Starting phenix.real_space_refine on Thu Sep 18 12:56:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqn_61730/09_2025/9jqn_61730.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqn_61730/09_2025/9jqn_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_61730/09_2025/9jqn_61730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqn_61730/09_2025/9jqn_61730.map" model { file = "/net/cci-nas-00/data/ceres_data/9jqn_61730/09_2025/9jqn_61730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqn_61730/09_2025/9jqn_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-2.0-5805/lib/python3.9/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: 5.12, per 1000 atoms: 0.31 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: 1.30 Conformation dependent library (CDL) restraints added in 962.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 2.15 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: 3.18 Time building geometry restraints manager: 1.72 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=" CB PRO A 898 " pdb=" CG PRO A 898 " ideal model delta sigma weight residual 1.492 1.584 -0.092 5.00e-02 4.00e+02 3.42e+00 bond pdb=" CG PRO A 898 " pdb=" CD PRO A 898 " ideal model delta sigma weight residual 1.503 1.537 -0.034 3.40e-02 8.65e+02 1.01e+00 bond pdb=" CG PRO C 521 " pdb=" CD PRO C 521 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.32e-01 bond pdb=" CB GLU A 576 " pdb=" CG GLU A 576 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.31e-01 bond pdb=" CA TYR C 982 " pdb=" CB TYR C 982 " ideal model delta sigma weight residual 1.526 1.540 -0.014 1.68e-02 3.54e+03 7.00e-01 ... (remaining 17084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 22988 1.45 - 2.90: 485 2.90 - 4.35: 86 4.35 - 5.79: 15 5.79 - 7.24: 2 Bond angle restraints: 23576 Sorted by residual: angle pdb=" CA PRO A 898 " pdb=" N PRO A 898 " pdb=" CD PRO A 898 " ideal model delta sigma weight residual 112.00 107.09 4.91 1.40e+00 5.10e-01 1.23e+01 angle pdb=" N GLY C 717 " pdb=" CA GLY C 717 " pdb=" C GLY C 717 " ideal model delta sigma weight residual 113.18 120.42 -7.24 2.37e+00 1.78e-01 9.34e+00 angle pdb=" N TYR C 514 " pdb=" CA TYR C 514 " pdb=" C TYR C 514 " ideal model delta sigma weight residual 114.56 110.82 3.74 1.27e+00 6.20e-01 8.70e+00 angle pdb=" N GLN C 914 " pdb=" CA GLN C 914 " pdb=" CB GLN C 914 " ideal model delta sigma weight residual 110.12 114.12 -4.00 1.47e+00 4.63e-01 7.41e+00 angle pdb=" N TYR C 982 " pdb=" CA TYR C 982 " pdb=" C TYR C 982 " ideal model delta sigma weight residual 110.44 113.59 -3.15 1.20e+00 6.94e-01 6.91e+00 ... (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 - 0.027: 1544 0.027 - 0.053: 631 0.053 - 0.080: 235 0.080 - 0.107: 118 0.107 - 0.133: 46 Chirality restraints: 2574 Sorted by residual: 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 chirality pdb=" CA ILE B 316 " pdb=" N ILE B 316 " pdb=" C ILE B 316 " pdb=" CB ILE B 316 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.400 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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= 0.114 Angle : 0.528 7.243 23580 Z= 0.289 Chirality : 0.039 0.133 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 aren 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 covalent geometry : bond 0.00251 (17089) covalent geometry : angle 0.52623 (23576) hydrogen bonds : bond 0.16212 ( 750) hydrogen bonds : angle 6.60729 ( 2086) metal coordination : bond 0.00669 ( 8) metal coordination : angle 3.37822 ( 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 : 0.630 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: 0.1340 time to fit residues: 58.4523 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 : 0.547 ------------------------------------------------------------------------------- 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: 0.0060 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: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN B 278 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 GLN C 581 GLN C 637 ASN C1006 HIS D 4 GLN D 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.096163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.069418 restraints weight = 84628.218| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.33 r_work: 0.2887 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17097 Z= 0.182 Angle : 0.602 7.742 23580 Z= 0.324 Chirality : 0.042 0.150 2574 Planarity : 0.004 0.046 2653 Dihedral : 20.203 74.382 3149 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.35 % Favored : 95.49 % Rotamer: Outliers : 2.04 % Allowed : 7.92 % Favored : 90.03 % 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 aren not related in a simple way. whole: 0.29 (0.20), residues: 1784 helix: 1.46 (0.23), residues: 563 sheet: 0.74 (0.28), residues: 340 loop : -0.88 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 915 TYR 0.015 0.001 TYR A 805 PHE 0.021 0.001 PHE C 936 TRP 0.046 0.002 TRP D 317 HIS 0.006 0.001 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00424 (17089) covalent geometry : angle 0.59872 (23576) hydrogen bonds : bond 0.04176 ( 750) hydrogen bonds : angle 4.98129 ( 2086) metal coordination : bond 0.00802 ( 8) metal coordination : angle 4.82867 ( 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 167 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8064 (ptt90) cc_final: 0.7355 (ptt90) REVERT: A 984 MET cc_start: 0.8714 (mmm) cc_final: 0.8371 (mmm) REVERT: C 659 LEU cc_start: 0.9067 (tp) cc_final: 0.8860 (mt) REVERT: C 691 MET cc_start: 0.8669 (ttm) cc_final: 0.8331 (ttm) REVERT: C 716 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8315 (mt-10) REVERT: C 770 GLU cc_start: 0.8876 (mp0) cc_final: 0.8610 (mp0) REVERT: C 983 GLU cc_start: 0.8706 (pp20) cc_final: 0.8166 (pp20) REVERT: D 4 GLN cc_start: 0.8554 (tp-100) cc_final: 0.8220 (tp-100) outliers start: 28 outliers final: 19 residues processed: 160 average time/residue: 0.1262 time to fit residues: 31.1050 Evaluate side-chains 141 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 143 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 847 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 288 SER Chi-restraints excluded: chain D residue 320 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: 0.9990 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 0.0770 chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 ASN C1000 GLN D 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.097163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.069751 restraints weight = 93207.209| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.61 r_work: 0.2882 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1997 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= 0.133 Angle : 0.532 6.871 23580 Z= 0.290 Chirality : 0.040 0.148 2574 Planarity : 0.004 0.042 2653 Dihedral : 20.215 80.286 3149 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer: Outliers : 1.85 % Allowed : 9.78 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.20), residues: 1784 helix: 1.53 (0.23), residues: 563 sheet: 0.67 (0.28), residues: 354 loop : -0.78 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 915 TYR 0.013 0.001 TYR A 757 PHE 0.009 0.001 PHE B 48 TRP 0.036 0.001 TRP B 317 HIS 0.004 0.001 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00304 (17089) covalent geometry : angle 0.52932 (23576) hydrogen bonds : bond 0.03477 ( 750) hydrogen bonds : angle 4.72278 ( 2086) metal coordination : bond 0.00564 ( 8) metal coordination : angle 4.17927 ( 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 167 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8105 (ptt90) cc_final: 0.7422 (ptt90) REVERT: A 602 MET cc_start: 0.8884 (mtp) cc_final: 0.8661 (mtt) REVERT: B 278 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8914 (mt0) REVERT: C 600 ASP cc_start: 0.8548 (t0) cc_final: 0.8321 (t0) REVERT: C 691 MET cc_start: 0.8692 (ttm) cc_final: 0.8463 (ttm) REVERT: C 716 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8215 (mt-10) REVERT: C 770 GLU cc_start: 0.8910 (mp0) cc_final: 0.8673 (mp0) REVERT: D 302 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8242 (pmm) outliers start: 25 outliers final: 20 residues processed: 159 average time/residue: 0.1232 time to fit residues: 29.8507 Evaluate side-chains 141 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 185 ILE Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 288 SER 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 631 ILE Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 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: 3.9990 chunk 92 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 96 optimal weight: 0.0970 chunk 36 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 809 GLN D 4 GLN D 27 GLN D 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.093824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.066338 restraints weight = 100379.049| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 4.65 r_work: 0.2817 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17097 Z= 0.185 Angle : 0.570 9.731 23580 Z= 0.306 Chirality : 0.041 0.147 2574 Planarity : 0.004 0.043 2653 Dihedral : 20.318 78.502 3149 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 2.88 % Allowed : 10.10 % Favored : 87.03 % 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 aren not related in a simple way. whole: 0.38 (0.20), residues: 1784 helix: 1.57 (0.23), residues: 565 sheet: 0.63 (0.28), residues: 354 loop : -0.80 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 915 TYR 0.014 0.001 TYR A 757 PHE 0.012 0.001 PHE A 916 TRP 0.039 0.002 TRP B 317 HIS 0.006 0.001 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00431 (17089) covalent geometry : angle 0.56709 (23576) hydrogen bonds : bond 0.03740 ( 750) hydrogen bonds : angle 4.63212 ( 2086) metal coordination : bond 0.00864 ( 8) metal coordination : angle 4.40481 ( 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 164 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8124 (ptt90) cc_final: 0.7458 (ptt90) REVERT: B 91 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: B 278 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8883 (mt0) REVERT: C 524 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8424 (ptmm) REVERT: C 716 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8252 (mt-10) REVERT: C 809 GLN cc_start: 0.8479 (tt0) cc_final: 0.8261 (tt0) REVERT: C 936 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8915 (m-10) outliers start: 41 outliers final: 30 residues processed: 154 average time/residue: 0.1282 time to fit residues: 30.0478 Evaluate side-chains 152 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 143 ASP 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 507 GLU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 597 GLU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 631 ILE 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 862 THR 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 22 MET Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 317 TRP 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: 4.9990 chunk 148 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3533 r_free = 0.3533 target = 0.094540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.067015 restraints weight = 105124.143| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 4.75 r_work: 0.2830 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17097 Z= 0.149 Angle : 0.534 8.523 23580 Z= 0.288 Chirality : 0.040 0.146 2574 Planarity : 0.004 0.042 2653 Dihedral : 20.291 79.531 3149 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 2.49 % Allowed : 11.37 % Favored : 86.13 % 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 aren not related in a simple way. whole: 0.40 (0.20), residues: 1784 helix: 1.61 (0.23), residues: 564 sheet: 0.63 (0.28), residues: 351 loop : -0.79 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 529 TYR 0.014 0.001 TYR A 757 PHE 0.011 0.001 PHE B 48 TRP 0.036 0.001 TRP B 317 HIS 0.005 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00346 (17089) covalent geometry : angle 0.53109 (23576) hydrogen bonds : bond 0.03367 ( 750) hydrogen bonds : angle 4.55675 ( 2086) metal coordination : bond 0.00675 ( 8) metal coordination : angle 4.18399 ( 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 157 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8081 (ptt90) cc_final: 0.7416 (ptt90) REVERT: B 91 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: B 278 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8906 (mt0) REVERT: C 524 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8423 (ptmm) REVERT: C 600 ASP cc_start: 0.8583 (t0) cc_final: 0.8361 (t0) REVERT: C 632 GLU cc_start: 0.8660 (tt0) cc_final: 0.8174 (tp30) REVERT: C 716 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8287 (mt-10) REVERT: C 883 MET cc_start: 0.8507 (tpp) cc_final: 0.8049 (tpt) REVERT: C 936 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8929 (m-10) outliers start: 36 outliers final: 26 residues processed: 149 average time/residue: 0.1304 time to fit residues: 29.6166 Evaluate side-chains 143 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 43 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 ASP 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 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 598 SER Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 862 THR 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 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: 1.9990 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 0.0370 chunk 183 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 19 optimal weight: 0.0170 chunk 39 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3550 r_free = 0.3550 target = 0.095609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.068294 restraints weight = 102660.219| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 4.69 r_work: 0.2853 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2531 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= 0.121 Angle : 0.518 8.170 23580 Z= 0.278 Chirality : 0.039 0.146 2574 Planarity : 0.004 0.041 2653 Dihedral : 20.251 80.264 3149 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.01 % Favored : 95.88 % Rotamer: Outliers : 1.98 % Allowed : 11.95 % Favored : 86.07 % 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 aren not related in a simple way. whole: 0.50 (0.20), residues: 1784 helix: 1.71 (0.23), residues: 564 sheet: 0.65 (0.28), residues: 351 loop : -0.73 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 148 TYR 0.014 0.001 TYR A 757 PHE 0.011 0.001 PHE B 48 TRP 0.034 0.001 TRP B 317 HIS 0.004 0.001 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00277 (17089) covalent geometry : angle 0.51580 (23576) hydrogen bonds : bond 0.03084 ( 750) hydrogen bonds : angle 4.42281 ( 2086) metal coordination : bond 0.00546 ( 8) metal coordination : angle 3.65666 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8043 (ptt90) cc_final: 0.7398 (ptt90) REVERT: A 883 MET cc_start: 0.8450 (tpt) cc_final: 0.7999 (tpt) REVERT: B 91 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: B 278 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8942 (mt0) REVERT: C 524 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8456 (ptmm) REVERT: C 600 ASP cc_start: 0.8544 (t0) cc_final: 0.8338 (t0) REVERT: C 632 GLU cc_start: 0.8609 (tt0) cc_final: 0.8174 (tp30) REVERT: C 818 HIS cc_start: 0.8324 (m90) cc_final: 0.8114 (m-70) REVERT: C 936 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8901 (m-10) outliers start: 28 outliers final: 23 residues processed: 144 average time/residue: 0.1185 time to fit residues: 26.2998 Evaluate side-chains 144 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 43 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 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 598 SER Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 714 GLU 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 982 TYR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 302 MET 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: 0.7980 chunk 117 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 129 optimal weight: 0.0370 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 154 optimal weight: 0.4980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.096514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.069306 restraints weight = 102352.718| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 4.68 r_work: 0.2875 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17097 Z= 0.111 Angle : 0.510 8.198 23580 Z= 0.273 Chirality : 0.039 0.142 2574 Planarity : 0.003 0.042 2653 Dihedral : 20.246 80.301 3149 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.56 % Favored : 96.33 % Rotamer: Outliers : 2.24 % Allowed : 11.69 % Favored : 86.07 % 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 aren not related in a simple way. whole: 0.60 (0.20), residues: 1784 helix: 1.83 (0.23), residues: 563 sheet: 0.73 (0.28), residues: 341 loop : -0.69 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 529 TYR 0.013 0.001 TYR A 757 PHE 0.011 0.001 PHE B 48 TRP 0.031 0.001 TRP B 317 HIS 0.004 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00253 (17089) covalent geometry : angle 0.50830 (23576) hydrogen bonds : bond 0.02917 ( 750) hydrogen bonds : angle 4.35852 ( 2086) metal coordination : bond 0.00519 ( 8) metal coordination : angle 3.47727 ( 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 156 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8053 (ptt90) cc_final: 0.7420 (ptt90) REVERT: B 91 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8569 (m-80) REVERT: B 278 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8939 (mt0) REVERT: B 312 LYS cc_start: 0.9338 (mtpt) cc_final: 0.8961 (mtpp) REVERT: C 524 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8482 (ptmm) REVERT: C 632 GLU cc_start: 0.8615 (tt0) cc_final: 0.8173 (tp30) REVERT: C 716 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7957 (mm-30) REVERT: C 818 HIS cc_start: 0.8329 (m90) cc_final: 0.8117 (m-70) REVERT: C 849 MET cc_start: 0.8431 (ttm) cc_final: 0.8190 (ttm) REVERT: C 936 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8924 (m-10) REVERT: D 280 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8753 (tp30) outliers start: 32 outliers final: 23 residues processed: 149 average time/residue: 0.1178 time to fit residues: 27.6058 Evaluate side-chains 142 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 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 598 SER Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 631 ILE 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 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 302 MET 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: 4.9990 chunk 88 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 174 optimal weight: 0.0670 chunk 132 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 830 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.096756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.069326 restraints weight = 101025.120| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 4.70 r_work: 0.2872 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17097 Z= 0.118 Angle : 0.522 10.151 23580 Z= 0.277 Chirality : 0.039 0.142 2574 Planarity : 0.003 0.041 2653 Dihedral : 20.276 80.260 3149 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.67 % Favored : 96.22 % Rotamer: Outliers : 1.98 % Allowed : 11.95 % Favored : 86.07 % 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 aren not related in a simple way. whole: 0.60 (0.20), residues: 1784 helix: 1.77 (0.22), residues: 565 sheet: 0.78 (0.28), residues: 341 loop : -0.67 (0.21), residues: 878 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 0.032 0.001 TRP B 317 HIS 0.004 0.001 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00272 (17089) covalent geometry : angle 0.51963 (23576) hydrogen bonds : bond 0.02960 ( 750) hydrogen bonds : angle 4.34884 ( 2086) metal coordination : bond 0.00542 ( 8) metal coordination : angle 3.58087 ( 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 146 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8062 (ptt90) cc_final: 0.7366 (ptt90) REVERT: A 883 MET cc_start: 0.8447 (tpt) cc_final: 0.7951 (tpt) REVERT: B 91 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.8544 (m-80) REVERT: B 278 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8934 (mt0) REVERT: C 524 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8487 (ptmm) REVERT: C 632 GLU cc_start: 0.8618 (tt0) cc_final: 0.8182 (tp30) REVERT: C 716 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8023 (mm-30) REVERT: C 818 HIS cc_start: 0.8329 (m90) cc_final: 0.8127 (m-70) REVERT: C 849 MET cc_start: 0.8391 (ttm) cc_final: 0.8156 (ttm) REVERT: C 883 MET cc_start: 0.8419 (tpp) cc_final: 0.7913 (tpt) REVERT: C 936 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8863 (m-10) REVERT: D 5 MET cc_start: 0.8320 (mmm) cc_final: 0.8113 (tpp) REVERT: D 280 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8776 (tp30) outliers start: 28 outliers final: 23 residues processed: 140 average time/residue: 0.1263 time to fit residues: 27.7338 Evaluate side-chains 141 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 43 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 VAL 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 598 SER Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 631 ILE 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 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 302 MET 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: 7.9990 chunk 57 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 HIS D 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.091796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064879 restraints weight = 75748.874| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 4.08 r_work: 0.2798 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17097 Z= 0.243 Angle : 0.595 8.877 23580 Z= 0.316 Chirality : 0.043 0.149 2574 Planarity : 0.004 0.044 2653 Dihedral : 20.535 77.926 3149 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.51 % Favored : 95.37 % Rotamer: Outliers : 2.30 % Allowed : 12.08 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.20), residues: 1784 helix: 1.58 (0.23), residues: 567 sheet: 0.79 (0.29), residues: 329 loop : -0.74 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 529 TYR 0.014 0.002 TYR A 757 PHE 0.016 0.001 PHE A 916 TRP 0.042 0.002 TRP B 317 HIS 0.006 0.001 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00565 (17089) covalent geometry : angle 0.59182 (23576) hydrogen bonds : bond 0.03977 ( 750) hydrogen bonds : angle 4.54926 ( 2086) metal coordination : bond 0.01327 ( 8) metal coordination : angle 4.53892 ( 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 143 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8069 (ptt90) cc_final: 0.7392 (ptt90) REVERT: A 602 MET cc_start: 0.8880 (mtm) cc_final: 0.8636 (mtt) REVERT: B 91 TYR cc_start: 0.8968 (OUTLIER) cc_final: 0.8457 (m-80) REVERT: C 524 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8479 (ptmm) REVERT: C 632 GLU cc_start: 0.8741 (tt0) cc_final: 0.8258 (tp30) REVERT: C 883 MET cc_start: 0.8599 (tpp) cc_final: 0.8295 (tpt) REVERT: C 936 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8941 (m-10) REVERT: C 983 GLU cc_start: 0.9007 (pp20) cc_final: 0.8518 (pp20) REVERT: D 5 MET cc_start: 0.8322 (mmm) cc_final: 0.8003 (tpp) outliers start: 33 outliers final: 23 residues processed: 137 average time/residue: 0.1145 time to fit residues: 24.4324 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 : 0.433 ------------------------------------------------------------------------------- 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 606 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 VAL 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 847 MET Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 341 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 145 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 168 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.094866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.067875 restraints weight = 90666.179| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 4.44 r_work: 0.2853 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17097 Z= 0.117 Angle : 0.532 9.038 23580 Z= 0.284 Chirality : 0.039 0.141 2574 Planarity : 0.003 0.040 2653 Dihedral : 20.364 81.256 3149 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.61 % Favored : 96.28 % Rotamer: Outliers : 1.79 % Allowed : 12.65 % Favored : 85.56 % 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 aren not related in a simple way. whole: 0.55 (0.20), residues: 1784 helix: 1.70 (0.22), residues: 565 sheet: 0.73 (0.28), residues: 342 loop : -0.68 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 529 TYR 0.015 0.001 TYR A 757 PHE 0.011 0.001 PHE B 48 TRP 0.035 0.001 TRP B 317 HIS 0.005 0.001 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00267 (17089) covalent geometry : angle 0.53028 (23576) hydrogen bonds : bond 0.03113 ( 750) hydrogen bonds : angle 4.40953 ( 2086) metal coordination : bond 0.00602 ( 8) metal coordination : angle 3.73198 ( 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 143 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.8069 (ptt90) cc_final: 0.7303 (ptt90) REVERT: A 602 MET cc_start: 0.8611 (mtm) cc_final: 0.8184 (mtp) REVERT: B 91 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.8593 (m-80) REVERT: C 524 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8486 (ptmm) REVERT: C 632 GLU cc_start: 0.8670 (tt0) cc_final: 0.8206 (tp30) REVERT: C 716 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7890 (mm-30) REVERT: C 770 GLU cc_start: 0.8977 (mp0) cc_final: 0.8684 (mp0) REVERT: C 883 MET cc_start: 0.8439 (tpp) cc_final: 0.8042 (tpt) REVERT: C 936 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8957 (m-10) REVERT: C 983 GLU cc_start: 0.8995 (pp20) cc_final: 0.8438 (pp20) REVERT: D 280 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8725 (tp30) outliers start: 25 outliers final: 21 residues processed: 140 average time/residue: 0.1166 time to fit residues: 25.4069 Evaluate side-chains 139 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 43 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 631 ILE 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 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: 0.6980 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3556 r_free = 0.3556 target = 0.095953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.068831 restraints weight = 89672.598| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 4.47 r_work: 0.2870 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17097 Z= 0.116 Angle : 0.525 10.220 23580 Z= 0.279 Chirality : 0.039 0.140 2574 Planarity : 0.003 0.042 2653 Dihedral : 20.320 81.295 3149 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.67 % Favored : 96.22 % Rotamer: Outliers : 1.60 % Allowed : 13.04 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.20), residues: 1784 helix: 1.77 (0.22), residues: 565 sheet: 0.80 (0.29), residues: 342 loop : -0.63 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 848 TYR 0.013 0.001 TYR A 757 PHE 0.011 0.001 PHE B 48 TRP 0.032 0.001 TRP B 317 HIS 0.004 0.001 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00266 (17089) covalent geometry : angle 0.52291 (23576) hydrogen bonds : bond 0.03011 ( 750) hydrogen bonds : angle 4.34253 ( 2086) metal coordination : bond 0.00551 ( 8) metal coordination : angle 3.43104 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3998.93 seconds wall clock time: 69 minutes 11.70 seconds (4151.70 seconds total)