Starting phenix.real_space_refine on Thu Aug 6 19:18:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqn_61730/08_2026/9jqn_61730.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqn_61730/08_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_61730/08_2026/9jqn_61730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqn_61730/08_2026/9jqn_61730.map" model { file = "/net/cci-nas-00/data/ceres_data/9jqn_61730/08_2026/9jqn_61730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqn_61730/08_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-2.2rc3-6140/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, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 5.22, per 1000 atoms: 0.32 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: 1.13 Conformation dependent library (CDL) restraints added in 903.0 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: 1.69 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: 3.31 Time building geometry restraints manager: 1.52 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.540 Find NCS groups from input model: 0.340 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.530 ------------------------------------------------------------------------------- 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 : 0.590 7.243 23580 Z= 0.425 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 0.58822 / 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 : 0.493 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: 0.1276 time to fit residues: 56.3297 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 : 0.465 ------------------------------------------------------------------------------- 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 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3582 r_free = 0.3582 target = 0.097649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.070772 restraints weight = 84365.844| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 4.35 r_work: 0.2910 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 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 = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (15 function evaluations) r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17097 Z= 0.188 Angle : 0.616 7.159 23580 Z= 0.337 Chirality : 0.044 0.196 2574 Planarity : 0.005 0.056 2653 Dihedral : 20.384 67.519 3149 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.01 % Favored : 95.77 % Rotamer: Outliers : 2.04 % Allowed : 7.35 % Favored : 90.61 % 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: 1.49 (0.23), residues: 562 sheet: 0.72 (0.28), residues: 358 loop : -0.93 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 529 TYR 0.016 0.001 TYR B 344 PHE 0.024 0.001 PHE C 936 TRP 0.041 0.002 TRP D 317 HIS 0.005 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (17089) covalent geometry : angle 0.61318 / 0.34 (23576) hydrogen bonds : bond 0.04653 / 3.26 ( 750) hydrogen bonds : angle 5.23253 / 3.62 ( 2086) metal coordination : bond 0.01061 / 0.74 ( 8) metal coordination : angle 4.46228 / 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: 28 poor density : 144 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8064 (ptt90) cc_final: 0.7376 (ptt90) REVERT: A 823 LYS cc_start: 0.8295 (mmmt) cc_final: 0.8091 (mmmt) REVERT: A 984 MET cc_start: 0.8570 (mmm) cc_final: 0.8151 (mmm) REVERT: C 716 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8073 (mt-10) REVERT: C 770 GLU cc_start: 0.8871 (mp0) cc_final: 0.8634 (mp0) REVERT: D 4 GLN cc_start: 0.8476 (tp-100) cc_final: 0.8154 (tp-100) outliers start: 28 outliers final: 20 residues processed: 161 average time/residue: 0.1039 time to fit residues: 25.9016 Evaluate side-chains 148 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 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 114 CYS Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 264 THR 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: 0.6980 chunk 43 optimal weight: 0.0970 chunk 91 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 182 optimal weight: 20.0000 chunk 141 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.098320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.071250 restraints weight = 91658.240| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 4.52 r_work: 0.2917 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17097 Z= 0.124 Angle : 0.543 6.816 23580 Z= 0.302 Chirality : 0.042 0.162 2574 Planarity : 0.004 0.051 2653 Dihedral : 20.418 81.319 3149 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.78 % Favored : 96.05 % Rotamer: Outliers : 1.73 % Allowed : 10.03 % Favored : 88.24 % 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: 0.36 (0.20), residues: 1784 helix: 1.52 (0.23), residues: 561 sheet: 0.70 (0.28), residues: 359 loop : -0.83 (0.21), residues: 864 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 D 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 0.00256 / 0.12 (17089) covalent geometry : angle 0.54057 / 0.30 (23576) hydrogen bonds : bond 0.03837 / 2.68 ( 750) hydrogen bonds : angle 4.96114 / 3.40 ( 2086) metal coordination : bond 0.00495 / 0.34 ( 8) metal coordination : angle 4.29134 / 2.33 ( 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 160 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8069 (ptt90) cc_final: 0.7381 (ptt90) REVERT: A 662 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7664 (tm-30) REVERT: A 984 MET cc_start: 0.8660 (mmm) cc_final: 0.8299 (mmm) REVERT: C 462 LEU cc_start: 0.8749 (mt) cc_final: 0.8487 (mt) REVERT: C 679 ARG cc_start: 0.9051 (ttp-170) cc_final: 0.8576 (ttp80) REVERT: C 770 GLU cc_start: 0.8878 (mp0) cc_final: 0.8673 (mp0) REVERT: C 983 GLU cc_start: 0.8662 (pp20) cc_final: 0.8288 (pp20) REVERT: D 317 TRP cc_start: 0.8436 (p90) cc_final: 0.7434 (p90) outliers start: 22 outliers final: 18 residues processed: 152 average time/residue: 0.1207 time to fit residues: 28.4250 Evaluate side-chains 142 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 287 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 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 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 302 MET 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: 1.9990 chunk 50 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN ** A 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN D 4 GLN D 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.093807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.066016 restraints weight = 101797.962| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.68 r_work: 0.2807 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17097 Z= 0.248 Angle : 0.620 10.930 23580 Z= 0.335 Chirality : 0.044 0.180 2574 Planarity : 0.004 0.052 2653 Dihedral : 20.690 75.421 3149 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.85 % Favored : 94.92 % Rotamer: Outliers : 2.11 % Allowed : 10.80 % Favored : 87.09 % 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: 0.31 (0.20), residues: 1784 helix: 1.49 (0.23), residues: 565 sheet: 0.56 (0.28), residues: 360 loop : -0.81 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 148 TYR 0.014 0.002 TYR A 805 PHE 0.015 0.001 PHE A 916 TRP 0.042 0.002 TRP B 317 HIS 0.007 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.25 (17089) covalent geometry : angle 0.61707 / 0.34 (23576) hydrogen bonds : bond 0.04478 / 3.11 ( 750) hydrogen bonds : angle 4.86772 / 3.34 ( 2086) metal coordination : bond 0.01332 / 0.89 ( 8) metal coordination : angle 4.65648 / 2.63 ( 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 151 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8115 (ptt90) cc_final: 0.7421 (ptt90) REVERT: A 662 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7872 (tm-30) REVERT: A 664 ASP cc_start: 0.8606 (t70) cc_final: 0.7817 (t70) REVERT: C 691 MET cc_start: 0.8794 (ttm) cc_final: 0.8532 (ttm) REVERT: D 5 MET cc_start: 0.8244 (tpp) cc_final: 0.7953 (tpp) outliers start: 30 outliers final: 25 residues processed: 143 average time/residue: 0.1289 time to fit residues: 28.0238 Evaluate side-chains 134 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 651 CYS Chi-restraints excluded: chain A residue 866 VAL 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 287 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 606 SER Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 803 GLU Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 947 ILE 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: 0.6980 chunk 16 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 0.0570 chunk 104 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 183 optimal weight: 50.0000 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.096175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.068300 restraints weight = 106069.221| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 4.83 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17097 Z= 0.120 Angle : 0.538 8.874 23580 Z= 0.296 Chirality : 0.041 0.167 2574 Planarity : 0.004 0.052 2653 Dihedral : 20.577 76.387 3149 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.12 % Favored : 95.71 % Rotamer: Outliers : 1.73 % Allowed : 11.44 % Favored : 86.84 % 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: 0.40 (0.20), residues: 1784 helix: 1.57 (0.23), residues: 565 sheet: 0.61 (0.28), residues: 354 loop : -0.76 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 529 TYR 0.013 0.001 TYR A 757 PHE 0.013 0.001 PHE D 48 TRP 0.037 0.001 TRP B 317 HIS 0.004 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (17089) covalent geometry : angle 0.53534 / 0.30 (23576) hydrogen bonds : bond 0.03595 / 2.51 ( 750) hydrogen bonds : angle 4.73915 / 3.24 ( 2086) metal coordination : bond 0.00597 / 0.42 ( 8) metal coordination : angle 4.38722 / 2.47 ( 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 145 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.7902 (ptt90) cc_final: 0.7211 (ptt90) REVERT: A 662 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 828 ARG cc_start: 0.8695 (mtp85) cc_final: 0.8386 (mmm160) REVERT: C 568 MET cc_start: 0.8916 (mmm) cc_final: 0.8601 (mmm) REVERT: C 691 MET cc_start: 0.8508 (ttm) cc_final: 0.8261 (ttm) REVERT: D 344 TYR cc_start: 0.8585 (m-10) cc_final: 0.8251 (m-10) outliers start: 24 outliers final: 21 residues processed: 139 average time/residue: 0.1357 time to fit residues: 28.7380 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 : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 575 LEU 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 208 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 317 TRP 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 663 SER Chi-restraints excluded: chain C residue 847 MET 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 317 TRP 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: 5.9990 chunk 73 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 183 optimal weight: 40.0000 chunk 56 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.093855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.066608 restraints weight = 102678.611| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.65 r_work: 0.2821 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17097 Z= 0.172 Angle : 0.556 8.290 23580 Z= 0.303 Chirality : 0.042 0.169 2574 Planarity : 0.004 0.088 2653 Dihedral : 20.638 75.688 3149 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.57 % Favored : 95.32 % Rotamer: Outliers : 1.92 % Allowed : 12.20 % Favored : 85.88 % 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: 0.39 (0.20), residues: 1784 helix: 1.62 (0.23), residues: 565 sheet: 0.53 (0.28), residues: 350 loop : -0.76 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 828 TYR 0.014 0.001 TYR A 757 PHE 0.011 0.001 PHE D 48 TRP 0.038 0.001 TRP B 317 HIS 0.005 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (17089) covalent geometry : angle 0.55337 / 0.30 (23576) hydrogen bonds : bond 0.03849 / 2.67 ( 750) hydrogen bonds : angle 4.65076 / 3.19 ( 2086) metal coordination : bond 0.00929 / 0.62 ( 8) metal coordination : angle 4.16801 / 2.37 ( 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 139 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8149 (ptt90) cc_final: 0.7480 (ptt90) REVERT: A 662 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7886 (tm-30) REVERT: C 524 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8416 (ptmm) REVERT: C 568 MET cc_start: 0.9284 (mmm) cc_final: 0.9043 (mmm) REVERT: C 691 MET cc_start: 0.8743 (ttm) cc_final: 0.8418 (ttm) REVERT: C 936 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8954 (m-10) outliers start: 27 outliers final: 25 residues processed: 133 average time/residue: 0.1393 time to fit residues: 28.4258 Evaluate side-chains 134 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 575 LEU 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 287 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 606 SER Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 736 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 131 optimal weight: 0.0270 chunk 117 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 0.0470 chunk 20 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.095670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.068246 restraints weight = 101647.472| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 4.69 r_work: 0.2859 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17097 Z= 0.112 Angle : 0.519 8.322 23580 Z= 0.285 Chirality : 0.041 0.164 2574 Planarity : 0.004 0.073 2653 Dihedral : 20.567 76.424 3149 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.84 % Favored : 96.05 % Rotamer: Outliers : 1.98 % Allowed : 12.78 % Favored : 85.24 % 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: 0.46 (0.20), residues: 1784 helix: 1.67 (0.23), residues: 565 sheet: 0.64 (0.28), residues: 351 loop : -0.75 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 529 TYR 0.014 0.001 TYR D 344 PHE 0.010 0.001 PHE B 48 TRP 0.036 0.001 TRP B 317 HIS 0.004 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (17089) covalent geometry : angle 0.51663 / 0.29 (23576) hydrogen bonds : bond 0.03351 / 2.34 ( 750) hydrogen bonds : angle 4.56236 / 3.12 ( 2086) metal coordination : bond 0.00579 / 0.41 ( 8) metal coordination : angle 4.03608 / 2.27 ( 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 143 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8138 (ptt90) cc_final: 0.7477 (ptt90) REVERT: A 662 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 883 MET cc_start: 0.8506 (tpt) cc_final: 0.8043 (tpt) REVERT: B 91 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: C 524 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8413 (ptmm) REVERT: C 600 ASP cc_start: 0.8637 (t0) cc_final: 0.8361 (t0) REVERT: C 691 MET cc_start: 0.8687 (ttm) cc_final: 0.8455 (ttm) REVERT: C 883 MET cc_start: 0.8303 (tpp) cc_final: 0.7866 (tpt) REVERT: C 936 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8927 (m-10) outliers start: 28 outliers final: 22 residues processed: 137 average time/residue: 0.1178 time to fit residues: 25.5531 Evaluate side-chains 140 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 575 LEU 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 208 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 287 CYS 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 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 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: 1.9990 chunk 51 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 181 optimal weight: 40.0000 chunk 63 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 914 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.093642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.066219 restraints weight = 99445.208| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 4.63 r_work: 0.2815 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 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 (9 function evaluations) r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 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 0.040 17097 Z= 0.178 Angle : 0.550 8.043 23580 Z= 0.299 Chirality : 0.042 0.167 2574 Planarity : 0.004 0.050 2653 Dihedral : 20.669 75.071 3149 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.46 % Favored : 95.43 % Rotamer: Outliers : 2.04 % Allowed : 12.78 % 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: 0.48 (0.20), residues: 1784 helix: 1.67 (0.23), residues: 565 sheet: 0.66 (0.28), residues: 348 loop : -0.73 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 828 TYR 0.014 0.001 TYR A 757 PHE 0.012 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 0.00400 / 0.18 (17089) covalent geometry : angle 0.54761 / 0.30 (23576) hydrogen bonds : bond 0.03772 / 2.62 ( 750) hydrogen bonds : angle 4.53880 / 3.11 ( 2086) metal coordination : bond 0.00962 / 0.65 ( 8) metal coordination : angle 4.16172 / 2.39 ( 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 141 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8102 (ptt90) cc_final: 0.7441 (ptt90) REVERT: A 662 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 91 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.8494 (m-80) REVERT: B 278 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8879 (mt0) REVERT: C 524 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8446 (ptmm) REVERT: C 936 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8961 (m-10) outliers start: 29 outliers final: 23 residues processed: 134 average time/residue: 0.1323 time to fit residues: 27.4623 Evaluate side-chains 137 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 575 LEU 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 278 GLN 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 736 GLU 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 C residue 982 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 162 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 147 optimal weight: 0.0050 chunk 161 optimal weight: 0.0270 chunk 140 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 overall best weight: 0.9456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.094968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.068071 restraints weight = 74500.407| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 4.13 r_work: 0.2866 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 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 = 0.2882 r_free = 0.2882 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: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2547 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= 0.124 Angle : 0.534 10.009 23580 Z= 0.290 Chirality : 0.041 0.163 2574 Planarity : 0.004 0.042 2653 Dihedral : 20.630 75.332 3149 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.18 % Favored : 95.71 % Rotamer: Outliers : 2.04 % Allowed : 12.91 % Favored : 85.05 % 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: 1.67 (0.23), residues: 565 sheet: 0.72 (0.29), residues: 342 loop : -0.72 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 529 TYR 0.013 0.001 TYR A 757 PHE 0.011 0.001 PHE B 48 TRP 0.036 0.001 TRP B 317 HIS 0.004 0.001 HIS C 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (17089) covalent geometry : angle 0.53179 / 0.29 (23576) hydrogen bonds : bond 0.03393 / 2.37 ( 750) hydrogen bonds : angle 4.50226 / 3.08 ( 2086) metal coordination : bond 0.00616 / 0.42 ( 8) metal coordination : angle 4.03607 / 2.30 ( 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 145 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8074 (ptt90) cc_final: 0.7414 (ptt90) REVERT: A 662 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7745 (tm-30) REVERT: B 91 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8477 (m-80) REVERT: B 278 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8913 (mt0) REVERT: C 524 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8396 (ptmm) REVERT: C 600 ASP cc_start: 0.8631 (t0) cc_final: 0.8407 (t0) REVERT: C 883 MET cc_start: 0.8515 (tpp) cc_final: 0.8038 (tpt) REVERT: C 936 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8938 (m-10) outliers start: 29 outliers final: 22 residues processed: 138 average time/residue: 0.1255 time to fit residues: 26.9650 Evaluate side-chains 137 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 575 LEU 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 218 ILE Chi-restraints excluded: chain B residue 278 GLN 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 736 GLU Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 982 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 145 optimal weight: 0.0870 chunk 74 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 0.0030 chunk 98 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 168 optimal weight: 0.0770 overall best weight: 0.3728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 47 HIS B ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS B Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.096674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.069616 restraints weight = 96897.976| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.60 r_work: 0.2886 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 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 = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17097 Z= 0.107 Angle : 0.526 10.073 23580 Z= 0.285 Chirality : 0.040 0.161 2574 Planarity : 0.003 0.043 2653 Dihedral : 20.547 76.986 3149 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.89 % Favored : 95.99 % Rotamer: Outliers : 1.41 % Allowed : 13.55 % Favored : 85.05 % 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: 1.78 (0.23), residues: 563 sheet: 0.68 (0.29), residues: 345 loop : -0.72 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 529 TYR 0.013 0.001 TYR A 757 PHE 0.010 0.001 PHE B 48 TRP 0.030 0.001 TRP B 317 HIS 0.004 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (17089) covalent geometry : angle 0.52415 / 0.28 (23576) hydrogen bonds : bond 0.03115 / 2.17 ( 750) hydrogen bonds : angle 4.42397 / 3.02 ( 2086) metal coordination : bond 0.00574 / 0.41 ( 8) metal coordination : angle 3.68836 / 2.07 ( 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 138 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8070 (ptt90) cc_final: 0.7430 (ptt90) REVERT: A 662 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7808 (tm-30) REVERT: A 828 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.8488 (mmm160) REVERT: B 91 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8567 (m-80) REVERT: B 278 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8935 (mt0) REVERT: B 331 ILE cc_start: 0.9361 (mm) cc_final: 0.9151 (tt) REVERT: C 524 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8414 (ptmm) REVERT: C 883 MET cc_start: 0.8547 (tpp) cc_final: 0.8119 (tpt) REVERT: C 936 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8897 (m-10) REVERT: D 5 MET cc_start: 0.8266 (mmm) cc_final: 0.7827 (tpt) outliers start: 19 outliers final: 15 residues processed: 134 average time/residue: 0.1365 time to fit residues: 28.6079 Evaluate side-chains 129 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 575 LEU 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 218 ILE Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 598 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 264 THR 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 34 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 16 optimal weight: 0.0030 chunk 92 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 99 optimal weight: 0.1980 chunk 58 optimal weight: 0.1980 overall best weight: 0.2790 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.098425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.071137 restraints weight = 97918.698| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 4.68 r_work: 0.2935 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17097 Z= 0.104 Angle : 0.517 9.832 23580 Z= 0.279 Chirality : 0.040 0.160 2574 Planarity : 0.003 0.043 2653 Dihedral : 20.544 76.948 3149 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.61 % Favored : 96.28 % Rotamer: Outliers : 1.47 % Allowed : 13.67 % Favored : 84.86 % 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: 0.58 (0.20), residues: 1784 helix: 1.78 (0.22), residues: 563 sheet: 0.74 (0.29), residues: 336 loop : -0.67 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 529 TYR 0.013 0.001 TYR A 757 PHE 0.010 0.001 PHE B 48 TRP 0.030 0.001 TRP B 317 HIS 0.004 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (17089) covalent geometry : angle 0.51513 / 0.28 (23576) hydrogen bonds : bond 0.03048 / 2.12 ( 750) hydrogen bonds : angle 4.39231 / 3.00 ( 2086) metal coordination : bond 0.00519 / 0.37 ( 8) metal coordination : angle 3.45236 / 1.96 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4062.38 seconds wall clock time: 70 minutes 15.89 seconds (4215.89 seconds total)