Starting phenix.real_space_refine on Fri Jul 3 23:31:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqn_61730/07_2026/9jqn_61730.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqn_61730/07_2026/9jqn_61730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jqn_61730/07_2026/9jqn_61730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqn_61730/07_2026/9jqn_61730.map" model { file = "/net/cci-nas-00/data/ceres_data/9jqn_61730/07_2026/9jqn_61730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqn_61730/07_2026/9jqn_61730.cif" } resolution = 3.03 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= -0.001 sd= 0.024 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 P 108 5.49 5 S 103 5.16 5 C 10090 2.51 5 N 2885 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 23 residue(s): 0.01s 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: 16485 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4411 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 548, 4405 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 522} Conformer: "B" Number of residues, atoms: 548, 4405 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 522} bond proxies already assigned to first conformer: 4495 Chain: "B" Number of atoms: 2701 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 344, 2680 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 344, 2680 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 2724 Chain: "C" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4394 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 521} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 2691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 345, 2681 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 345, 2681 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 2737 Chain: "G" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 306 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "L" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "M" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 306 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "F" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "H" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 262 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "E" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 262 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "J" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2074 SG CYS A 727 86.792 82.624 50.837 1.00 55.72 S ATOM 2095 SG CYS A 730 90.033 82.972 48.678 1.00 56.56 S ATOM 9186 SG CYS C 727 21.312 65.719 50.743 1.00 56.25 S ATOM 9207 SG CYS C 730 18.118 65.043 48.572 1.00 55.58 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS A 907 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 907 " occ=0.50 residue: pdb=" N AHIS B 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 47 " occ=0.50 residue: pdb=" N AARG B 237 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 237 " occ=0.50 residue: pdb=" N AHIS D 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 47 " occ=0.50 residue: pdb=" P DT I 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT I 15 " occ=0.85 residue: pdb=" P DT J 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT J 15 " occ=0.85 Time building chain proxies: 4.95, per 1000 atoms: 0.30 Number of scatterers: 16485 At special positions: 0 Unit cell: (110.24, 150.52, 114.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 103 16.00 P 108 15.00 O 3295 8.00 N 2885 7.00 C 10090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 868.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " Number of angles added : 4 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3348 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 17 sheets defined 35.3% alpha, 24.8% beta 53 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.639A pdb=" N LYS A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 814 removed outlier: 3.870A pdb=" N GLY A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 842 Processing helix chain 'A' and resid 850 through 858 removed outlier: 3.646A pdb=" N ALA A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.716A pdb=" N VAL A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 890 Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 902 through 924 removed outlier: 4.765A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE A 911 " --> pdb=" O ACYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.613A pdb=" N ARG A 969 " --> pdb=" O ASN A 965 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 970 " --> pdb=" O LYS A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.535A pdb=" N ILE B 15 " --> pdb=" O ILE B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.523A pdb=" N TRP B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.580A pdb=" N ALA B 338 " --> pdb=" O ASN B 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 511 removed outlier: 4.096A pdb=" N VAL C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 665 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 749 through 763 removed outlier: 3.566A pdb=" N ASN C 753 " --> pdb=" O SER C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 813 removed outlier: 3.970A pdb=" N GLY C 813 " --> pdb=" O GLN C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 842 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.815A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 901 Processing helix chain 'C' and resid 902 through 908 removed outlier: 3.799A pdb=" N GLN C 908 " --> pdb=" O GLU C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 950 Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.503A pdb=" N ALA C 957 " --> pdb=" O GLY C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.972A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 995 Processing helix chain 'C' and resid 996 through 1001 Processing helix chain 'C' and resid 1002 through 1004 No H-bonds generated for 'chain 'C' and resid 1002 through 1004' Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.767A pdb=" N ILE D 15 " --> pdb=" O ILE D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 519 removed outlier: 6.399A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU A 655 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 519 removed outlier: 6.399A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 631 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.655A pdb=" N PHE B 328 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 320 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 24 removed outlier: 4.554A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 removed outlier: 5.836A pdb=" N TYR B 108 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS B 127 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N MET B 110 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR B 125 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL B 112 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG B 123 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.489A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS B 191 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.562A pdb=" N VAL B 208 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 246 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 267 removed outlier: 3.614A pdb=" N THR B 264 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 517 through 520 removed outlier: 5.880A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR C 705 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLU C 597 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 517 through 520 removed outlier: 5.880A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR C 705 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLU C 597 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN C 636 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 24 removed outlier: 4.548A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 58 " --> pdb=" O AHIS D 47 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU D 55 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 6 " --> pdb=" O PHE D 345 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL D 8 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 9.605A pdb=" N PHE D 343 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 328 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 320 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 318 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.373A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N CYS D 124 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.194A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB7, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.581A pdb=" N VAL D 208 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 246 " --> pdb=" O ASP D 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 262 through 267 removed outlier: 3.575A pdb=" N THR D 264 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL D 272 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR D 266 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 134 hydrogen bonds 268 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4779 1.34 - 1.46: 3425 1.46 - 1.57: 8515 1.57 - 1.69: 213 1.69 - 1.81: 157 Bond restraints: 17089 Sorted by residual: bond pdb=" C3' DG G 41 " pdb=" C2' DG G 41 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.42e+00 bond pdb=" C3' DT G 28 " pdb=" C2' DT G 28 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.17e+00 bond pdb=" C3' DA H 48 " pdb=" C2' DA H 48 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.93e+00 bond pdb=" C3' DG F 30 " pdb=" C2' DG F 30 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.27e+00 bond pdb=" C3' DC F 24 " pdb=" C2' DC F 24 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.81e+00 ... (remaining 17084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 22715 1.45 - 2.90: 755 2.90 - 4.35: 89 4.35 - 5.79: 15 5.79 - 7.24: 2 Bond angle restraints: 23576 Sorted by residual: angle pdb=" O4' DT F 29 " pdb=" C4' DT F 29 " pdb=" C3' DT F 29 " ideal model delta sigma weight residual 106.00 102.88 3.12 6.00e-01 2.78e+00 2.71e+01 angle pdb=" N3 DT L 22 " pdb=" C4 DT L 22 " pdb=" O4 DT L 22 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" N3 DT G 28 " pdb=" C4 DT G 28 " pdb=" O4 DT G 28 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT G 38 " pdb=" C4 DT G 38 " pdb=" O4 DT G 38 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT M 25 " pdb=" C4 DT M 25 " pdb=" O4 DT M 25 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 23571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 8284 16.83 - 33.67: 1048 33.67 - 50.50: 455 50.50 - 67.34: 168 67.34 - 84.17: 19 Dihedral angle restraints: 9974 sinusoidal: 4772 harmonic: 5202 Sorted by residual: dihedral pdb=" CA ILE D 316 " pdb=" C ILE D 316 " pdb=" N TRP D 317 " pdb=" CA TRP D 317 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ILE B 316 " pdb=" C ILE B 316 " pdb=" N TRP B 317 " pdb=" CA TRP B 317 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA TYR C 928 " pdb=" C TYR C 928 " pdb=" N GLU C 929 " pdb=" CA GLU C 929 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 9971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1502 0.030 - 0.060: 674 0.060 - 0.090: 249 0.090 - 0.120: 136 0.120 - 0.150: 13 Chirality restraints: 2574 Sorted by residual: chirality pdb=" C3' DT L 22 " pdb=" C4' DT L 22 " pdb=" O3' DT L 22 " pdb=" C2' DT L 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA TYR C 982 " pdb=" N TYR C 982 " pdb=" C TYR C 982 " pdb=" CB TYR C 982 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE A 870 " pdb=" N ILE A 870 " pdb=" C ILE A 870 " pdb=" CB ILE A 870 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 2571 not shown) Planarity restraints: 2653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 317 " -0.020 2.00e-02 2.50e+03 1.84e-02 8.49e+00 pdb=" CG TRP D 317 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP D 317 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 317 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 317 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 317 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 317 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 317 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 317 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP D 317 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 317 " -0.020 2.00e-02 2.50e+03 1.76e-02 7.76e+00 pdb=" CG TRP B 317 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 317 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 317 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 317 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 317 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 317 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 317 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 317 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 317 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 897 " 0.037 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO A 898 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 898 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 898 " 0.030 5.00e-02 4.00e+02 ... (remaining 2650 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1340 2.74 - 3.28: 15375 3.28 - 3.82: 28280 3.82 - 4.36: 33447 4.36 - 4.90: 55538 Nonbonded interactions: 133980 Sorted by model distance: nonbonded pdb=" ND2 ASN B 23 " pdb=" O MET B 322 " model vdw 2.203 3.120 nonbonded pdb=" OH TYR A 805 " pdb=" OD1 ASP A 834 " model vdw 2.231 3.040 nonbonded pdb=" OE2 GLU C 811 " pdb=" OH TYR C 926 " model vdw 2.236 3.040 nonbonded pdb=" OE1 GLU A 662 " pdb=" NZ LYS A 710 " model vdw 2.245 3.120 nonbonded pdb=" OD2 ASP C 792 " pdb=" ND1 HIS C 795 " model vdw 2.253 3.120 ... (remaining 133975 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 461 through 833 or (resid 834 and (name N or name CA or na \ me C or name O or name CB )) or resid 835 through 906 or resid 908 through 1006 \ or (resid 1007 and (name N or name CA or name C or name O or name CB )) or resid \ 1101 through 1102)) selection = (chain 'C' and (resid 461 through 906 or resid 908 through 1102)) } ncs_group { reference = (chain 'B' and (resid 1 through 46 or resid 48 through 117 or (resid 118 and (na \ me N or name CA or name C or name O or name CB )) or resid 119 through 236 or re \ sid 238 through 350)) selection = (chain 'D' and (resid 1 through 46 or resid 48 through 236 or resid 238 through \ 350)) } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.900 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.003 0.092 17097 Z= 0.275 Angle : 0.588 7.243 23580 Z= 0.424 Chirality : 0.042 0.150 2574 Planarity : 0.004 0.054 2653 Dihedral : 18.577 84.171 6626 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.12 % Favored : 95.71 % Rotamer: Outliers : 0.26 % Allowed : 0.19 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1784 helix: 1.44 (0.23), residues: 561 sheet: 0.57 (0.28), residues: 375 loop : -1.07 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 977 TYR 0.015 0.001 TYR C 982 PHE 0.014 0.001 PHE D 48 TRP 0.049 0.002 TRP D 317 HIS 0.006 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.28 (17089) covalent geometry : angle 0.58674 / 0.42 (23576) hydrogen bonds : bond 0.16212 / 11.07 ( 750) hydrogen bonds : angle 6.60729 / 4.62 ( 2086) metal coordination : bond 0.00669 / 0.42 ( 8) metal coordination : angle 3.37822 / 1.83 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.462 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: C 462 LEU cc_start: 0.8510 (mt) cc_final: 0.8163 (mt) REVERT: D 135 GLU cc_start: 0.7609 (pt0) cc_final: 0.7367 (pt0) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1290 time to fit residues: 56.3668 Evaluate side-chains 148 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN B 278 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 GLN C 637 ASN ** C 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1006 HIS D 4 GLN D 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.097590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.070700 restraints weight = 84372.751| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 4.36 r_work: 0.2909 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (15 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17097 Z= 0.193 Angle : 0.614 7.164 23580 Z= 0.336 Chirality : 0.044 0.235 2574 Planarity : 0.005 0.053 2653 Dihedral : 20.395 67.737 3149 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.18 % Favored : 95.60 % Rotamer: Outliers : 2.11 % Allowed : 7.16 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.20), residues: 1784 helix: 1.50 (0.23), residues: 562 sheet: 0.70 (0.28), residues: 358 loop : -0.92 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 927 TYR 0.017 0.001 TYR B 344 PHE 0.025 0.001 PHE C 936 TRP 0.038 0.002 TRP D 317 HIS 0.005 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (17089) covalent geometry : angle 0.61129 / 0.34 (23576) hydrogen bonds : bond 0.04734 / 3.30 ( 750) hydrogen bonds : angle 5.23649 / 3.62 ( 2086) metal coordination : bond 0.00983 / 0.69 ( 8) metal coordination : angle 4.45244 / 2.47 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8044 (ptt90) cc_final: 0.7358 (ptt90) REVERT: A 823 LYS cc_start: 0.8284 (mmmt) cc_final: 0.8080 (mmmt) REVERT: A 984 MET cc_start: 0.8581 (mmm) cc_final: 0.8174 (mmm) REVERT: C 716 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8098 (mt-10) REVERT: C 770 GLU cc_start: 0.8863 (mp0) cc_final: 0.8624 (mp0) REVERT: D 4 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8161 (tp-100) REVERT: D 5 MET cc_start: 0.8011 (tpp) cc_final: 0.7721 (tpt) outliers start: 29 outliers final: 20 residues processed: 159 average time/residue: 0.1184 time to fit residues: 29.0636 Evaluate side-chains 144 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 341 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 118 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 182 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 744 HIS B 166 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.098036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.070560 restraints weight = 93116.863| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 4.57 r_work: 0.2903 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17097 Z= 0.136 Angle : 0.552 6.980 23580 Z= 0.306 Chirality : 0.042 0.159 2574 Planarity : 0.004 0.044 2653 Dihedral : 20.449 79.401 3149 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.89 % Favored : 95.88 % Rotamer: Outliers : 1.60 % Allowed : 10.03 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1784 helix: 1.50 (0.23), residues: 562 sheet: 0.69 (0.28), residues: 359 loop : -0.84 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 529 TYR 0.013 0.001 TYR B 344 PHE 0.010 0.001 PHE B 24 TRP 0.035 0.001 TRP B 317 HIS 0.004 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (17089) covalent geometry : angle 0.54907 / 0.31 (23576) hydrogen bonds : bond 0.03968 / 2.77 ( 750) hydrogen bonds : angle 4.97894 / 3.42 ( 2086) metal coordination : bond 0.00579 / 0.39 ( 8) metal coordination : angle 4.36891 / 2.39 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8080 (ptt90) cc_final: 0.7385 (ptt90) REVERT: A 662 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7790 (tm-30) REVERT: A 984 MET cc_start: 0.8678 (mmm) cc_final: 0.8339 (mmm) REVERT: C 679 ARG cc_start: 0.9065 (ttp-170) cc_final: 0.8617 (ttp80) REVERT: C 691 MET cc_start: 0.8624 (ttm) cc_final: 0.8301 (ttm) REVERT: C 716 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8194 (mt-10) REVERT: C 770 GLU cc_start: 0.8888 (mp0) cc_final: 0.8671 (mp0) REVERT: C 809 GLN cc_start: 0.8251 (tt0) cc_final: 0.7964 (tt0) REVERT: C 983 GLU cc_start: 0.8693 (pp20) cc_final: 0.8265 (pp20) outliers start: 20 outliers final: 17 residues processed: 147 average time/residue: 0.1221 time to fit residues: 27.7380 Evaluate side-chains 141 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 341 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 56 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 chunk 96 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 151 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 147 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 ASN D 4 GLN D 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.098226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.071032 restraints weight = 99665.524| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 4.69 r_work: 0.2908 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17097 Z= 0.119 Angle : 0.536 9.918 23580 Z= 0.296 Chirality : 0.041 0.161 2574 Planarity : 0.004 0.048 2653 Dihedral : 20.445 77.824 3149 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.06 % Favored : 95.77 % Rotamer: Outliers : 1.73 % Allowed : 10.99 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.20), residues: 1784 helix: 1.55 (0.23), residues: 563 sheet: 0.77 (0.28), residues: 359 loop : -0.81 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 529 TYR 0.012 0.001 TYR A 757 PHE 0.008 0.001 PHE B 48 TRP 0.034 0.001 TRP B 317 HIS 0.003 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (17089) covalent geometry : angle 0.53335 / 0.30 (23576) hydrogen bonds : bond 0.03589 / 2.51 ( 750) hydrogen bonds : angle 4.82112 / 3.30 ( 2086) metal coordination : bond 0.00508 / 0.36 ( 8) metal coordination : angle 4.05443 / 2.18 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8109 (ptt90) cc_final: 0.7422 (ptt90) REVERT: A 662 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7733 (tm-30) REVERT: C 691 MET cc_start: 0.8654 (ttm) cc_final: 0.8303 (ttm) REVERT: C 716 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8251 (mt-10) REVERT: C 770 GLU cc_start: 0.8909 (mp0) cc_final: 0.8688 (mp0) REVERT: C 983 GLU cc_start: 0.8618 (pp20) cc_final: 0.8324 (pp20) REVERT: D 4 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8450 (tp40) outliers start: 22 outliers final: 16 residues processed: 153 average time/residue: 0.1117 time to fit residues: 26.6475 Evaluate side-chains 130 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 341 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 183 optimal weight: 50.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN D 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.069880 restraints weight = 104474.643| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 4.75 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17097 Z= 0.128 Angle : 0.531 8.696 23580 Z= 0.291 Chirality : 0.041 0.162 2574 Planarity : 0.004 0.046 2653 Dihedral : 20.483 77.948 3149 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.01 % Favored : 95.88 % Rotamer: Outliers : 1.92 % Allowed : 11.88 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.20), residues: 1784 helix: 1.60 (0.23), residues: 565 sheet: 0.69 (0.29), residues: 344 loop : -0.77 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 828 TYR 0.014 0.001 TYR D 344 PHE 0.014 0.001 PHE D 48 TRP 0.034 0.001 TRP B 317 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (17089) covalent geometry : angle 0.52867 / 0.29 (23576) hydrogen bonds : bond 0.03532 / 2.46 ( 750) hydrogen bonds : angle 4.68601 / 3.21 ( 2086) metal coordination : bond 0.00536 / 0.35 ( 8) metal coordination : angle 3.88582 / 2.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.7914 (ptt90) cc_final: 0.7243 (ptt90) REVERT: A 662 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7483 (tm-30) REVERT: B 91 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: B 331 ILE cc_start: 0.9336 (mm) cc_final: 0.9115 (tt) REVERT: C 691 MET cc_start: 0.8524 (ttm) cc_final: 0.8279 (ttm) REVERT: C 716 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7820 (mt-10) REVERT: C 770 GLU cc_start: 0.8663 (mp0) cc_final: 0.8422 (mp0) REVERT: C 983 GLU cc_start: 0.8523 (pp20) cc_final: 0.8109 (pp20) REVERT: D 344 TYR cc_start: 0.8694 (m-10) cc_final: 0.8323 (m-10) outliers start: 27 outliers final: 21 residues processed: 137 average time/residue: 0.1335 time to fit residues: 28.4809 Evaluate side-chains 137 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 341 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 45 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 183 optimal weight: 50.0000 chunk 56 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 49 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 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 = 0.3587 r_free = 0.3587 target = 0.097817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.070578 restraints weight = 102604.468| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 4.75 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17097 Z= 0.110 Angle : 0.518 9.681 23580 Z= 0.283 Chirality : 0.040 0.160 2574 Planarity : 0.003 0.044 2653 Dihedral : 20.461 77.851 3149 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.12 % Favored : 95.77 % Rotamer: Outliers : 1.85 % Allowed : 12.46 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1784 helix: 1.67 (0.23), residues: 565 sheet: 0.70 (0.28), residues: 348 loop : -0.72 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 529 TYR 0.012 0.001 TYR D 344 PHE 0.010 0.001 PHE B 48 TRP 0.032 0.001 TRP B 317 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (17089) covalent geometry : angle 0.51555 / 0.28 (23576) hydrogen bonds : bond 0.03291 / 2.30 ( 750) hydrogen bonds : angle 4.59892 / 3.14 ( 2086) metal coordination : bond 0.00485 / 0.34 ( 8) metal coordination : angle 3.61063 / 2.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.7951 (ptt90) cc_final: 0.7234 (ptt90) REVERT: A 662 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7420 (tm-30) REVERT: B 91 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: B 331 ILE cc_start: 0.9323 (mm) cc_final: 0.9103 (tt) REVERT: C 524 LYS cc_start: 0.8703 (mmmt) cc_final: 0.8356 (ptmm) REVERT: C 572 GLU cc_start: 0.8771 (pm20) cc_final: 0.8551 (pm20) REVERT: C 600 ASP cc_start: 0.8375 (t0) cc_final: 0.8162 (t0) REVERT: C 691 MET cc_start: 0.8494 (ttm) cc_final: 0.8209 (ttm) REVERT: C 770 GLU cc_start: 0.8669 (mp0) cc_final: 0.8426 (mp0) REVERT: C 936 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8744 (m-10) REVERT: C 983 GLU cc_start: 0.8444 (pp20) cc_final: 0.7876 (pp20) REVERT: D 285 MET cc_start: 0.9265 (mmp) cc_final: 0.8897 (mmm) REVERT: D 344 TYR cc_start: 0.8696 (m-10) cc_final: 0.8306 (m-10) outliers start: 26 outliers final: 21 residues processed: 140 average time/residue: 0.1235 time to fit residues: 26.7449 Evaluate side-chains 139 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 341 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 131 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 ASN ** C 473 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 = 0.3557 r_free = 0.3557 target = 0.095969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.068562 restraints weight = 101927.097| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 4.71 r_work: 0.2864 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17097 Z= 0.144 Angle : 0.533 9.068 23580 Z= 0.289 Chirality : 0.041 0.161 2574 Planarity : 0.004 0.044 2653 Dihedral : 20.556 76.680 3149 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.06 % Favored : 95.82 % Rotamer: Outliers : 2.04 % Allowed : 12.33 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.20), residues: 1784 helix: 1.74 (0.23), residues: 565 sheet: 0.67 (0.28), residues: 351 loop : -0.73 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 148 TYR 0.012 0.001 TYR A 757 PHE 0.010 0.001 PHE D 48 TRP 0.034 0.001 TRP B 317 HIS 0.005 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (17089) covalent geometry : angle 0.53045 / 0.29 (23576) hydrogen bonds : bond 0.03522 / 2.45 ( 750) hydrogen bonds : angle 4.54376 / 3.11 ( 2086) metal coordination : bond 0.00720 / 0.47 ( 8) metal coordination : angle 3.73852 / 2.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8167 (ptt90) cc_final: 0.7440 (ptt90) REVERT: A 662 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7793 (tm-30) REVERT: B 91 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.8469 (m-80) REVERT: B 331 ILE cc_start: 0.9378 (mm) cc_final: 0.9161 (tt) REVERT: C 524 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8403 (ptmm) REVERT: C 572 GLU cc_start: 0.8979 (pm20) cc_final: 0.8765 (pm20) REVERT: C 691 MET cc_start: 0.8685 (ttm) cc_final: 0.8426 (ttm) REVERT: C 883 MET cc_start: 0.8383 (tpp) cc_final: 0.7854 (tpt) REVERT: C 936 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8893 (m-10) REVERT: C 983 GLU cc_start: 0.8759 (pp20) cc_final: 0.8298 (pp20) REVERT: D 344 TYR cc_start: 0.9083 (m-10) cc_final: 0.8707 (m-10) outliers start: 29 outliers final: 19 residues processed: 136 average time/residue: 0.1242 time to fit residues: 26.1219 Evaluate side-chains 132 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 341 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 181 optimal weight: 40.0000 chunk 63 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 174 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 830 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.093477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.065947 restraints weight = 99322.964| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 4.63 r_work: 0.2813 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17097 Z= 0.194 Angle : 0.584 12.219 23580 Z= 0.312 Chirality : 0.043 0.177 2574 Planarity : 0.004 0.045 2653 Dihedral : 20.718 74.106 3149 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.35 % Favored : 95.54 % Rotamer: Outliers : 1.85 % Allowed : 12.84 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.20), residues: 1784 helix: 1.69 (0.23), residues: 565 sheet: 0.63 (0.28), residues: 348 loop : -0.73 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 894 TYR 0.014 0.001 TYR A 757 PHE 0.013 0.001 PHE A 916 TRP 0.040 0.002 TRP B 317 HIS 0.006 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (17089) covalent geometry : angle 0.58079 / 0.31 (23576) hydrogen bonds : bond 0.03907 / 2.71 ( 750) hydrogen bonds : angle 4.58480 / 3.15 ( 2086) metal coordination : bond 0.01090 / 0.74 ( 8) metal coordination : angle 4.35792 / 2.53 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8121 (ptt90) cc_final: 0.7450 (ptt90) REVERT: A 662 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7842 (tm-30) REVERT: B 91 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: C 524 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8410 (ptmm) REVERT: C 883 MET cc_start: 0.8637 (tpp) cc_final: 0.8249 (tpt) REVERT: C 936 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.8979 (m-10) REVERT: D 344 TYR cc_start: 0.9097 (m-10) cc_final: 0.8670 (m-10) outliers start: 26 outliers final: 20 residues processed: 132 average time/residue: 0.1357 time to fit residues: 27.2850 Evaluate side-chains 135 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 341 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 162 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 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 = 0.3528 r_free = 0.3528 target = 0.094148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.067152 restraints weight = 74624.608| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 4.11 r_work: 0.2850 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17097 Z= 0.157 Angle : 0.551 8.139 23580 Z= 0.299 Chirality : 0.042 0.160 2574 Planarity : 0.004 0.042 2653 Dihedral : 20.699 74.292 3149 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.06 % Favored : 95.82 % Rotamer: Outliers : 1.66 % Allowed : 13.16 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1784 helix: 1.70 (0.23), residues: 565 sheet: 0.63 (0.28), residues: 348 loop : -0.71 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 529 TYR 0.013 0.001 TYR A 757 PHE 0.010 0.001 PHE A 916 TRP 0.038 0.001 TRP B 317 HIS 0.005 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (17089) covalent geometry : angle 0.54847 / 0.30 (23576) hydrogen bonds : bond 0.03603 / 2.51 ( 750) hydrogen bonds : angle 4.52842 / 3.10 ( 2086) metal coordination : bond 0.00839 / 0.56 ( 8) metal coordination : angle 4.16493 / 2.41 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8087 (ptt90) cc_final: 0.7427 (ptt90) REVERT: A 662 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7769 (tm-30) REVERT: B 91 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: C 524 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8436 (ptmm) REVERT: C 568 MET cc_start: 0.9203 (mmm) cc_final: 0.8999 (mmm) REVERT: C 936 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8931 (m-10) REVERT: D 344 TYR cc_start: 0.9062 (m-10) cc_final: 0.8616 (m-10) outliers start: 23 outliers final: 19 residues processed: 132 average time/residue: 0.1360 time to fit residues: 27.4225 Evaluate side-chains 129 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 341 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 145 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 128 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 914 GLN B 47 HIS B ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.095929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.068763 restraints weight = 89436.762| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 4.46 r_work: 0.2876 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17097 Z= 0.116 Angle : 0.535 9.516 23580 Z= 0.290 Chirality : 0.041 0.157 2574 Planarity : 0.004 0.043 2653 Dihedral : 20.624 75.739 3149 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.18 % Favored : 95.71 % Rotamer: Outliers : 1.60 % Allowed : 13.10 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.20), residues: 1784 helix: 1.80 (0.23), residues: 565 sheet: 0.65 (0.29), residues: 342 loop : -0.71 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 529 TYR 0.013 0.001 TYR A 757 PHE 0.011 0.001 PHE B 48 TRP 0.034 0.001 TRP B 317 HIS 0.004 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (17089) covalent geometry : angle 0.53233 / 0.29 (23576) hydrogen bonds : bond 0.03262 / 2.28 ( 750) hydrogen bonds : angle 4.46114 / 3.05 ( 2086) metal coordination : bond 0.00602 / 0.42 ( 8) metal coordination : angle 3.82931 / 2.21 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8082 (ptt90) cc_final: 0.7320 (ptt90) REVERT: A 662 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7769 (tm-30) REVERT: B 91 TYR cc_start: 0.8968 (OUTLIER) cc_final: 0.8504 (m-80) REVERT: C 524 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8407 (ptmm) REVERT: C 936 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8924 (m-10) REVERT: D 344 TYR cc_start: 0.9045 (m-10) cc_final: 0.8561 (m-10) outliers start: 21 outliers final: 16 residues processed: 132 average time/residue: 0.1334 time to fit residues: 26.9107 Evaluate side-chains 126 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 341 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 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 = 0.3553 r_free = 0.3553 target = 0.095735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.068532 restraints weight = 88743.318| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 4.45 r_work: 0.2871 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17097 Z= 0.122 Angle : 0.532 9.151 23580 Z= 0.288 Chirality : 0.041 0.157 2574 Planarity : 0.004 0.043 2653 Dihedral : 20.632 75.701 3149 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 1.60 % Allowed : 13.42 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1784 helix: 1.79 (0.23), residues: 565 sheet: 0.67 (0.29), residues: 342 loop : -0.70 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 529 TYR 0.013 0.001 TYR A 757 PHE 0.015 0.001 PHE C 924 TRP 0.034 0.001 TRP B 317 HIS 0.004 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (17089) covalent geometry : angle 0.52992 / 0.29 (23576) hydrogen bonds : bond 0.03284 / 2.29 ( 750) hydrogen bonds : angle 4.42499 / 3.03 ( 2086) metal coordination : bond 0.00623 / 0.42 ( 8) metal coordination : angle 3.68574 / 2.14 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3928.17 seconds wall clock time: 68 minutes 3.91 seconds (4083.91 seconds total)