.058191 restraints weight = 129874.848| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 5.93 r_work: 0.2939 rms_B_bonded: 5.78 restraints_weight: 2.0000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18982 Z= 0.218 Angle : 0.642 12.363 25601 Z= 0.324 Chirality : 0.042 0.249 2855 Planarity : 0.004 0.039 3135 Dihedral : 6.291 73.029 2687 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.82 % Favored : 98.09 % Rotamer: Outliers : 1.60 % Allowed : 11.30 % Favored : 87.10 % 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: 1.85 (0.18), residues: 2306 helix: 2.60 (0.14), residues: 1353 sheet: -1.82 (0.34), residues: 172 loop : -0.55 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 765 TYR 0.016 0.001 TYR D 754 PHE 0.018 0.001 PHE A 563 TRP 0.012 0.001 TRP B 693 HIS 0.005 0.001 HIS G 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (18966) covalent geometry : angle 0.64210 / 0.32 (25577) SS BOND : bond 0.00268 / 0.21 ( 12) SS BOND : angle 0.49907 / 0.28 ( 24) hydrogen bonds : bond 0.04036 / 2.60 ( 1067) hydrogen bonds : angle 4.17117 / 2.88 ( 3090) Misc. bond : bond 0.00023 / 0.01 ( 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 165 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.768 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 607 MET cc_start: 0.9529 (tpp) cc_final: 0.9084 (mmm) REVERT: C 423 MET cc_start: 0.6672 (mmt) cc_final: 0.6432 (mmt) REVERT: C 429 MET cc_start: 0.8030 (mtm) cc_final: 0.7500 (mpp) REVERT: D 485 MET cc_start: 0.7003 (mpp) cc_final: 0.6443 (mpp) REVERT: D 525 MET cc_start: 0.8527 (tmm) cc_final: 0.8274 (tmm) REVERT: F 58 MET cc_start: 0.8205 (mmm) cc_final: 0.7976 (mmm) REVERT: F 149 ASN cc_start: 0.9406 (t0) cc_final: 0.9183 (t0) REVERT: H 174 TYR cc_start: 0.8674 (p90) cc_final: 0.8435 (p90) outliers start: 31 outliers final: 25 residues processed: 158 average time/residue: 0.1331 time to fit residues: 33.5860 Evaluate side-chains 154 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 A residue 768 VAL 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 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 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: 6.9990 chunk 197 optimal weight: 2.9990 chunk 192 optimal weight: 0.5980 chunk 154 optimal weight: 6.9990 chunk 194 optimal weight: 0.1980 chunk 199 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.101449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.059841 restraints weight = 134583.459| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 6.16 r_work: 0.2967 rms_B_bonded: 5.60 restraints_weight: 2.0000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 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 = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18982 Z= 0.128 Angle : 0.612 11.424 25601 Z= 0.303 Chirality : 0.041 0.245 2855 Planarity : 0.003 0.037 3135 Dihedral : 5.919 70.765 2687 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.52 % Favored : 98.39 % Rotamer: Outliers : 1.34 % Allowed : 11.87 % Favored : 86.79 % 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: 2.74 (0.14), residues: 1355 sheet: -1.77 (0.34), residues: 186 loop : -0.44 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 697 TYR 0.012 0.001 TYR D 754 PHE 0.025 0.001 PHE H 116 TRP 0.042 0.001 TRP C 693 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (18966) covalent geometry : angle 0.61230 / 0.30 (25577) SS BOND : bond 0.00127 / 0.10 ( 12) SS BOND : angle 0.32470 / 0.20 ( 24) hydrogen bonds : bond 0.03645 / 2.37 ( 1067) hydrogen bonds : angle 3.97466 / 2.74 ( 3090) Misc. bond : bond 0.00014 / 0.01 ( 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 164 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.605 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 607 MET cc_start: 0.9468 (tpp) cc_final: 0.8997 (mmm) REVERT: C 423 MET cc_start: 0.6444 (mmt) cc_final: 0.6198 (mmt) REVERT: C 429 MET cc_start: 0.7965 (mtm) cc_final: 0.7448 (mpp) REVERT: D 436 MET cc_start: 0.7469 (ppp) cc_final: 0.7183 (pmm) REVERT: D 485 MET cc_start: 0.6982 (mpp) cc_final: 0.6273 (mpp) REVERT: D 525 MET cc_start: 0.8575 (tmm) cc_final: 0.8355 (tmm) REVERT: E 174 TYR cc_start: 0.9068 (p90) cc_final: 0.8751 (p90) REVERT: F 58 MET cc_start: 0.8214 (mmm) cc_final: 0.8007 (mmm) REVERT: F 95 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8563 (tm-30) REVERT: F 149 ASN cc_start: 0.9371 (t0) cc_final: 0.9124 (t0) REVERT: H 174 TYR cc_start: 0.8654 (p90) cc_final: 0.8385 (p90) REVERT: H 191 GLU cc_start: 0.9368 (mm-30) cc_final: 0.9078 (mm-30) outliers start: 26 outliers final: 22 residues processed: 158 average time/residue: 0.1225 time to fit residues: 30.4624 Evaluate side-chains 158 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 12 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 143 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 148 optimal weight: 20.0000 chunk 127 optimal weight: 0.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.100509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.058875 restraints weight = 115208.646| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 5.64 r_work: 0.2953 rms_B_bonded: 5.29 restraints_weight: 2.0000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18982 Z= 0.184 Angle : 0.642 11.048 25601 Z= 0.320 Chirality : 0.042 0.245 2855 Planarity : 0.003 0.038 3135 Dihedral : 5.934 67.509 2687 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.65 % Favored : 98.26 % Rotamer: Outliers : 1.39 % Allowed : 12.23 % Favored : 86.38 % 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: 2.00 (0.18), residues: 2306 helix: 2.70 (0.14), residues: 1353 sheet: -1.76 (0.35), residues: 172 loop : -0.44 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 683 TYR 0.012 0.001 TYR A 695 PHE 0.025 0.001 PHE H 116 TRP 0.043 0.001 TRP C 693 HIS 0.004 0.001 HIS G 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (18966) covalent geometry : angle 0.64231 / 0.32 (25577) SS BOND : bond 0.00225 / 0.17 ( 12) SS BOND : angle 0.46399 / 0.27 ( 24) hydrogen bonds : bond 0.03823 / 2.47 ( 1067) hydrogen bonds : angle 4.09064 / 2.84 ( 3090) Misc. bond : bond 0.00019 / 0.01 ( 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 162 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.758 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: 0.9495 (tpp) cc_final: 0.8996 (mmm) REVERT: C 423 MET cc_start: 0.6544 (mmt) cc_final: 0.6299 (mmt) REVERT: C 429 MET cc_start: 0.8021 (mtm) cc_final: 0.7477 (mpp) REVERT: D 436 MET cc_start: 0.7474 (ppp) cc_final: 0.7162 (pmm) REVERT: D 485 MET cc_start: 0.7080 (mpp) cc_final: 0.6547 (mpp) REVERT: D 520 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7133 (pt) REVERT: D 525 MET cc_start: 0.8576 (tmm) cc_final: 0.8349 (tmm) REVERT: F 58 MET cc_start: 0.8210 (mmm) cc_final: 0.7997 (mmm) REVERT: F 149 ASN cc_start: 0.9393 (t0) cc_final: 0.9150 (t0) REVERT: H 174 TYR cc_start: 0.8705 (p90) cc_final: 0.8162 (p90) outliers start: 27 outliers final: 23 residues processed: 154 average time/residue: 0.1264 time to fit residues: 30.9927 Evaluate side-chains 155 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 C residue 549 MET 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 70 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 12 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 228 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.101295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.059828 restraints weight = 112447.666| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 5.48 r_work: 0.2993 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 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 = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.5165 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= 0.137 Angle : 0.634 13.456 25601 Z= 0.312 Chirality : 0.041 0.246 2855 Planarity : 0.003 0.046 3135 Dihedral : 5.765 63.571 2687 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.61 % Favored : 98.31 % Rotamer: Outliers : 1.39 % Allowed : 12.23 % Favored : 86.38 % 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: 2.78 (0.14), residues: 1354 sheet: -1.79 (0.35), residues: 172 loop : -0.47 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 683 TYR 0.011 0.001 TYR E 174 PHE 0.028 0.001 PHE F 116 TRP 0.040 0.001 TRP C 693 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (18966) covalent geometry : angle 0.63390 / 0.31 (25577) SS BOND : bond 0.00138 / 0.11 ( 12) SS BOND : angle 0.36690 / 0.23 ( 24) hydrogen bonds : bond 0.03643 / 2.36 ( 1067) hydrogen bonds : angle 3.98694 / 2.77 ( 3090) Misc. bond : bond 0.00013 / 0.01 ( 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 161 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.825 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: 0.9437 (tpp) cc_final: 0.8945 (mmm) REVERT: C 423 MET cc_start: 0.6449 (mmt) cc_final: 0.6186 (mmt) REVERT: C 429 MET cc_start: 0.7999 (mtm) cc_final: 0.7444 (mpp) REVERT: D 436 MET cc_start: 0.7428 (ppp) cc_final: 0.7101 (pmm) REVERT: D 485 MET cc_start: 0.6997 (mpp) cc_final: 0.6314 (mpp) REVERT: D 520 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7076 (pt) REVERT: D 525 MET cc_start: 0.8586 (tmm) cc_final: 0.8367 (tmm) REVERT: F 58 MET cc_start: 0.8185 (mmm) cc_final: 0.7958 (mmm) REVERT: F 149 ASN cc_start: 0.9361 (t0) cc_final: 0.9117 (t0) REVERT: H 191 GLU cc_start: 0.9327 (mm-30) cc_final: 0.9081 (mm-30) outliers start: 27 outliers final: 25 residues processed: 152 average time/residue: 0.1346 time to fit residues: 32.4527 Evaluate side-chains 157 residues out of total 1963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 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 C residue 549 MET Chi-restraints excluded: chain C residue 730 MET 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 140 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 11 LEU 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 12 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 182 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.099336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.057735 restraints weight = 95047.165| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 5.00 r_work: 0.2934 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 18982 Z= 0.279 Angle : 0.717 12.530 25601 Z= 0.358 Chirality : 0.043 0.251 2855 Planarity : 0.004 0.045 3135 Dihedral : 6.176 61.852 2687 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.78 % Rotamer: Outliers : 1.55 % Allowed : 12.38 % 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: 1.83 (0.18), residues: 2306 helix: 2.55 (0.14), residues: 1354 sheet: -1.89 (0.36), residues: 160 loop : -0.49 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 765 TYR 0.017 0.001 TYR A 819 PHE 0.026 0.002 PHE F 116 TRP 0.043 0.002 TRP C 693 HIS 0.009 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.28 (18966) covalent geometry : angle 0.71735 / 0.36 (25577) SS BOND : bond 0.00319 / 0.25 ( 12) SS BOND : angle 0.66271 / 0.37 ( 24) hydrogen bonds : bond 0.04105 / 2.65 ( 1067) hydrogen bonds : angle 4.30329 / 2.99 ( 3090) Misc. bond : bond 0.00031 / 0.02 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5684.64 seconds wall clock time: 97 minutes 50.38 seconds (5870.38 seconds total)