Starting phenix.real_space_refine on Tue Apr 7 01:28:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10or_75340/04_2026/10or_75340_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/10or_75340/04_2026/10or_75340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10or_75340/04_2026/10or_75340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10or_75340/04_2026/10or_75340.map" model { file = "/net/cci-nas-00/data/ceres_data/10or_75340/04_2026/10or_75340_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10or_75340/04_2026/10or_75340_neut.cif" } resolution = 2.46 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= 0.000 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 14610 2.51 5 N 3981 2.21 5 O 4563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23250 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1407 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 169} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 955 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1407 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 169} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 955 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1407 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 169} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 955 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 935 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 828 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "I" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 935 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 828 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "K" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 935 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 828 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "M" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 964 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "N" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 799 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "O" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 964 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "P" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 799 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "Q" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 964 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "R" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 799 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "S" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "T" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "U" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "V" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "W" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "X" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.27, per 1000 atoms: 0.23 Number of scatterers: 23250 At special positions: 0 Unit cell: (135.29, 135.29, 154.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 4563 8.00 N 3981 7.00 C 14610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.04 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.02 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.03 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 Links applied ALPHA1-3 " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA Y 3 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG Y 1 " - " ASN B 563 " " NAG Z 1 " - " ASN D 563 " " NAG a 1 " - " ASN F 563 " Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 956.4 milliseconds 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5406 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 69 sheets defined 12.1% alpha, 44.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.893A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 576 removed outlier: 4.854A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 Processing helix chain 'B' and resid 612 through 629 removed outlier: 3.585A pdb=" N ASN B 618 " --> pdb=" O ASP B 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.871A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 576 removed outlier: 4.845A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 Processing helix chain 'D' and resid 612 through 629 removed outlier: 3.589A pdb=" N ASN D 618 " --> pdb=" O ASP D 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 84 removed outlier: 3.844A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 576 removed outlier: 4.861A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 Processing helix chain 'F' and resid 612 through 629 removed outlier: 3.577A pdb=" N ASN F 618 " --> pdb=" O ASP F 614 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.764A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.630A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.600A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.793A pdb=" N HIS M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.591A pdb=" N LEU M 64 " --> pdb=" O GLN M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.720A pdb=" N GLU N 83 " --> pdb=" O THR N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.733A pdb=" N HIS O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.579A pdb=" N LEU O 64 " --> pdb=" O GLN O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.759A pdb=" N GLU P 83 " --> pdb=" O THR P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.798A pdb=" N HIS Q 32 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 64 removed outlier: 3.558A pdb=" N LEU Q 64 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 61 through 64' Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.719A pdb=" N GLU R 83 " --> pdb=" O THR R 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 64 removed outlier: 3.610A pdb=" N LYS S 64 " --> pdb=" O PRO S 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 61 through 64' Processing helix chain 'S' and resid 83 through 87 Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.629A pdb=" N PHE T 83 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 61 through 64 removed outlier: 3.612A pdb=" N LYS U 64 " --> pdb=" O PRO U 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 61 through 64' Processing helix chain 'U' and resid 83 through 87 Processing helix chain 'V' and resid 79 through 83 removed outlier: 3.621A pdb=" N PHE V 83 " --> pdb=" O PRO V 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 61 through 64 removed outlier: 3.613A pdb=" N LYS W 64 " --> pdb=" O PRO W 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 61 through 64' Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'X' and resid 79 through 83 removed outlier: 3.635A pdb=" N PHE X 83 " --> pdb=" O PRO X 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 46 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 7.030A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA5, first strand: chain 'A' and resid 105 through 111 removed outlier: 6.186A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASN A 110 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG A 136 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL A 138 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLN A 142 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 46 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 46 removed outlier: 7.001A pdb=" N VAL C 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AB1, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.180A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ALA C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN C 110 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG C 136 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL C 138 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLN C 142 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 42 through 46 Processing sheet with id=AB3, first strand: chain 'E' and resid 42 through 46 removed outlier: 6.926A pdb=" N VAL E 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AB5, first strand: chain 'E' and resid 101 through 103 Processing sheet with id=AB6, first strand: chain 'E' and resid 105 through 111 removed outlier: 6.176A pdb=" N GLU E 106 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N HIS E 139 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ALA E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN E 110 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG E 136 " --> pdb=" O SER E 216 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU E 218 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL E 138 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TYR E 220 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS E 140 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE E 222 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLN E 142 " --> pdb=" O ILE E 222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.690A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AC1, first strand: chain 'H' and resid 9 through 13 removed outlier: 6.400A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 9 through 13 Processing sheet with id=AC3, first strand: chain 'H' and resid 19 through 24 Processing sheet with id=AC4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.655A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AC7, first strand: chain 'J' and resid 9 through 13 removed outlier: 6.402A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 9 through 13 Processing sheet with id=AC9, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AD1, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.602A pdb=" N MET K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.418A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AD6, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AD7, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.458A pdb=" N VAL M 34 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.739A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.778A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.778A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE4, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.408A pdb=" N VAL O 34 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG O 50 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.775A pdb=" N CYS O 92 " --> pdb=" O TRP O 103 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TRP O 103 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.772A pdb=" N VAL P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA P 84 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.772A pdb=" N VAL P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA P 84 " --> pdb=" O VAL P 104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AF1, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.460A pdb=" N VAL Q 34 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG Q 50 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.765A pdb=" N CYS Q 92 " --> pdb=" O TRP Q 103 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TRP Q 103 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ARG Q 94 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 9 through 13 removed outlier: 6.722A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA R 84 " --> pdb=" O VAL R 104 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 9 through 13 removed outlier: 6.722A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA R 84 " --> pdb=" O VAL R 104 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 19 through 24 Processing sheet with id=AF7, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.263A pdb=" N TRP S 35A" --> pdb=" O ASN S 50 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN S 50 " --> pdb=" O TRP S 35A" (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP S 36 " --> pdb=" O ILE S 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 11 through 12 removed outlier: 7.341A pdb=" N CYS S 92 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL S 102 " --> pdb=" O CYS S 92 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG S 94 " --> pdb=" O MET S 100G" (cutoff:3.500A) removed outlier: 5.084A pdb=" N MET S 100G" --> pdb=" O ARG S 94 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ARG S 96 " --> pdb=" O TYR S 100E" (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG S 98 " --> pdb=" O HIS S 100C" (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS S 100C" --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'T' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.519A pdb=" N LEU T 11 " --> pdb=" O GLU T 105 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.519A pdb=" N LEU T 11 " --> pdb=" O GLU T 105 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER T 97 " --> pdb=" O GLN T 90 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'U' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'U' and resid 11 through 12 removed outlier: 6.287A pdb=" N TRP U 35A" --> pdb=" O ASN U 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASN U 50 " --> pdb=" O TRP U 35A" (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP U 36 " --> pdb=" O ILE U 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'U' and resid 11 through 12 removed outlier: 7.301A pdb=" N CYS U 92 " --> pdb=" O VAL U 102 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL U 102 " --> pdb=" O CYS U 92 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG U 94 " --> pdb=" O MET U 100G" (cutoff:3.500A) removed outlier: 4.915A pdb=" N MET U 100G" --> pdb=" O ARG U 94 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ARG U 96 " --> pdb=" O TYR U 100E" (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG U 98 " --> pdb=" O HIS U 100C" (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS U 100C" --> pdb=" O ARG U 98 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'V' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'V' and resid 10 through 13 removed outlier: 6.510A pdb=" N LEU V 11 " --> pdb=" O GLU V 105 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU V 33 " --> pdb=" O TYR V 49 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR V 49 " --> pdb=" O LEU V 33 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'V' and resid 10 through 13 removed outlier: 6.510A pdb=" N LEU V 11 " --> pdb=" O GLU V 105 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER V 97 " --> pdb=" O GLN V 90 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'W' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'W' and resid 11 through 12 removed outlier: 6.270A pdb=" N TRP W 35A" --> pdb=" O ASN W 50 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN W 50 " --> pdb=" O TRP W 35A" (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP W 36 " --> pdb=" O ILE W 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'W' and resid 11 through 12 removed outlier: 7.346A pdb=" N CYS W 92 " --> pdb=" O VAL W 102 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL W 102 " --> pdb=" O CYS W 92 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG W 94 " --> pdb=" O MET W 100G" (cutoff:3.500A) removed outlier: 5.025A pdb=" N MET W 100G" --> pdb=" O ARG W 94 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ARG W 96 " --> pdb=" O TYR W 100E" (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG W 98 " --> pdb=" O HIS W 100C" (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS W 100C" --> pdb=" O ARG W 98 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'X' and resid 4 through 7 Processing sheet with id=AH5, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.675A pdb=" N LEU X 33 " --> pdb=" O TYR X 49 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR X 49 " --> pdb=" O LEU X 33 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP X 35 " --> pdb=" O LEU X 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 10 through 13 removed outlier: 4.025A pdb=" N SER X 97 " --> pdb=" O GLN X 90 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2394 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.60 Time building geometry restraints manager: 2.55 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: 7520 1.34 - 1.46: 5980 1.46 - 1.58: 10170 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 23796 Sorted by residual: bond pdb=" CG1 ILE F 626 " pdb=" CD1 ILE F 626 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.82e+00 bond pdb=" C5 MAN a 5 " pdb=" O5 MAN a 5 " ideal model delta sigma weight residual 1.418 1.447 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C5 MAN Y 5 " pdb=" O5 MAN Y 5 " ideal model delta sigma weight residual 1.418 1.447 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C5 MAN Z 5 " pdb=" O5 MAN Z 5 " ideal model delta sigma weight residual 1.418 1.446 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C VAL K 40 " pdb=" N PRO K 41 " ideal model delta sigma weight residual 1.331 1.348 -0.017 1.20e-02 6.94e+03 1.91e+00 ... (remaining 23791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 32093 3.38 - 6.77: 235 6.77 - 10.15: 9 10.15 - 13.53: 0 13.53 - 16.92: 3 Bond angle restraints: 32340 Sorted by residual: angle pdb=" C ASN B 550 " pdb=" CA ASN B 550 " pdb=" CB ASN B 550 " ideal model delta sigma weight residual 117.23 110.94 6.29 1.36e+00 5.41e-01 2.14e+01 angle pdb=" C LYS K 100B" pdb=" N ASP K 100C" pdb=" CA ASP K 100C" ideal model delta sigma weight residual 121.54 129.35 -7.81 1.91e+00 2.74e-01 1.67e+01 angle pdb=" N ILE W 100A" pdb=" CA ILE W 100A" pdb=" C ILE W 100A" ideal model delta sigma weight residual 113.07 107.68 5.39 1.36e+00 5.41e-01 1.57e+01 angle pdb=" N ILE U 100A" pdb=" CA ILE U 100A" pdb=" C ILE U 100A" ideal model delta sigma weight residual 113.07 107.79 5.28 1.36e+00 5.41e-01 1.51e+01 angle pdb=" N VAL G 63 " pdb=" CA VAL G 63 " pdb=" C VAL G 63 " ideal model delta sigma weight residual 112.29 108.85 3.44 9.40e-01 1.13e+00 1.34e+01 ... (remaining 32335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 12918 21.58 - 43.15: 1030 43.15 - 64.72: 172 64.72 - 86.30: 43 86.30 - 107.87: 12 Dihedral angle restraints: 14175 sinusoidal: 5622 harmonic: 8553 Sorted by residual: dihedral pdb=" CA ILE F 627 " pdb=" C ILE F 627 " pdb=" N HIS F 628 " pdb=" CA HIS F 628 " ideal model delta harmonic sigma weight residual 180.00 149.51 30.49 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CB CYS B 511 " pdb=" SG CYS B 511 " pdb=" SG CYS B 556 " pdb=" CB CYS B 556 " ideal model delta sinusoidal sigma weight residual -86.00 -134.21 48.21 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" CB CYS F 511 " pdb=" SG CYS F 511 " pdb=" SG CYS F 556 " pdb=" CB CYS F 556 " ideal model delta sinusoidal sigma weight residual -86.00 -133.74 47.74 1 1.00e+01 1.00e-02 3.14e+01 ... (remaining 14172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2901 0.054 - 0.108: 542 0.108 - 0.162: 120 0.162 - 0.215: 7 0.215 - 0.269: 6 Chirality restraints: 3576 Sorted by residual: chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C5 BMA Y 3 " pdb=" C4 BMA Y 3 " pdb=" C6 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA Z 3 " pdb=" C4 BMA Z 3 " pdb=" C6 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3573 not shown) Planarity restraints: 4143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO J 7 " -0.059 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO J 8 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO J 8 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO J 8 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 52 " -0.025 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYR S 52 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR S 52 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR S 52 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR S 52 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR S 52 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR S 52 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR S 52 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 53 " 0.009 2.00e-02 2.50e+03 1.73e-02 5.96e+00 pdb=" CG TYR S 53 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR S 53 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR S 53 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR S 53 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR S 53 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR S 53 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR S 53 " -0.003 2.00e-02 2.50e+03 ... (remaining 4140 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 718 2.69 - 3.24: 21689 3.24 - 3.80: 37808 3.80 - 4.35: 51931 4.35 - 4.90: 84975 Nonbonded interactions: 197121 Sorted by model distance: nonbonded pdb=" OD2 ASP I 72 " pdb=" NZ LYS I 75 " model vdw 2.141 3.120 nonbonded pdb=" OE1 GLN B 625 " pdb=" OH TYR S 53 " model vdw 2.161 3.040 nonbonded pdb=" OG1 THR A 60 " pdb=" OD1 ASP D 591 " model vdw 2.174 3.040 nonbonded pdb=" OG1 THR C 60 " pdb=" OD1 ASP F 591 " model vdw 2.182 3.040 nonbonded pdb=" N GLU J 81 " pdb=" OE1 GLU J 81 " model vdw 2.182 3.120 ... (remaining 197116 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' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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=1.00 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: 8.610 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.700 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 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:8.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 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 : 0.004 0.065 23841 Z= 0.163 Angle : 0.717 16.918 32445 Z= 0.370 Chirality : 0.046 0.269 3576 Planarity : 0.006 0.090 4140 Dihedral : 15.855 107.874 8679 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 2.52 % Allowed : 18.97 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 2961 helix: 0.68 (0.38), residues: 168 sheet: 0.72 (0.15), residues: 1188 loop : -0.21 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Q 62 TYR 0.062 0.002 TYR S 52 PHE 0.023 0.001 PHE G 67 TRP 0.011 0.001 TRP O 47 HIS 0.020 0.001 HIS F 628 Details of bonding type rmsd covalent geometry : bond 0.00352 (23796) covalent geometry : angle 0.71442 (32340) SS BOND : bond 0.00301 ( 30) SS BOND : angle 0.64344 ( 60) hydrogen bonds : bond 0.11534 ( 894) hydrogen bonds : angle 6.31521 ( 2394) link_ALPHA1-3 : bond 0.00186 ( 3) link_ALPHA1-3 : angle 1.90003 ( 9) link_ALPHA1-6 : bond 0.00354 ( 3) link_ALPHA1-6 : angle 1.75422 ( 9) link_BETA1-4 : bond 0.00182 ( 6) link_BETA1-4 : angle 1.56474 ( 18) link_NAG-ASN : bond 0.00405 ( 3) link_NAG-ASN : angle 2.65726 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 336 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 63 VAL cc_start: 0.8835 (m) cc_final: 0.8631 (m) REVERT: H 52 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7497 (mm-30) REVERT: I 100 LYS cc_start: 0.8555 (ttpp) cc_final: 0.8273 (tmmt) REVERT: M 51 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9082 (tp) REVERT: R 18 ARG cc_start: 0.8650 (mtp85) cc_final: 0.8365 (ttm-80) outliers start: 63 outliers final: 54 residues processed: 392 average time/residue: 0.6975 time to fit residues: 309.1350 Evaluate side-chains 387 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 332 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 609 CYS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 609 CYS Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 100 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain T residue 6 GLN Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain X residue 6 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 514 ASN D 550 ASN E 50 GLN E 107 ASN F 514 ASN G 73 ASN L 34 GLN L 79 GLN R 37 GLN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 6 GLN ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.137232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.073325 restraints weight = 46252.362| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 4.67 r_work: 0.2602 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23841 Z= 0.209 Angle : 0.634 16.632 32445 Z= 0.323 Chirality : 0.046 0.200 3576 Planarity : 0.005 0.065 4140 Dihedral : 8.809 80.896 3665 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.12 % Rotamer: Outliers : 3.84 % Allowed : 16.33 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 2961 helix: 0.80 (0.39), residues: 171 sheet: 0.71 (0.15), residues: 1170 loop : -0.23 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 82B TYR 0.032 0.001 TYR U 52 PHE 0.012 0.001 PHE E 176 TRP 0.014 0.001 TRP A 86 HIS 0.008 0.001 HIS F 628 Details of bonding type rmsd covalent geometry : bond 0.00478 (23796) covalent geometry : angle 0.62843 (32340) SS BOND : bond 0.00398 ( 30) SS BOND : angle 0.62721 ( 60) hydrogen bonds : bond 0.03587 ( 894) hydrogen bonds : angle 5.27458 ( 2394) link_ALPHA1-3 : bond 0.00718 ( 3) link_ALPHA1-3 : angle 2.65853 ( 9) link_ALPHA1-6 : bond 0.00139 ( 3) link_ALPHA1-6 : angle 1.61151 ( 9) link_BETA1-4 : bond 0.00425 ( 6) link_BETA1-4 : angle 2.16879 ( 18) link_NAG-ASN : bond 0.00442 ( 3) link_NAG-ASN : angle 2.44513 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 341 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.8607 (tpp80) cc_final: 0.8087 (tpt-90) REVERT: A 140 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8459 (mtpp) REVERT: B 567 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: E 44 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8141 (tp30) REVERT: G 11 LEU cc_start: 0.8598 (tp) cc_final: 0.8283 (tm) REVERT: G 100 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8248 (tmmt) REVERT: G 100 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7573 (p0) REVERT: H 52 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7887 (mm-30) REVERT: I 100 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8440 (tmmt) REVERT: K 11 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8341 (tm) REVERT: L 17 GLN cc_start: 0.8851 (tt0) cc_final: 0.8080 (pt0) REVERT: M 10 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6755 (tm-30) REVERT: M 12 LYS cc_start: 0.8624 (mttp) cc_final: 0.8271 (mttp) outliers start: 96 outliers final: 46 residues processed: 412 average time/residue: 0.7269 time to fit residues: 337.1753 Evaluate side-chains 375 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 323 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 609 CYS Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 584 ILE Chi-restraints excluded: chain F residue 609 CYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 100 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 139 optimal weight: 0.0050 chunk 132 optimal weight: 9.9990 chunk 233 optimal weight: 50.0000 chunk 169 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 276 optimal weight: 50.0000 chunk 191 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN G 73 ASN H 34 GLN N 37 GLN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.137640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.072494 restraints weight = 46355.339| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 5.19 r_work: 0.2591 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23841 Z= 0.175 Angle : 0.612 16.230 32445 Z= 0.313 Chirality : 0.045 0.181 3576 Planarity : 0.005 0.055 4140 Dihedral : 8.200 77.167 3608 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.88 % Favored : 96.01 % Rotamer: Outliers : 3.80 % Allowed : 16.97 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 2961 helix: 0.73 (0.39), residues: 174 sheet: 0.69 (0.15), residues: 1167 loop : -0.24 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 82B TYR 0.030 0.001 TYR U 52 PHE 0.015 0.001 PHE K 67 TRP 0.014 0.001 TRP O 47 HIS 0.004 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00398 (23796) covalent geometry : angle 0.60892 (32340) SS BOND : bond 0.00355 ( 30) SS BOND : angle 0.59174 ( 60) hydrogen bonds : bond 0.03319 ( 894) hydrogen bonds : angle 5.07041 ( 2394) link_ALPHA1-3 : bond 0.00758 ( 3) link_ALPHA1-3 : angle 1.86754 ( 9) link_ALPHA1-6 : bond 0.00366 ( 3) link_ALPHA1-6 : angle 1.73731 ( 9) link_BETA1-4 : bond 0.00290 ( 6) link_BETA1-4 : angle 1.69509 ( 18) link_NAG-ASN : bond 0.00389 ( 3) link_NAG-ASN : angle 2.31705 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 338 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8624 (mmtm) REVERT: A 136 ARG cc_start: 0.8644 (tpp80) cc_final: 0.8110 (tpt-90) REVERT: A 140 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8507 (mtpp) REVERT: E 220 TYR cc_start: 0.8479 (m-80) cc_final: 0.8089 (m-80) REVERT: F 595 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7663 (ttt-90) REVERT: G 100 LYS cc_start: 0.8806 (ttpp) cc_final: 0.8173 (tmmt) REVERT: G 100 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7663 (p0) REVERT: H 17 GLN cc_start: 0.8814 (tt0) cc_final: 0.8085 (pt0) REVERT: H 52 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7910 (mm-30) REVERT: I 46 GLU cc_start: 0.9229 (tt0) cc_final: 0.8836 (tt0) REVERT: I 100 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8454 (tmmt) REVERT: L 17 GLN cc_start: 0.8786 (tt0) cc_final: 0.7994 (pt0) REVERT: L 90 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8681 (p) REVERT: M 10 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6583 (tm-30) REVERT: M 12 LYS cc_start: 0.8659 (mttp) cc_final: 0.8224 (mttp) outliers start: 95 outliers final: 46 residues processed: 406 average time/residue: 0.7084 time to fit residues: 323.8799 Evaluate side-chains 373 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 321 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 584 ILE Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 625 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 100 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain W residue 52 TYR Chi-restraints excluded: chain X residue 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 172 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 272 optimal weight: 40.0000 chunk 107 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 514 ASN G 73 ASN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.136968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.070752 restraints weight = 46196.310| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 5.13 r_work: 0.2588 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23841 Z= 0.207 Angle : 0.621 16.311 32445 Z= 0.317 Chirality : 0.045 0.207 3576 Planarity : 0.005 0.066 4140 Dihedral : 7.883 72.731 3604 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.15 % Favored : 95.74 % Rotamer: Outliers : 3.76 % Allowed : 17.73 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 2961 helix: 0.80 (0.40), residues: 174 sheet: 0.66 (0.15), residues: 1158 loop : -0.26 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 62 TYR 0.032 0.001 TYR U 52 PHE 0.021 0.001 PHE G 67 TRP 0.015 0.001 TRP O 47 HIS 0.004 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00473 (23796) covalent geometry : angle 0.61683 (32340) SS BOND : bond 0.00400 ( 30) SS BOND : angle 0.63165 ( 60) hydrogen bonds : bond 0.03341 ( 894) hydrogen bonds : angle 4.99026 ( 2394) link_ALPHA1-3 : bond 0.00686 ( 3) link_ALPHA1-3 : angle 2.08066 ( 9) link_ALPHA1-6 : bond 0.00388 ( 3) link_ALPHA1-6 : angle 1.70198 ( 9) link_BETA1-4 : bond 0.00386 ( 6) link_BETA1-4 : angle 1.74174 ( 18) link_NAG-ASN : bond 0.00513 ( 3) link_NAG-ASN : angle 2.44303 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 336 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.8639 (tpp80) cc_final: 0.8081 (tpt-90) REVERT: E 44 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8103 (tp30) REVERT: E 220 TYR cc_start: 0.8640 (m-80) cc_final: 0.8226 (m-80) REVERT: F 595 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7645 (ttt-90) REVERT: G 100 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8268 (tmmt) REVERT: G 100 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7791 (p0) REVERT: H 17 GLN cc_start: 0.8773 (tt0) cc_final: 0.8013 (pt0) REVERT: H 52 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7904 (mm-30) REVERT: I 46 GLU cc_start: 0.9192 (tt0) cc_final: 0.8785 (tt0) REVERT: I 100 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8474 (tmmt) REVERT: L 17 GLN cc_start: 0.8770 (tt0) cc_final: 0.7984 (pt0) REVERT: L 90 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8638 (p) REVERT: M 10 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6588 (tm-30) REVERT: M 12 LYS cc_start: 0.8728 (mttp) cc_final: 0.8329 (mttp) REVERT: M 69 MET cc_start: 0.9298 (mtt) cc_final: 0.9098 (mtt) REVERT: O 83 ARG cc_start: 0.8549 (mpp80) cc_final: 0.8062 (mpt-90) outliers start: 94 outliers final: 54 residues processed: 405 average time/residue: 0.7173 time to fit residues: 326.4537 Evaluate side-chains 381 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 321 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 584 ILE Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 625 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 100 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain W residue 52 TYR Chi-restraints excluded: chain X residue 11 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 293 optimal weight: 50.0000 chunk 288 optimal weight: 0.0270 chunk 208 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 222 optimal weight: 0.0020 chunk 239 optimal weight: 50.0000 chunk 76 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 37 GLN ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.138122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.072528 restraints weight = 46058.765| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 5.13 r_work: 0.2633 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23841 Z= 0.125 Angle : 0.599 14.903 32445 Z= 0.305 Chirality : 0.044 0.211 3576 Planarity : 0.005 0.058 4140 Dihedral : 7.323 66.851 3603 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.98 % Rotamer: Outliers : 3.52 % Allowed : 18.49 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 2961 helix: 0.81 (0.39), residues: 174 sheet: 0.70 (0.15), residues: 1158 loop : -0.24 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 62 TYR 0.028 0.001 TYR U 52 PHE 0.021 0.001 PHE K 67 TRP 0.015 0.001 TRP O 47 HIS 0.004 0.001 HIS F 628 Details of bonding type rmsd covalent geometry : bond 0.00282 (23796) covalent geometry : angle 0.59681 (32340) SS BOND : bond 0.00278 ( 30) SS BOND : angle 0.51000 ( 60) hydrogen bonds : bond 0.03011 ( 894) hydrogen bonds : angle 4.85033 ( 2394) link_ALPHA1-3 : bond 0.00812 ( 3) link_ALPHA1-3 : angle 1.62002 ( 9) link_ALPHA1-6 : bond 0.00556 ( 3) link_ALPHA1-6 : angle 1.89656 ( 9) link_BETA1-4 : bond 0.00170 ( 6) link_BETA1-4 : angle 1.34572 ( 18) link_NAG-ASN : bond 0.00104 ( 3) link_NAG-ASN : angle 1.89864 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 338 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.8637 (tpp80) cc_final: 0.8055 (tpt-90) REVERT: E 220 TYR cc_start: 0.8802 (m-80) cc_final: 0.8336 (m-80) REVERT: F 595 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7545 (ttt-90) REVERT: G 100 LYS cc_start: 0.8822 (ttpp) cc_final: 0.8249 (tmmt) REVERT: G 100 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7744 (p0) REVERT: H 52 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7798 (mm-30) REVERT: I 46 GLU cc_start: 0.9097 (tt0) cc_final: 0.8696 (tt0) REVERT: I 100 LYS cc_start: 0.8769 (ttpp) cc_final: 0.8501 (tmmt) REVERT: K 100 LYS cc_start: 0.8834 (tmmt) cc_final: 0.8585 (tmmt) REVERT: L 17 GLN cc_start: 0.8628 (tt0) cc_final: 0.7886 (pt0) REVERT: L 90 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8559 (p) REVERT: M 10 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6390 (tm-30) REVERT: M 12 LYS cc_start: 0.8737 (mttp) cc_final: 0.8298 (mttp) REVERT: O 43 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8270 (mp10) outliers start: 88 outliers final: 46 residues processed: 405 average time/residue: 0.7116 time to fit residues: 324.9549 Evaluate side-chains 377 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 327 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 584 ILE Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 625 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain W residue 52 TYR Chi-restraints excluded: chain X residue 11 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 82 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 272 optimal weight: 50.0000 chunk 142 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 260 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 ASN V 37 GLN ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 89 GLN ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.137965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.073466 restraints weight = 46301.465| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 4.89 r_work: 0.2609 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23841 Z= 0.136 Angle : 0.601 16.355 32445 Z= 0.304 Chirality : 0.044 0.229 3576 Planarity : 0.005 0.060 4140 Dihedral : 7.008 63.566 3599 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.19 % Favored : 95.71 % Rotamer: Outliers : 3.48 % Allowed : 19.33 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 2961 helix: 0.91 (0.40), residues: 174 sheet: 0.72 (0.15), residues: 1167 loop : -0.26 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 62 TYR 0.027 0.001 TYR U 52 PHE 0.024 0.001 PHE K 67 TRP 0.013 0.001 TRP O 47 HIS 0.006 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00309 (23796) covalent geometry : angle 0.59793 (32340) SS BOND : bond 0.00283 ( 30) SS BOND : angle 0.50150 ( 60) hydrogen bonds : bond 0.03024 ( 894) hydrogen bonds : angle 4.79041 ( 2394) link_ALPHA1-3 : bond 0.00847 ( 3) link_ALPHA1-3 : angle 1.88058 ( 9) link_ALPHA1-6 : bond 0.00611 ( 3) link_ALPHA1-6 : angle 1.85888 ( 9) link_BETA1-4 : bond 0.00183 ( 6) link_BETA1-4 : angle 1.36704 ( 18) link_NAG-ASN : bond 0.00191 ( 3) link_NAG-ASN : angle 2.00176 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 328 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.8640 (tpp80) cc_final: 0.8095 (tpt-90) REVERT: D 591 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8425 (m-30) REVERT: E 220 TYR cc_start: 0.8358 (m-80) cc_final: 0.7763 (m-80) REVERT: F 595 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7609 (ttt-90) REVERT: G 100 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8207 (tmmt) REVERT: G 100 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7907 (p0) REVERT: H 52 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7854 (mm-30) REVERT: I 46 GLU cc_start: 0.9219 (tt0) cc_final: 0.8850 (tt0) REVERT: I 100 LYS cc_start: 0.8701 (ttpp) cc_final: 0.8453 (tmmt) REVERT: K 43 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8804 (mptp) REVERT: K 100 LYS cc_start: 0.8836 (tmmt) cc_final: 0.8616 (tmmt) REVERT: L 17 GLN cc_start: 0.8789 (tt0) cc_final: 0.8030 (pt0) REVERT: L 90 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8618 (p) REVERT: M 10 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6388 (tm-30) REVERT: M 12 LYS cc_start: 0.8473 (mttp) cc_final: 0.8041 (mttp) REVERT: O 43 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8346 (mp10) REVERT: Q 46 GLU cc_start: 0.8514 (pt0) cc_final: 0.8177 (pt0) REVERT: Q 62 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.8210 (ttm110) REVERT: T 42 GLN cc_start: 0.4717 (OUTLIER) cc_final: 0.4146 (pp30) REVERT: X 42 GLN cc_start: 0.4091 (OUTLIER) cc_final: 0.3856 (pp30) outliers start: 87 outliers final: 52 residues processed: 395 average time/residue: 0.7267 time to fit residues: 323.1477 Evaluate side-chains 379 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 319 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 584 ILE Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 625 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 42 GLN Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain W residue 52 TYR Chi-restraints excluded: chain X residue 11 LEU Chi-restraints excluded: chain X residue 42 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 93 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 281 optimal weight: 50.0000 chunk 116 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 5 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 6 GLN ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.136297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.069218 restraints weight = 46168.167| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 5.20 r_work: 0.2570 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 23841 Z= 0.253 Angle : 0.648 14.628 32445 Z= 0.331 Chirality : 0.046 0.238 3576 Planarity : 0.005 0.063 4140 Dihedral : 7.091 65.188 3599 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.51 % Rotamer: Outliers : 3.88 % Allowed : 19.25 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 2961 helix: 0.96 (0.40), residues: 174 sheet: 0.62 (0.15), residues: 1158 loop : -0.29 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 62 TYR 0.027 0.002 TYR S 52 PHE 0.015 0.001 PHE E 176 TRP 0.015 0.001 TRP A 86 HIS 0.011 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00584 (23796) covalent geometry : angle 0.64449 (32340) SS BOND : bond 0.00441 ( 30) SS BOND : angle 0.60515 ( 60) hydrogen bonds : bond 0.03411 ( 894) hydrogen bonds : angle 4.87638 ( 2394) link_ALPHA1-3 : bond 0.00735 ( 3) link_ALPHA1-3 : angle 2.07952 ( 9) link_ALPHA1-6 : bond 0.00517 ( 3) link_ALPHA1-6 : angle 1.66820 ( 9) link_BETA1-4 : bond 0.00434 ( 6) link_BETA1-4 : angle 1.72014 ( 18) link_NAG-ASN : bond 0.00595 ( 3) link_NAG-ASN : angle 2.43750 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 321 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.8639 (tpp80) cc_final: 0.8073 (tpt-90) REVERT: D 591 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: E 44 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8070 (tp30) REVERT: E 51 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8468 (tp) REVERT: E 220 TYR cc_start: 0.8592 (m-80) cc_final: 0.8020 (m-80) REVERT: F 595 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7569 (ttt-90) REVERT: G 100 LYS cc_start: 0.8867 (ttpp) cc_final: 0.8309 (tmmt) REVERT: H 52 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7901 (mm-30) REVERT: I 46 GLU cc_start: 0.9084 (tt0) cc_final: 0.8700 (tt0) REVERT: I 100 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8508 (tmmt) REVERT: K 100 LYS cc_start: 0.8854 (tmmt) cc_final: 0.8623 (tmmt) REVERT: L 17 GLN cc_start: 0.8342 (tt0) cc_final: 0.7677 (pt0) REVERT: L 90 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8543 (p) REVERT: M 10 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6409 (tm-30) REVERT: M 12 LYS cc_start: 0.8561 (mttp) cc_final: 0.8222 (mttp) REVERT: O 43 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8285 (mp10) REVERT: Q 62 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8213 (ttm110) outliers start: 97 outliers final: 59 residues processed: 399 average time/residue: 0.6982 time to fit residues: 314.4718 Evaluate side-chains 378 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 313 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 584 ILE Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 625 GLN Chi-restraints excluded: chain F residue 628 HIS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 100 ARG Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain W residue 52 TYR Chi-restraints excluded: chain X residue 11 LEU Chi-restraints excluded: chain X residue 91 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 30 optimal weight: 0.1980 chunk 108 optimal weight: 0.8980 chunk 276 optimal weight: 40.0000 chunk 186 optimal weight: 0.6980 chunk 204 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 GLN ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 6 GLN ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.138057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.072045 restraints weight = 45990.127| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 4.99 r_work: 0.2622 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23841 Z= 0.124 Angle : 0.613 14.423 32445 Z= 0.310 Chirality : 0.044 0.227 3576 Planarity : 0.005 0.063 4140 Dihedral : 6.644 59.832 3598 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.78 % Rotamer: Outliers : 3.36 % Allowed : 20.25 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 2961 helix: 0.98 (0.40), residues: 174 sheet: 0.65 (0.15), residues: 1158 loop : -0.24 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 62 TYR 0.024 0.001 TYR U 52 PHE 0.014 0.001 PHE G 67 TRP 0.015 0.001 TRP O 47 HIS 0.006 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00281 (23796) covalent geometry : angle 0.61069 (32340) SS BOND : bond 0.00259 ( 30) SS BOND : angle 0.49787 ( 60) hydrogen bonds : bond 0.03015 ( 894) hydrogen bonds : angle 4.76429 ( 2394) link_ALPHA1-3 : bond 0.00889 ( 3) link_ALPHA1-3 : angle 1.56329 ( 9) link_ALPHA1-6 : bond 0.00699 ( 3) link_ALPHA1-6 : angle 1.88137 ( 9) link_BETA1-4 : bond 0.00192 ( 6) link_BETA1-4 : angle 1.21316 ( 18) link_NAG-ASN : bond 0.00067 ( 3) link_NAG-ASN : angle 1.81707 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 327 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.8645 (tpp80) cc_final: 0.8072 (tpt-90) REVERT: D 540 GLU cc_start: 0.8775 (pm20) cc_final: 0.8257 (pp20) REVERT: E 51 LEU cc_start: 0.8740 (tt) cc_final: 0.8445 (tp) REVERT: E 220 TYR cc_start: 0.8731 (m-80) cc_final: 0.8157 (m-80) REVERT: F 595 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7586 (ttt-90) REVERT: G 100 LYS cc_start: 0.8848 (ttpp) cc_final: 0.8377 (tmmt) REVERT: H 52 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7763 (mm-30) REVERT: I 46 GLU cc_start: 0.9157 (tt0) cc_final: 0.8697 (tt0) REVERT: I 100 LYS cc_start: 0.8700 (ttpp) cc_final: 0.8448 (tmmt) REVERT: K 46 GLU cc_start: 0.9128 (tt0) cc_final: 0.8792 (tt0) REVERT: K 100 LYS cc_start: 0.8899 (tmmt) cc_final: 0.8610 (tmmt) REVERT: L 17 GLN cc_start: 0.8748 (tt0) cc_final: 0.7986 (pt0) REVERT: L 90 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8628 (p) REVERT: M 12 LYS cc_start: 0.8762 (mttp) cc_final: 0.8301 (mttp) REVERT: O 43 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8328 (mp10) REVERT: O 46 GLU cc_start: 0.8572 (pt0) cc_final: 0.8087 (pt0) REVERT: Q 46 GLU cc_start: 0.8561 (pt0) cc_final: 0.8265 (pt0) REVERT: Q 62 ARG cc_start: 0.8669 (ttp-110) cc_final: 0.8237 (ttm110) REVERT: T 42 GLN cc_start: 0.4564 (OUTLIER) cc_final: 0.4007 (pp30) outliers start: 84 outliers final: 57 residues processed: 397 average time/residue: 0.7093 time to fit residues: 317.3929 Evaluate side-chains 378 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 318 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 625 GLN Chi-restraints excluded: chain F residue 628 HIS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain S residue 100 ARG Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 42 GLN Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain W residue 52 TYR Chi-restraints excluded: chain X residue 91 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 286 optimal weight: 40.0000 chunk 159 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 289 optimal weight: 0.0270 chunk 108 optimal weight: 0.0770 chunk 27 optimal weight: 20.0000 chunk 238 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 34 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 = 0.4086 r_free = 0.4086 target = 0.137569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.072701 restraints weight = 46242.769| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 4.82 r_work: 0.2611 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23841 Z= 0.162 Angle : 0.634 15.889 32445 Z= 0.321 Chirality : 0.045 0.240 3576 Planarity : 0.005 0.069 4140 Dihedral : 6.498 58.224 3596 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.78 % Rotamer: Outliers : 2.84 % Allowed : 20.49 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 2961 helix: 1.03 (0.40), residues: 174 sheet: 0.69 (0.15), residues: 1143 loop : -0.24 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 62 TYR 0.025 0.001 TYR U 52 PHE 0.011 0.001 PHE W 78 TRP 0.013 0.001 TRP O 47 HIS 0.005 0.001 HIS F 628 Details of bonding type rmsd covalent geometry : bond 0.00372 (23796) covalent geometry : angle 0.63160 (32340) SS BOND : bond 0.00314 ( 30) SS BOND : angle 0.50944 ( 60) hydrogen bonds : bond 0.03105 ( 894) hydrogen bonds : angle 4.77491 ( 2394) link_ALPHA1-3 : bond 0.00835 ( 3) link_ALPHA1-3 : angle 1.82223 ( 9) link_ALPHA1-6 : bond 0.00704 ( 3) link_ALPHA1-6 : angle 1.75886 ( 9) link_BETA1-4 : bond 0.00192 ( 6) link_BETA1-4 : angle 1.37327 ( 18) link_NAG-ASN : bond 0.00246 ( 3) link_NAG-ASN : angle 2.09346 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 318 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8081 (tpt-90) REVERT: D 540 GLU cc_start: 0.8783 (pm20) cc_final: 0.8264 (pp20) REVERT: D 591 ASP cc_start: 0.8758 (t70) cc_final: 0.8251 (m-30) REVERT: E 51 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8493 (tp) REVERT: E 220 TYR cc_start: 0.8675 (m-80) cc_final: 0.8062 (m-80) REVERT: F 595 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7671 (ttt-90) REVERT: G 100 LYS cc_start: 0.8853 (ttpp) cc_final: 0.8392 (tmmt) REVERT: G 100 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7829 (p0) REVERT: H 52 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7833 (mm-30) REVERT: I 46 GLU cc_start: 0.9181 (tt0) cc_final: 0.8839 (tt0) REVERT: I 100 LYS cc_start: 0.8688 (ttpp) cc_final: 0.8470 (tmmt) REVERT: K 46 GLU cc_start: 0.9143 (tt0) cc_final: 0.8805 (tt0) REVERT: K 100 LYS cc_start: 0.8908 (tmmt) cc_final: 0.8634 (tmmt) REVERT: L 90 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8699 (p) REVERT: M 10 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6478 (tm-30) REVERT: M 12 LYS cc_start: 0.8635 (mttp) cc_final: 0.8182 (mttp) REVERT: O 43 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8359 (mp10) REVERT: Q 46 GLU cc_start: 0.8545 (pt0) cc_final: 0.8252 (pt0) REVERT: Q 62 ARG cc_start: 0.8684 (ttp-110) cc_final: 0.8254 (ttm110) REVERT: T 42 GLN cc_start: 0.4542 (OUTLIER) cc_final: 0.3994 (pp30) outliers start: 71 outliers final: 57 residues processed: 376 average time/residue: 0.7012 time to fit residues: 297.7482 Evaluate side-chains 378 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 315 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 625 GLN Chi-restraints excluded: chain F residue 628 HIS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain S residue 100 ARG Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 42 GLN Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain W residue 52 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 74 optimal weight: 0.8980 chunk 269 optimal weight: 50.0000 chunk 167 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 108 optimal weight: 0.1980 chunk 212 optimal weight: 3.9990 chunk 242 optimal weight: 50.0000 chunk 241 optimal weight: 50.0000 chunk 275 optimal weight: 30.0000 chunk 54 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 6 GLN ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.137153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.070647 restraints weight = 45965.545| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 4.95 r_work: 0.2587 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23841 Z= 0.177 Angle : 0.641 14.605 32445 Z= 0.326 Chirality : 0.045 0.243 3576 Planarity : 0.005 0.070 4140 Dihedral : 6.443 56.395 3596 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.19 % Favored : 95.64 % Rotamer: Outliers : 2.72 % Allowed : 20.93 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 2961 helix: 1.06 (0.40), residues: 174 sheet: 0.68 (0.15), residues: 1143 loop : -0.25 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 62 TYR 0.025 0.001 TYR U 52 PHE 0.011 0.001 PHE E 176 TRP 0.012 0.001 TRP M 47 HIS 0.005 0.001 HIS F 628 Details of bonding type rmsd covalent geometry : bond 0.00404 (23796) covalent geometry : angle 0.63893 (32340) SS BOND : bond 0.00328 ( 30) SS BOND : angle 0.53145 ( 60) hydrogen bonds : bond 0.03181 ( 894) hydrogen bonds : angle 4.78977 ( 2394) link_ALPHA1-3 : bond 0.00787 ( 3) link_ALPHA1-3 : angle 1.73505 ( 9) link_ALPHA1-6 : bond 0.00746 ( 3) link_ALPHA1-6 : angle 1.58801 ( 9) link_BETA1-4 : bond 0.00213 ( 6) link_BETA1-4 : angle 1.38509 ( 18) link_NAG-ASN : bond 0.00282 ( 3) link_NAG-ASN : angle 2.15091 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 317 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.9047 (p0) cc_final: 0.8847 (p0) REVERT: A 136 ARG cc_start: 0.8605 (tpp80) cc_final: 0.8051 (tpt-90) REVERT: D 540 GLU cc_start: 0.8799 (pm20) cc_final: 0.8286 (pp20) REVERT: D 591 ASP cc_start: 0.8750 (t70) cc_final: 0.8219 (m-30) REVERT: E 51 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8495 (tp) REVERT: E 220 TYR cc_start: 0.8586 (m-80) cc_final: 0.8028 (m-80) REVERT: F 595 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7599 (ttt-90) REVERT: G 100 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8378 (tmmt) REVERT: H 52 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7844 (mm-30) REVERT: I 46 GLU cc_start: 0.9166 (tt0) cc_final: 0.8823 (tt0) REVERT: I 100 LYS cc_start: 0.8699 (ttpp) cc_final: 0.8481 (tmmt) REVERT: K 46 GLU cc_start: 0.9133 (tt0) cc_final: 0.8784 (tt0) REVERT: K 100 LYS cc_start: 0.8894 (tmmt) cc_final: 0.8617 (tmmt) REVERT: L 90 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8632 (p) REVERT: M 10 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.5926 (tm-30) REVERT: M 12 LYS cc_start: 0.8558 (mttp) cc_final: 0.7950 (mmmm) REVERT: O 43 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8283 (mp10) REVERT: Q 62 ARG cc_start: 0.8671 (ttp-110) cc_final: 0.8220 (ttm110) REVERT: T 42 GLN cc_start: 0.4957 (OUTLIER) cc_final: 0.4584 (pp30) outliers start: 68 outliers final: 53 residues processed: 374 average time/residue: 0.7063 time to fit residues: 297.6274 Evaluate side-chains 369 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 311 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 625 GLN Chi-restraints excluded: chain F residue 628 HIS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 52 TYR Chi-restraints excluded: chain S residue 100 ARG Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 42 GLN Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain W residue 52 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 179 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 chunk 293 optimal weight: 50.0000 chunk 276 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 277 optimal weight: 30.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN M 3 GLN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 6 GLN ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.137898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.072400 restraints weight = 46018.517| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 4.83 r_work: 0.2629 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23841 Z= 0.136 Angle : 0.641 14.231 32445 Z= 0.324 Chirality : 0.044 0.261 3576 Planarity : 0.005 0.070 4140 Dihedral : 6.177 52.536 3594 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.29 % Favored : 95.54 % Rotamer: Outliers : 2.68 % Allowed : 21.09 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 2961 helix: 1.07 (0.40), residues: 174 sheet: 0.72 (0.15), residues: 1134 loop : -0.23 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG R 18 TYR 0.023 0.001 TYR U 52 PHE 0.011 0.001 PHE W 78 TRP 0.014 0.001 TRP Q 47 HIS 0.006 0.001 HIS F 628 Details of bonding type rmsd covalent geometry : bond 0.00311 (23796) covalent geometry : angle 0.63953 (32340) SS BOND : bond 0.00297 ( 30) SS BOND : angle 0.52831 ( 60) hydrogen bonds : bond 0.03004 ( 894) hydrogen bonds : angle 4.75504 ( 2394) link_ALPHA1-3 : bond 0.00873 ( 3) link_ALPHA1-3 : angle 1.56459 ( 9) link_ALPHA1-6 : bond 0.00858 ( 3) link_ALPHA1-6 : angle 1.59263 ( 9) link_BETA1-4 : bond 0.00197 ( 6) link_BETA1-4 : angle 1.19074 ( 18) link_NAG-ASN : bond 0.00087 ( 3) link_NAG-ASN : angle 1.90845 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15383.66 seconds wall clock time: 261 minutes 5.76 seconds (15665.76 seconds total)