Starting phenix.real_space_refine on Tue Apr 7 01:43:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10op_75339/04_2026/10op_75339_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/10op_75339/04_2026/10op_75339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10op_75339/04_2026/10op_75339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10op_75339/04_2026/10op_75339.map" model { file = "/net/cci-nas-00/data/ceres_data/10op_75339/04_2026/10op_75339_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10op_75339/04_2026/10op_75339_neut.cif" } resolution = 2.63 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= 0.011 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 14682 2.51 5 N 3978 2.21 5 O 4581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 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: 23337 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: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 923 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "H" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 869 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "I" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 923 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 869 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "K" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 923 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 869 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} 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: 5.61, per 1000 atoms: 0.24 Number of scatterers: 23337 At special positions: 0 Unit cell: (135.29, 136.95, 156.87, 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 4581 8.00 N 3978 7.00 C 14682 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=3, 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 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.2 seconds 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5448 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 69 sheets defined 12.1% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 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 83 through 87 Processing helix chain 'H' and resid 27C through 31 removed outlier: 3.592A pdb=" N THR H 30 " --> pdb=" O ASN H 27C" (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.982A pdb=" N GLU H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 27C through 31 removed outlier: 3.524A pdb=" N THR J 30 " --> pdb=" O ASN J 27C" (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.515A pdb=" N ASP J 82 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 27C through 31 removed outlier: 3.543A pdb=" N THR L 30 " --> pdb=" O ASN L 27C" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.515A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for '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: 7.623A pdb=" N SER G 34 " --> pdb=" O SER G 52 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N SER G 52 " --> pdb=" O SER G 34 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.713A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASP G 96 " --> pdb=" O LEU G 100C" (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU G 100C" --> pdb=" O ASP G 96 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AC2, first strand: chain 'H' and resid 9 through 13 removed outlier: 6.696A pdb=" N LEU H 11 " --> pdb=" O THR H 105 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE H 33 " --> pdb=" O ARG H 49 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG H 49 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 9 through 13 removed outlier: 6.696A pdb=" N LEU H 11 " --> pdb=" O THR H 105 " (cutoff:3.500A) 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: 3.828A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.835A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP I 96 " --> pdb=" O LEU I 100C" (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU I 100C" --> pdb=" O ASP I 96 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AC8, first strand: chain 'J' and resid 9 through 13 removed outlier: 3.617A pdb=" N LEU J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN J 37 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP J 54A" --> pdb=" O LYS J 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 9 through 13 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: 7.650A pdb=" N SER K 34 " --> pdb=" O SER K 52 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER K 52 " --> pdb=" O SER K 34 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TRP K 35A" --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR K 50 " --> pdb=" O TRP K 35A" (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.765A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ASP K 96 " --> pdb=" O LEU K 100C" (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU K 100C" --> pdb=" O ASP K 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AD5, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.586A pdb=" N LEU L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN L 37 " --> pdb=" O TYR L 46 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 9 through 13 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) 1010 hydrogen bonds defined for protein. 2448 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: 5.67 Time building geometry restraints manager: 2.73 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: 7489 1.34 - 1.46: 6105 1.46 - 1.58: 10184 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 23904 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=" CB GLN K 1 " pdb=" CG GLN K 1 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.92e+00 ... (remaining 23899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 32256 3.38 - 6.77: 220 6.77 - 10.15: 17 10.15 - 13.53: 0 13.53 - 16.92: 3 Bond angle restraints: 32496 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=" 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=" CA GLN K 1 " pdb=" CB GLN K 1 " pdb=" CG GLN K 1 " ideal model delta sigma weight residual 114.10 121.41 -7.31 2.00e+00 2.50e-01 1.33e+01 angle pdb=" CA GLN I 1 " pdb=" CB GLN I 1 " pdb=" CG GLN I 1 " ideal model delta sigma weight residual 114.10 121.32 -7.22 2.00e+00 2.50e-01 1.30e+01 ... (remaining 32491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.57: 12996 21.57 - 43.15: 1000 43.15 - 64.72: 181 64.72 - 86.30: 43 86.30 - 107.87: 12 Dihedral angle restraints: 14232 sinusoidal: 5619 harmonic: 8613 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 14229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2932 0.054 - 0.108: 534 0.108 - 0.162: 113 0.162 - 0.215: 5 0.215 - 0.269: 4 Chirality restraints: 3588 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 3585 not shown) Planarity restraints: 4143 Sorted by residual: 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 delta sigma weight rms_deltas residual plane pdb=" C ARG U 98 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.37e+00 pdb=" N PRO U 99 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO U 99 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO U 99 " -0.032 5.00e-02 4.00e+02 ... (remaining 4140 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 5 2.04 - 2.75: 2913 2.75 - 3.47: 31502 3.47 - 4.18: 59971 4.18 - 4.90: 103751 Nonbonded interactions: 198142 Sorted by model distance: nonbonded pdb=" O HIS E 229 " pdb=" OG SER I 56 " model vdw 1.322 3.040 nonbonded pdb=" ND2 ASN E 224 " pdb=" OG SER I 56 " model vdw 1.796 3.120 nonbonded pdb=" ND1 HIS C 229 " pdb=" CA SER K 56 " model vdw 1.978 3.550 nonbonded pdb=" ND1 HIS E 229 " pdb=" CA SER I 56 " model vdw 2.012 3.550 nonbonded pdb=" ND1 HIS A 229 " pdb=" CA SER G 56 " model vdw 2.035 3.550 ... (remaining 198137 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: 0.01 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: 7.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.050 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 : 0.005 0.386 23952 Z= 0.414 Angle : 0.710 16.918 32601 Z= 0.361 Chirality : 0.045 0.269 3588 Planarity : 0.005 0.064 4140 Dihedral : 15.834 107.874 8694 Min Nonbonded Distance : 1.322 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.06 % Favored : 96.84 % Rotamer: Outliers : 2.43 % Allowed : 18.84 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.40 (0.16), residues: 2970 helix: 0.68 (0.38), residues: 168 sheet: 0.65 (0.15), residues: 1188 loop : 0.01 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Q 62 TYR 0.062 0.001 TYR S 52 PHE 0.010 0.001 PHE U 78 TRP 0.013 0.001 TRP H 96 HIS 0.020 0.001 HIS F 628 Details of bonding type rmsd covalent geometry : bond 0.00354 (23904) covalent geometry : angle 0.70729 (32496) SS BOND : bond 0.00298 ( 30) SS BOND : angle 0.70139 ( 60) hydrogen bonds : bond 0.12726 ( 902) hydrogen bonds : angle 6.86796 ( 2448) Misc. bond : bond 0.34130 ( 3) 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) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 334 time to evaluate : 0.897 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: A 55 ASP cc_start: 0.8132 (m-30) cc_final: 0.7791 (m-30) REVERT: A 127 ASP cc_start: 0.8769 (t0) cc_final: 0.8452 (t0) REVERT: A 136 ARG cc_start: 0.7165 (tpp80) cc_final: 0.6704 (tpt90) REVERT: A 224 ASN cc_start: 0.6504 (m-40) cc_final: 0.6154 (t0) REVERT: B 540 GLU cc_start: 0.7761 (pm20) cc_final: 0.7431 (pm20) REVERT: C 55 ASP cc_start: 0.8132 (m-30) cc_final: 0.7801 (m-30) REVERT: C 127 ASP cc_start: 0.8831 (t0) cc_final: 0.8513 (t0) REVERT: C 136 ARG cc_start: 0.7203 (tpt-90) cc_final: 0.6950 (tpt90) REVERT: D 540 GLU cc_start: 0.7616 (pm20) cc_final: 0.7360 (pm20) REVERT: E 54 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8855 (ttpp) REVERT: E 127 ASP cc_start: 0.8855 (t0) cc_final: 0.8632 (t0) REVERT: E 136 ARG cc_start: 0.7298 (tpt-90) cc_final: 0.7047 (tpt90) REVERT: F 540 GLU cc_start: 0.7614 (pm20) cc_final: 0.7412 (pm20) REVERT: I 13 LYS cc_start: 0.7757 (mppt) cc_final: 0.7507 (mmpt) REVERT: I 16 GLN cc_start: 0.7976 (mm110) cc_final: 0.7611 (mt0) REVERT: I 89 VAL cc_start: 0.8484 (t) cc_final: 0.8176 (p) REVERT: K 16 GLN cc_start: 0.7676 (mm110) cc_final: 0.7336 (mt0) REVERT: K 89 VAL cc_start: 0.8443 (t) cc_final: 0.8221 (p) REVERT: M 3 GLN cc_start: 0.9048 (tt0) cc_final: 0.8846 (tt0) REVERT: M 13 LYS cc_start: 0.8362 (mmtm) cc_final: 0.8115 (tppp) REVERT: M 105 LYS cc_start: 0.9396 (mptm) cc_final: 0.9170 (mmmt) REVERT: N 18 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8185 (mtp85) REVERT: N 79 GLN cc_start: 0.8270 (mt0) cc_final: 0.7708 (mp10) REVERT: O 13 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7990 (tppp) REVERT: O 62 ARG cc_start: 0.8440 (ttp-110) cc_final: 0.7929 (ttp-110) REVERT: O 105 LYS cc_start: 0.9385 (mptm) cc_final: 0.9160 (mmmt) REVERT: P 18 ARG cc_start: 0.8701 (mtp85) cc_final: 0.8376 (mtp-110) REVERT: P 79 GLN cc_start: 0.8024 (mt0) cc_final: 0.7606 (mp10) REVERT: Q 13 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7769 (tppp) REVERT: R 18 ARG cc_start: 0.8712 (mtp85) cc_final: 0.8287 (mtp-110) REVERT: R 79 GLN cc_start: 0.7996 (mt0) cc_final: 0.7531 (mp10) REVERT: T 3 GLN cc_start: 0.8534 (tp-100) cc_final: 0.7960 (tm-30) REVERT: T 4 MET cc_start: 0.2067 (mmt) cc_final: -0.1108 (mpt) REVERT: T 6 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7231 (mm-40) REVERT: T 90 GLN cc_start: 0.2127 (pp30) cc_final: 0.0835 (tt0) REVERT: T 100 GLN cc_start: 0.8449 (mm110) cc_final: 0.7900 (mp10) REVERT: V 3 GLN cc_start: 0.8572 (tp40) cc_final: 0.8027 (tm-30) REVERT: V 4 MET cc_start: 0.1364 (mmt) cc_final: -0.2226 (mpt) REVERT: V 6 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.6530 (mm-40) REVERT: V 90 GLN cc_start: 0.2046 (pp30) cc_final: 0.1005 (tm-30) REVERT: V 100 GLN cc_start: 0.8290 (mm110) cc_final: 0.7605 (mp10) REVERT: X 3 GLN cc_start: 0.8518 (tp-100) cc_final: 0.7961 (tm-30) REVERT: X 4 MET cc_start: 0.1547 (mmt) cc_final: -0.2552 (mpt) REVERT: X 6 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7232 (mm-40) REVERT: X 90 GLN cc_start: 0.2343 (pp30) cc_final: 0.1715 (tt0) REVERT: X 100 GLN cc_start: 0.8328 (mm110) cc_final: 0.7710 (mp10) outliers start: 61 outliers final: 43 residues processed: 388 average time/residue: 0.6892 time to fit residues: 302.7998 Evaluate side-chains 349 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 303 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 579 LEU Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 65 SER 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 609 CYS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 609 CYS Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 THR 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 39 LEU Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain P residue 102 THR 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 U residue 52 TYR Chi-restraints excluded: chain V residue 6 GLN 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: 0.4980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 560 GLN B 628 HIS ** D 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN I 40 HIS N 37 GLN P 37 GLN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 GLN T 55 GLN ** U 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 GLN V 55 GLN ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 89 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.129967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.072019 restraints weight = 51982.911| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 4.21 r_work: 0.2660 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 23952 Z= 0.190 Angle : 0.648 16.202 32601 Z= 0.328 Chirality : 0.045 0.200 3588 Planarity : 0.006 0.138 4140 Dihedral : 8.767 94.548 3657 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.60 % Rotamer: Outliers : 3.54 % Allowed : 17.56 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2970 helix: 0.87 (0.40), residues: 171 sheet: 0.83 (0.15), residues: 1092 loop : -0.04 (0.16), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG K 97 TYR 0.024 0.002 TYR V 36 PHE 0.014 0.001 PHE K 78 TRP 0.017 0.002 TRP B 615 HIS 0.006 0.001 HIS F 628 Details of bonding type rmsd covalent geometry : bond 0.00442 (23904) covalent geometry : angle 0.64340 (32496) SS BOND : bond 0.00284 ( 30) SS BOND : angle 0.54312 ( 60) hydrogen bonds : bond 0.03544 ( 902) hydrogen bonds : angle 5.51227 ( 2448) Misc. bond : bond 0.01250 ( 3) link_ALPHA1-3 : bond 0.00643 ( 3) link_ALPHA1-3 : angle 2.32432 ( 9) link_ALPHA1-6 : bond 0.00312 ( 3) link_ALPHA1-6 : angle 1.99704 ( 9) link_BETA1-4 : bond 0.00551 ( 6) link_BETA1-4 : angle 2.01672 ( 18) link_NAG-ASN : bond 0.00257 ( 3) link_NAG-ASN : angle 2.27002 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 311 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8258 (m-30) cc_final: 0.7973 (m-30) REVERT: A 83 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.8955 (p) REVERT: A 136 ARG cc_start: 0.8765 (tpp80) cc_final: 0.8269 (tpt90) REVERT: B 540 GLU cc_start: 0.8548 (pm20) cc_final: 0.8180 (pm20) REVERT: C 55 ASP cc_start: 0.8156 (m-30) cc_final: 0.7853 (m-30) REVERT: C 61 ASP cc_start: 0.9159 (p0) cc_final: 0.8949 (OUTLIER) REVERT: C 100 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8582 (mm-30) REVERT: C 136 ARG cc_start: 0.8571 (tpt-90) cc_final: 0.8325 (tpt90) REVERT: C 219 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8627 (mm-30) REVERT: D 540 GLU cc_start: 0.8596 (pm20) cc_final: 0.8256 (pm20) REVERT: E 77 THR cc_start: 0.9457 (p) cc_final: 0.9049 (m) REVERT: E 83 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.8930 (p) REVERT: E 136 ARG cc_start: 0.8679 (tpt-90) cc_final: 0.8362 (tpt90) REVERT: F 540 GLU cc_start: 0.8600 (pm20) cc_final: 0.8281 (pm20) REVERT: G 13 LYS cc_start: 0.8661 (mmpt) cc_final: 0.8353 (mmpt) REVERT: H 27 ASN cc_start: 0.8933 (t0) cc_final: 0.8592 (t0) REVERT: I 13 LYS cc_start: 0.8654 (mppt) cc_final: 0.8369 (mmpt) REVERT: I 16 GLN cc_start: 0.8597 (mm110) cc_final: 0.8385 (mt0) REVERT: I 81 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7822 (mmmm) REVERT: I 89 VAL cc_start: 0.8924 (t) cc_final: 0.8569 (p) REVERT: K 89 VAL cc_start: 0.8874 (t) cc_final: 0.8624 (p) REVERT: L 33 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8984 (mm) REVERT: M 105 LYS cc_start: 0.9602 (mptm) cc_final: 0.9290 (mmmt) REVERT: N 79 GLN cc_start: 0.7944 (mt0) cc_final: 0.7529 (mp10) REVERT: N 82 ASP cc_start: 0.7786 (m-30) cc_final: 0.7545 (m-30) REVERT: O 1 GLN cc_start: 0.8537 (pm20) cc_final: 0.8301 (pp30) REVERT: O 13 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8209 (tppp) REVERT: P 79 GLN cc_start: 0.7806 (mt0) cc_final: 0.7535 (mp10) REVERT: Q 1 GLN cc_start: 0.8599 (pm20) cc_final: 0.8361 (pp30) REVERT: Q 13 LYS cc_start: 0.8408 (mmtt) cc_final: 0.8105 (tppp) REVERT: R 60 ASP cc_start: 0.9068 (m-30) cc_final: 0.8833 (t0) REVERT: R 79 GLN cc_start: 0.7930 (mt0) cc_final: 0.7531 (mp10) REVERT: R 82 ASP cc_start: 0.7881 (m-30) cc_final: 0.7646 (m-30) REVERT: T 3 GLN cc_start: 0.8731 (tp-100) cc_final: 0.8164 (tm-30) REVERT: T 4 MET cc_start: 0.5933 (mmt) cc_final: 0.2683 (mpt) REVERT: T 55 GLN cc_start: 0.3465 (OUTLIER) cc_final: 0.2714 (pm20) REVERT: T 90 GLN cc_start: 0.2757 (pp30) cc_final: 0.2128 (tt0) REVERT: T 100 GLN cc_start: 0.8417 (mm110) cc_final: 0.7905 (mp10) REVERT: V 3 GLN cc_start: 0.8826 (tp-100) cc_final: 0.8311 (tm-30) REVERT: V 4 MET cc_start: 0.5287 (mmt) cc_final: 0.1301 (mpt) REVERT: V 6 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8397 (mm-40) REVERT: V 33 LEU cc_start: 0.2306 (OUTLIER) cc_final: 0.1971 (tt) REVERT: V 100 GLN cc_start: 0.8413 (mm110) cc_final: 0.7912 (mp10) REVERT: X 3 GLN cc_start: 0.8881 (tp-100) cc_final: 0.8394 (tm-30) REVERT: X 4 MET cc_start: 0.5431 (mmt) cc_final: 0.1345 (mpt) REVERT: X 6 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8524 (mm-40) REVERT: X 100 GLN cc_start: 0.8424 (mm110) cc_final: 0.7874 (mp10) outliers start: 89 outliers final: 39 residues processed: 379 average time/residue: 0.7415 time to fit residues: 316.4601 Evaluate side-chains 345 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 297 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain D residue 609 CYS Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 609 CYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 110 THR 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 110 THR Chi-restraints excluded: chain R residue 45 LYS Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 55 GLN Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 55 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 228 optimal weight: 50.0000 chunk 13 optimal weight: 1.9990 chunk 231 optimal weight: 50.0000 chunk 179 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS B 514 ASN D 560 GLN ** D 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN F 514 ASN I 40 HIS O 3 GLN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 ASN T 42 GLN T 55 GLN ** V 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 GLN V 55 GLN ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 GLN ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.128156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.069818 restraints weight = 51953.355| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 4.05 r_work: 0.2611 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 23952 Z= 0.269 Angle : 0.671 15.153 32601 Z= 0.339 Chirality : 0.046 0.218 3588 Planarity : 0.006 0.136 4140 Dihedral : 8.018 83.104 3614 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.09 % Rotamer: Outliers : 3.94 % Allowed : 17.92 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.32 (0.16), residues: 2970 helix: 0.93 (0.40), residues: 171 sheet: 0.76 (0.15), residues: 1092 loop : -0.17 (0.16), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG I 97 TYR 0.018 0.002 TYR W 91 PHE 0.014 0.001 PHE K 78 TRP 0.016 0.002 TRP L 96 HIS 0.004 0.001 HIS E 229 Details of bonding type rmsd covalent geometry : bond 0.00621 (23904) covalent geometry : angle 0.66736 (32496) SS BOND : bond 0.00379 ( 30) SS BOND : angle 0.62914 ( 60) hydrogen bonds : bond 0.03621 ( 902) hydrogen bonds : angle 5.38051 ( 2448) Misc. bond : bond 0.01310 ( 3) link_ALPHA1-3 : bond 0.00413 ( 3) link_ALPHA1-3 : angle 1.72654 ( 9) link_ALPHA1-6 : bond 0.00149 ( 3) link_ALPHA1-6 : angle 2.06044 ( 9) link_BETA1-4 : bond 0.00550 ( 6) link_BETA1-4 : angle 1.61339 ( 18) link_NAG-ASN : bond 0.00567 ( 3) link_NAG-ASN : angle 2.32388 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 295 time to evaluate : 0.895 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: A 55 ASP cc_start: 0.8293 (m-30) cc_final: 0.8063 (m-30) REVERT: A 114 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8565 (mttp) REVERT: A 136 ARG cc_start: 0.8803 (tpp80) cc_final: 0.8361 (tpt90) REVERT: B 540 GLU cc_start: 0.8613 (pm20) cc_final: 0.8246 (pm20) REVERT: C 55 ASP cc_start: 0.8265 (m-30) cc_final: 0.8014 (m-30) REVERT: C 100 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8727 (mm-30) REVERT: C 136 ARG cc_start: 0.8553 (tpt-90) cc_final: 0.8322 (tpt90) REVERT: C 219 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8581 (mm-30) REVERT: D 540 GLU cc_start: 0.8626 (pm20) cc_final: 0.8232 (pm20) REVERT: E 136 ARG cc_start: 0.8597 (tpt-90) cc_final: 0.8358 (tpt90) REVERT: F 540 GLU cc_start: 0.8646 (pm20) cc_final: 0.8319 (pm20) REVERT: G 3 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7487 (tm-30) REVERT: G 64 GLU cc_start: 0.8122 (pm20) cc_final: 0.7899 (pm20) REVERT: H 27 ASN cc_start: 0.9034 (t0) cc_final: 0.8313 (t0) REVERT: H 29 ASP cc_start: 0.9320 (m-30) cc_final: 0.8918 (m-30) REVERT: I 13 LYS cc_start: 0.8561 (mppt) cc_final: 0.7898 (mppt) REVERT: I 16 GLN cc_start: 0.8467 (mm110) cc_final: 0.8173 (mt0) REVERT: I 81 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7709 (mmmm) REVERT: J 45 GLN cc_start: 0.8516 (mm110) cc_final: 0.8299 (mm110) REVERT: J 66 ASP cc_start: 0.8514 (t0) cc_final: 0.8112 (t70) REVERT: K 89 VAL cc_start: 0.8776 (t) cc_final: 0.8542 (p) REVERT: L 27 ASN cc_start: 0.9050 (t0) cc_final: 0.8841 (t0) REVERT: L 33 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8928 (mm) REVERT: L 45 GLN cc_start: 0.8462 (mm110) cc_final: 0.8212 (mm110) REVERT: M 105 LYS cc_start: 0.9604 (mptm) cc_final: 0.9301 (mmmt) REVERT: N 79 GLN cc_start: 0.7967 (mt0) cc_final: 0.7478 (mp10) REVERT: N 82 ASP cc_start: 0.7820 (m-30) cc_final: 0.7563 (m-30) REVERT: O 1 GLN cc_start: 0.8641 (pm20) cc_final: 0.8412 (pp30) REVERT: O 13 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8426 (tppp) REVERT: O 43 GLN cc_start: 0.8896 (mp10) cc_final: 0.8404 (mp10) REVERT: P 79 GLN cc_start: 0.7925 (mt0) cc_final: 0.7619 (mp10) REVERT: Q 1 GLN cc_start: 0.8721 (pm20) cc_final: 0.8437 (pp30) REVERT: Q 13 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8440 (tppp) REVERT: Q 43 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8180 (mp10) REVERT: Q 105 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9168 (mmmt) REVERT: R 79 GLN cc_start: 0.7982 (mt0) cc_final: 0.7524 (mp10) REVERT: R 82 ASP cc_start: 0.7933 (m-30) cc_final: 0.7676 (m-30) REVERT: T 3 GLN cc_start: 0.8629 (tp-100) cc_final: 0.7957 (tm-30) REVERT: T 4 MET cc_start: 0.4128 (mmt) cc_final: 0.0706 (mpp) REVERT: T 6 GLN cc_start: 0.8233 (mm-40) cc_final: 0.8026 (mm-40) REVERT: T 55 GLN cc_start: -0.0060 (mt0) cc_final: -0.1326 (mm-40) REVERT: T 90 GLN cc_start: 0.2747 (pp30) cc_final: 0.2105 (tt0) REVERT: T 100 GLN cc_start: 0.8431 (mm110) cc_final: 0.7878 (mp10) REVERT: U 100 MET cc_start: -0.3053 (OUTLIER) cc_final: -0.3267 (pp-130) REVERT: V 3 GLN cc_start: 0.8666 (tp-100) cc_final: 0.8182 (tp40) REVERT: V 4 MET cc_start: 0.1545 (mmt) cc_final: -0.4375 (tpp) REVERT: V 6 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7356 (mm-40) REVERT: V 55 GLN cc_start: 0.0144 (mt0) cc_final: -0.0993 (mm-40) REVERT: V 100 GLN cc_start: 0.8334 (mm110) cc_final: 0.7848 (mp10) REVERT: X 3 GLN cc_start: 0.8603 (tp-100) cc_final: 0.7978 (tm-30) REVERT: X 4 MET cc_start: 0.2281 (mmt) cc_final: -0.0816 (mpt) REVERT: X 6 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7729 (mm-40) REVERT: X 100 GLN cc_start: 0.8331 (mm110) cc_final: 0.7720 (mp10) outliers start: 99 outliers final: 39 residues processed: 375 average time/residue: 0.7304 time to fit residues: 311.2075 Evaluate side-chains 335 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 287 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain F residue 584 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 19 VAL 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 105 LYS Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 100 MET Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 10 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 219 optimal weight: 0.9980 chunk 293 optimal weight: 50.0000 chunk 285 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 263 optimal weight: 40.0000 chunk 183 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS C 50 GLN C 56 HIS D 514 ASN ** D 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS E 224 ASN J 79 GLN N 37 GLN ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 GLN ** V 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 GLN ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN X 55 GLN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.126868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.067411 restraints weight = 51977.578| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 4.44 r_work: 0.2531 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 23952 Z= 0.377 Angle : 0.711 14.216 32601 Z= 0.362 Chirality : 0.048 0.242 3588 Planarity : 0.006 0.125 4140 Dihedral : 7.936 85.023 3607 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.72 % Rotamer: Outliers : 4.14 % Allowed : 18.52 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.19 (0.15), residues: 2970 helix: 1.05 (0.40), residues: 171 sheet: 0.64 (0.15), residues: 1089 loop : -0.27 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 97 TYR 0.018 0.002 TYR U 91 PHE 0.020 0.002 PHE X 71 TRP 0.021 0.002 TRP H 96 HIS 0.004 0.001 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00868 (23904) covalent geometry : angle 0.70783 (32496) SS BOND : bond 0.00499 ( 30) SS BOND : angle 0.73148 ( 60) hydrogen bonds : bond 0.03784 ( 902) hydrogen bonds : angle 5.32948 ( 2448) Misc. bond : bond 0.01415 ( 3) link_ALPHA1-3 : bond 0.00170 ( 3) link_ALPHA1-3 : angle 1.86972 ( 9) link_ALPHA1-6 : bond 0.00083 ( 3) link_ALPHA1-6 : angle 2.00822 ( 9) link_BETA1-4 : bond 0.00746 ( 6) link_BETA1-4 : angle 1.74274 ( 18) link_NAG-ASN : bond 0.00703 ( 3) link_NAG-ASN : angle 2.31451 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 290 time to evaluate : 0.912 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: A 54 LYS cc_start: 0.9458 (ttpp) cc_final: 0.9251 (ttpp) REVERT: A 55 ASP cc_start: 0.8434 (m-30) cc_final: 0.8082 (m-30) REVERT: A 114 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8551 (mttp) REVERT: A 136 ARG cc_start: 0.8888 (tpp80) cc_final: 0.8291 (tpt90) REVERT: B 540 GLU cc_start: 0.8756 (pm20) cc_final: 0.8385 (pm20) REVERT: C 55 ASP cc_start: 0.8283 (m-30) cc_final: 0.8014 (m-30) REVERT: C 100 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8697 (mm-30) REVERT: C 136 ARG cc_start: 0.8711 (tpt-90) cc_final: 0.8346 (tpt90) REVERT: C 219 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8378 (mm-30) REVERT: D 540 GLU cc_start: 0.8762 (pm20) cc_final: 0.8303 (pm20) REVERT: E 44 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8561 (tt0) REVERT: E 136 ARG cc_start: 0.8731 (tpt-90) cc_final: 0.8404 (tpt90) REVERT: F 540 GLU cc_start: 0.8786 (pm20) cc_final: 0.8450 (pm20) REVERT: G 3 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7329 (tm-30) REVERT: G 64 GLU cc_start: 0.8319 (pm20) cc_final: 0.7960 (pm20) REVERT: H 27 ASN cc_start: 0.9046 (t0) cc_final: 0.8764 (t0) REVERT: J 45 GLN cc_start: 0.8614 (mm110) cc_final: 0.8369 (mm110) REVERT: J 66 ASP cc_start: 0.8511 (t0) cc_final: 0.8102 (t0) REVERT: L 27 ASN cc_start: 0.9060 (t0) cc_final: 0.8804 (t0) REVERT: L 33 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8929 (mm) REVERT: L 45 GLN cc_start: 0.8527 (mm110) cc_final: 0.8261 (mm110) REVERT: L 51 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8161 (tptm) REVERT: N 79 GLN cc_start: 0.7818 (mt0) cc_final: 0.7424 (mp10) REVERT: O 1 GLN cc_start: 0.8679 (pm20) cc_final: 0.8460 (pp30) REVERT: O 43 GLN cc_start: 0.8956 (mp10) cc_final: 0.8395 (mp10) REVERT: P 79 GLN cc_start: 0.7710 (mt0) cc_final: 0.7365 (mp10) REVERT: Q 13 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8631 (tppp) REVERT: Q 43 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8800 (mp10) REVERT: R 79 GLN cc_start: 0.7862 (mt0) cc_final: 0.7452 (mp10) REVERT: T 3 GLN cc_start: 0.8776 (tp-100) cc_final: 0.8182 (tm-30) REVERT: T 4 MET cc_start: 0.6217 (mmt) cc_final: 0.3707 (mpp) REVERT: T 90 GLN cc_start: 0.2864 (pp30) cc_final: 0.2528 (tm-30) REVERT: T 91 ILE cc_start: 0.5286 (OUTLIER) cc_final: 0.4998 (mm) REVERT: T 100 GLN cc_start: 0.8451 (mm110) cc_final: 0.7962 (mp10) REVERT: V 3 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8362 (tp40) REVERT: V 4 MET cc_start: 0.4651 (mmt) cc_final: -0.1124 (tpp) REVERT: V 6 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8252 (mm-40) REVERT: V 100 GLN cc_start: 0.8391 (mm110) cc_final: 0.7941 (mp10) REVERT: X 3 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8127 (tm-30) REVERT: X 4 MET cc_start: 0.4486 (mmt) cc_final: 0.1418 (mpt) REVERT: X 6 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8452 (mm-40) REVERT: X 95 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.6022 (pmm) REVERT: X 100 GLN cc_start: 0.8381 (mm110) cc_final: 0.7867 (mp10) outliers start: 104 outliers final: 51 residues processed: 371 average time/residue: 0.7165 time to fit residues: 300.5121 Evaluate side-chains 338 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 277 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 584 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 45 LYS Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain T residue 91 ILE Chi-restraints excluded: chain T residue 95 MET Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 55 GLN Chi-restraints excluded: chain X residue 95 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 149 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 260 optimal weight: 50.0000 chunk 78 optimal weight: 0.8980 chunk 287 optimal weight: 30.0000 chunk 218 optimal weight: 7.9990 chunk 258 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN K 40 HIS S 50 ASN T 42 GLN T 55 GLN ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 GLN V 55 GLN ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.129316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.070879 restraints weight = 51387.993| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 4.21 r_work: 0.2619 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23952 Z= 0.139 Angle : 0.629 14.706 32601 Z= 0.317 Chirality : 0.044 0.220 3588 Planarity : 0.005 0.079 4140 Dihedral : 7.175 65.152 3604 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.09 % Rotamer: Outliers : 2.91 % Allowed : 19.83 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.28 (0.16), residues: 2970 helix: 1.10 (0.40), residues: 171 sheet: 0.69 (0.16), residues: 1083 loop : -0.19 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 62 TYR 0.017 0.001 TYR W 91 PHE 0.015 0.001 PHE T 71 TRP 0.014 0.001 TRP O 47 HIS 0.004 0.001 HIS K 40 Details of bonding type rmsd covalent geometry : bond 0.00321 (23904) covalent geometry : angle 0.62713 (32496) SS BOND : bond 0.00285 ( 30) SS BOND : angle 0.54722 ( 60) hydrogen bonds : bond 0.03078 ( 902) hydrogen bonds : angle 5.09592 ( 2448) Misc. bond : bond 0.00649 ( 3) link_ALPHA1-3 : bond 0.00668 ( 3) link_ALPHA1-3 : angle 1.43791 ( 9) link_ALPHA1-6 : bond 0.00426 ( 3) link_ALPHA1-6 : angle 1.99880 ( 9) link_BETA1-4 : bond 0.00200 ( 6) link_BETA1-4 : angle 1.13023 ( 18) link_NAG-ASN : bond 0.00120 ( 3) link_NAG-ASN : angle 1.41856 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 311 time to evaluate : 0.890 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: A 54 LYS cc_start: 0.9451 (ttpp) cc_final: 0.9242 (ttpp) REVERT: A 55 ASP cc_start: 0.8376 (m-30) cc_final: 0.7947 (m-30) REVERT: A 136 ARG cc_start: 0.8862 (tpp80) cc_final: 0.8390 (tpt90) REVERT: B 540 GLU cc_start: 0.8689 (pm20) cc_final: 0.8310 (pm20) REVERT: C 55 ASP cc_start: 0.8239 (m-30) cc_final: 0.7837 (m-30) REVERT: C 100 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8764 (mm-30) REVERT: C 136 ARG cc_start: 0.8688 (tpt-90) cc_final: 0.8368 (tpt90) REVERT: C 219 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8549 (mm-30) REVERT: D 540 GLU cc_start: 0.8726 (pm20) cc_final: 0.8260 (pm20) REVERT: E 100 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8709 (mp0) REVERT: E 136 ARG cc_start: 0.8687 (tpt-90) cc_final: 0.8389 (tpt90) REVERT: F 540 GLU cc_start: 0.8762 (pm20) cc_final: 0.8426 (pm20) REVERT: G 3 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7530 (tm-30) REVERT: G 64 GLU cc_start: 0.8361 (pm20) cc_final: 0.7966 (pm20) REVERT: G 72 ASP cc_start: 0.8088 (t0) cc_final: 0.7305 (t0) REVERT: G 89 VAL cc_start: 0.8797 (t) cc_final: 0.8504 (p) REVERT: H 27 ASN cc_start: 0.8986 (t0) cc_final: 0.8744 (t0) REVERT: I 3 GLN cc_start: 0.7711 (tm130) cc_final: 0.7467 (tm-30) REVERT: I 13 LYS cc_start: 0.8457 (mppt) cc_final: 0.8036 (mmpt) REVERT: I 16 GLN cc_start: 0.8519 (mm110) cc_final: 0.8252 (mt0) REVERT: I 89 VAL cc_start: 0.8761 (t) cc_final: 0.8456 (p) REVERT: J 45 GLN cc_start: 0.8595 (mm110) cc_final: 0.8320 (mm110) REVERT: J 66 ASP cc_start: 0.8480 (t0) cc_final: 0.8068 (t0) REVERT: K 16 GLN cc_start: 0.8385 (mm110) cc_final: 0.8110 (mt0) REVERT: K 89 VAL cc_start: 0.8838 (t) cc_final: 0.8627 (p) REVERT: L 27 ASN cc_start: 0.9064 (t0) cc_final: 0.8799 (t0) REVERT: L 45 GLN cc_start: 0.8513 (mm110) cc_final: 0.8224 (mm110) REVERT: M 105 LYS cc_start: 0.9599 (mmtp) cc_final: 0.9255 (mmmt) REVERT: N 79 GLN cc_start: 0.7953 (mt0) cc_final: 0.7555 (mp10) REVERT: O 1 GLN cc_start: 0.8668 (pm20) cc_final: 0.8464 (pp30) REVERT: O 43 GLN cc_start: 0.8934 (mp10) cc_final: 0.8474 (mp10) REVERT: O 105 LYS cc_start: 0.9557 (mmtm) cc_final: 0.9264 (mmmt) REVERT: P 79 GLN cc_start: 0.7956 (mt0) cc_final: 0.7629 (mp10) REVERT: Q 13 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8633 (tppp) REVERT: Q 43 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8747 (mp10) REVERT: Q 105 LYS cc_start: 0.9510 (mmtm) cc_final: 0.9169 (mmmt) REVERT: R 79 GLN cc_start: 0.8081 (mt0) cc_final: 0.7719 (mp10) REVERT: T 3 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8205 (tm-30) REVERT: T 4 MET cc_start: 0.5841 (mmt) cc_final: 0.2576 (mmt) REVERT: T 55 GLN cc_start: 0.0160 (OUTLIER) cc_final: -0.0379 (pm20) REVERT: T 90 GLN cc_start: 0.2632 (pp30) cc_final: 0.2257 (tm-30) REVERT: T 100 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: V 3 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8256 (tp40) REVERT: V 4 MET cc_start: 0.3199 (mmt) cc_final: -0.3219 (tpp) REVERT: V 6 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7705 (mm-40) REVERT: V 55 GLN cc_start: 0.1605 (OUTLIER) cc_final: 0.1016 (pm20) REVERT: V 100 GLN cc_start: 0.8439 (mm110) cc_final: 0.7927 (mp10) REVERT: X 3 GLN cc_start: 0.8624 (tp-100) cc_final: 0.8109 (tm-30) REVERT: X 4 MET cc_start: 0.3650 (mmt) cc_final: 0.0033 (mpt) REVERT: X 6 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7984 (mm-40) REVERT: X 55 GLN cc_start: 0.1246 (OUTLIER) cc_final: 0.0717 (pm20) REVERT: X 100 GLN cc_start: 0.8374 (mm110) cc_final: 0.7892 (mp10) outliers start: 73 outliers final: 30 residues processed: 362 average time/residue: 0.7292 time to fit residues: 297.6630 Evaluate side-chains 330 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 292 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 584 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 45 LYS Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 55 GLN Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 55 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 73 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 203 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 265 optimal weight: 30.0000 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 8 optimal weight: 0.0270 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS C 56 HIS ** D 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 HIS J 79 GLN K 5 GLN K 40 HIS N 37 GLN T 42 GLN ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 GLN V 55 GLN ** X 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN X 55 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.128882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.070253 restraints weight = 52146.603| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 4.42 r_work: 0.2604 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 23952 Z= 0.185 Angle : 0.641 13.281 32601 Z= 0.324 Chirality : 0.044 0.240 3588 Planarity : 0.007 0.231 4140 Dihedral : 7.037 63.322 3603 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.03 % Rotamer: Outliers : 2.71 % Allowed : 20.35 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.28 (0.16), residues: 2970 helix: 1.22 (0.41), residues: 171 sheet: 0.68 (0.16), residues: 1089 loop : -0.20 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.001 ARG K 97 TYR 0.014 0.001 TYR W 91 PHE 0.013 0.001 PHE K 78 TRP 0.014 0.001 TRP H 96 HIS 0.004 0.001 HIS K 40 Details of bonding type rmsd covalent geometry : bond 0.00446 (23904) covalent geometry : angle 0.63901 (32496) SS BOND : bond 0.00301 ( 30) SS BOND : angle 0.55394 ( 60) hydrogen bonds : bond 0.03125 ( 902) hydrogen bonds : angle 5.04415 ( 2448) Misc. bond : bond 0.02072 ( 3) link_ALPHA1-3 : bond 0.00599 ( 3) link_ALPHA1-3 : angle 1.72543 ( 9) link_ALPHA1-6 : bond 0.00463 ( 3) link_ALPHA1-6 : angle 1.83617 ( 9) link_BETA1-4 : bond 0.00240 ( 6) link_BETA1-4 : angle 1.27023 ( 18) link_NAG-ASN : bond 0.00160 ( 3) link_NAG-ASN : angle 1.74171 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 295 time to evaluate : 0.817 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: A 54 LYS cc_start: 0.9417 (ttpp) cc_final: 0.9216 (ttpp) REVERT: A 55 ASP cc_start: 0.8324 (m-30) cc_final: 0.7953 (m-30) REVERT: A 136 ARG cc_start: 0.8887 (tpp80) cc_final: 0.8352 (tpt90) REVERT: B 523 GLN cc_start: 0.8425 (tp-100) cc_final: 0.8060 (tp-100) REVERT: B 540 GLU cc_start: 0.8736 (pm20) cc_final: 0.8354 (pm20) REVERT: C 55 ASP cc_start: 0.8043 (m-30) cc_final: 0.7814 (m-30) REVERT: C 100 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8740 (mm-30) REVERT: C 136 ARG cc_start: 0.8737 (tpt-90) cc_final: 0.8367 (tpt90) REVERT: C 219 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8538 (mm-30) REVERT: D 540 GLU cc_start: 0.8781 (pm20) cc_final: 0.8352 (pm20) REVERT: E 44 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8515 (tt0) REVERT: E 100 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8701 (mm-30) REVERT: E 136 ARG cc_start: 0.8757 (tpt-90) cc_final: 0.8386 (tpt90) REVERT: F 540 GLU cc_start: 0.8787 (pm20) cc_final: 0.8452 (pm20) REVERT: G 3 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7448 (tm130) REVERT: G 64 GLU cc_start: 0.8368 (pm20) cc_final: 0.7931 (pm20) REVERT: G 72 ASP cc_start: 0.8004 (t0) cc_final: 0.7168 (t0) REVERT: G 89 VAL cc_start: 0.8633 (t) cc_final: 0.8331 (p) REVERT: H 27 ASN cc_start: 0.8963 (t0) cc_final: 0.8416 (t0) REVERT: H 29 ASP cc_start: 0.9321 (m-30) cc_final: 0.9004 (m-30) REVERT: I 13 LYS cc_start: 0.8269 (mppt) cc_final: 0.7739 (mppt) REVERT: I 16 GLN cc_start: 0.8462 (mm110) cc_final: 0.8123 (mt0) REVERT: I 75 LYS cc_start: 0.9533 (mttt) cc_final: 0.9228 (mtmm) REVERT: I 89 VAL cc_start: 0.8647 (t) cc_final: 0.8324 (p) REVERT: J 66 ASP cc_start: 0.8403 (t0) cc_final: 0.7986 (t0) REVERT: K 89 VAL cc_start: 0.8729 (t) cc_final: 0.8515 (p) REVERT: L 27 ASN cc_start: 0.9084 (t0) cc_final: 0.8833 (t0) REVERT: L 33 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8883 (mm) REVERT: L 45 GLN cc_start: 0.8466 (mm110) cc_final: 0.8218 (mm110) REVERT: M 105 LYS cc_start: 0.9659 (mmtp) cc_final: 0.9299 (mmmt) REVERT: N 79 GLN cc_start: 0.8030 (mt0) cc_final: 0.7648 (mp10) REVERT: O 1 GLN cc_start: 0.8683 (pm20) cc_final: 0.8460 (pp30) REVERT: O 43 GLN cc_start: 0.8919 (mp10) cc_final: 0.8417 (mp10) REVERT: O 105 LYS cc_start: 0.9596 (mmtm) cc_final: 0.9298 (mmmt) REVERT: P 79 GLN cc_start: 0.8038 (mt0) cc_final: 0.7686 (mp10) REVERT: Q 43 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8739 (mp10) REVERT: Q 105 LYS cc_start: 0.9599 (mmtm) cc_final: 0.9235 (mmmt) REVERT: R 79 GLN cc_start: 0.8134 (mt0) cc_final: 0.7747 (mp10) REVERT: T 3 GLN cc_start: 0.8787 (tp-100) cc_final: 0.8170 (tm-30) REVERT: T 4 MET cc_start: 0.5743 (mmt) cc_final: 0.2430 (mmt) REVERT: T 55 GLN cc_start: -0.0573 (OUTLIER) cc_final: -0.0903 (pm20) REVERT: T 90 GLN cc_start: 0.2723 (pp30) cc_final: 0.2481 (tm-30) REVERT: T 100 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: V 3 GLN cc_start: 0.8724 (tp-100) cc_final: 0.8285 (tp40) REVERT: V 4 MET cc_start: 0.2491 (mmt) cc_final: -0.4309 (mpt) REVERT: V 6 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7216 (mm-40) REVERT: V 55 GLN cc_start: 0.0879 (OUTLIER) cc_final: 0.0474 (pm20) REVERT: V 100 GLN cc_start: 0.8453 (mm110) cc_final: 0.7932 (mp10) REVERT: X 3 GLN cc_start: 0.8610 (tp-100) cc_final: 0.8093 (tm-30) REVERT: X 4 MET cc_start: 0.3109 (mmt) cc_final: -0.0507 (mpt) REVERT: X 6 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7853 (mm-40) REVERT: X 55 GLN cc_start: 0.1254 (OUTLIER) cc_final: 0.0770 (pm20) REVERT: X 100 GLN cc_start: 0.8383 (mm110) cc_final: 0.7875 (mp10) outliers start: 68 outliers final: 38 residues processed: 348 average time/residue: 0.7392 time to fit residues: 289.9841 Evaluate side-chains 335 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 287 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 98 SER Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 45 LYS Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 55 GLN Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 55 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 67 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 273 optimal weight: 40.0000 chunk 163 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 274 optimal weight: 50.0000 chunk 157 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 10 optimal weight: 0.0670 chunk 12 optimal weight: 1.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS C 56 HIS ** D 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN N 37 GLN T 42 GLN T 55 GLN ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 GLN V 55 GLN ** X 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN X 55 GLN ** X 89 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 = 0.4013 r_free = 0.4013 target = 0.129197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.069888 restraints weight = 51744.833| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 4.62 r_work: 0.2607 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 23952 Z= 0.166 Angle : 0.646 12.810 32601 Z= 0.327 Chirality : 0.044 0.241 3588 Planarity : 0.007 0.284 4140 Dihedral : 6.873 60.589 3603 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.09 % Rotamer: Outliers : 2.95 % Allowed : 20.71 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.16), residues: 2970 helix: 1.03 (0.40), residues: 174 sheet: 0.71 (0.16), residues: 1089 loop : -0.19 (0.16), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.001 ARG G 97 TYR 0.012 0.001 TYR G 91 PHE 0.013 0.001 PHE K 78 TRP 0.013 0.001 TRP H 96 HIS 0.002 0.001 HIS W 35 Details of bonding type rmsd covalent geometry : bond 0.00403 (23904) covalent geometry : angle 0.64448 (32496) SS BOND : bond 0.00278 ( 30) SS BOND : angle 0.50497 ( 60) hydrogen bonds : bond 0.03041 ( 902) hydrogen bonds : angle 5.00693 ( 2448) Misc. bond : bond 0.01816 ( 3) link_ALPHA1-3 : bond 0.00691 ( 3) link_ALPHA1-3 : angle 1.70287 ( 9) link_ALPHA1-6 : bond 0.00532 ( 3) link_ALPHA1-6 : angle 1.78785 ( 9) link_BETA1-4 : bond 0.00200 ( 6) link_BETA1-4 : angle 1.20729 ( 18) link_NAG-ASN : bond 0.00065 ( 3) link_NAG-ASN : angle 1.64678 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 298 time to evaluate : 0.993 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: A 54 LYS cc_start: 0.9459 (ttpp) cc_final: 0.9255 (ttpp) REVERT: A 55 ASP cc_start: 0.8382 (m-30) cc_final: 0.7981 (m-30) REVERT: A 136 ARG cc_start: 0.8807 (tpp80) cc_final: 0.8369 (tpt90) REVERT: B 523 GLN cc_start: 0.8375 (tp-100) cc_final: 0.8041 (tp-100) REVERT: B 540 GLU cc_start: 0.8759 (pm20) cc_final: 0.8374 (pm20) REVERT: C 55 ASP cc_start: 0.8213 (m-30) cc_final: 0.7954 (m-30) REVERT: C 100 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8815 (mm-30) REVERT: C 136 ARG cc_start: 0.8644 (tpt-90) cc_final: 0.8350 (tpt90) REVERT: C 219 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8504 (mm-30) REVERT: D 540 GLU cc_start: 0.8793 (pm20) cc_final: 0.8370 (pm20) REVERT: E 44 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8526 (tt0) REVERT: E 100 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8725 (mp0) REVERT: E 136 ARG cc_start: 0.8652 (tpt-90) cc_final: 0.8359 (tpt90) REVERT: F 540 GLU cc_start: 0.8819 (pm20) cc_final: 0.8486 (pm20) REVERT: G 3 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7354 (tm-30) REVERT: G 64 GLU cc_start: 0.8433 (pm20) cc_final: 0.8060 (pm20) REVERT: G 72 ASP cc_start: 0.8068 (t0) cc_final: 0.7169 (t0) REVERT: G 75 LYS cc_start: 0.9539 (mttt) cc_final: 0.9172 (pttt) REVERT: G 89 VAL cc_start: 0.8760 (t) cc_final: 0.8472 (p) REVERT: H 27 ASN cc_start: 0.8965 (t0) cc_final: 0.8412 (t0) REVERT: H 29 ASP cc_start: 0.9338 (m-30) cc_final: 0.9037 (m-30) REVERT: I 3 GLN cc_start: 0.7639 (tm130) cc_final: 0.7358 (tm-30) REVERT: I 13 LYS cc_start: 0.8329 (mppt) cc_final: 0.7704 (mppt) REVERT: I 16 GLN cc_start: 0.8432 (mm110) cc_final: 0.8112 (mt0) REVERT: I 75 LYS cc_start: 0.9529 (mttt) cc_final: 0.9190 (mtmm) REVERT: I 89 VAL cc_start: 0.8724 (t) cc_final: 0.8414 (p) REVERT: J 66 ASP cc_start: 0.8432 (t0) cc_final: 0.8018 (t0) REVERT: K 72 ASP cc_start: 0.8126 (t0) cc_final: 0.7398 (t0) REVERT: K 89 VAL cc_start: 0.8787 (t) cc_final: 0.8560 (p) REVERT: L 27 ASN cc_start: 0.9098 (t0) cc_final: 0.8865 (t0) REVERT: L 33 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8940 (mm) REVERT: L 45 GLN cc_start: 0.8529 (mm110) cc_final: 0.8278 (mm110) REVERT: M 105 LYS cc_start: 0.9603 (mmtp) cc_final: 0.9248 (mmmt) REVERT: N 79 GLN cc_start: 0.7985 (mt0) cc_final: 0.7595 (mp10) REVERT: O 1 GLN cc_start: 0.8713 (pm20) cc_final: 0.8497 (pp30) REVERT: O 43 GLN cc_start: 0.8927 (mp10) cc_final: 0.8476 (mp10) REVERT: O 105 LYS cc_start: 0.9554 (mmtm) cc_final: 0.9261 (mmmt) REVERT: P 79 GLN cc_start: 0.7995 (mt0) cc_final: 0.7657 (mp10) REVERT: Q 43 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8744 (mp10) REVERT: Q 105 LYS cc_start: 0.9500 (mmtm) cc_final: 0.9163 (mmmt) REVERT: R 79 GLN cc_start: 0.8106 (mt0) cc_final: 0.7741 (mp10) REVERT: T 3 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8288 (pp30) REVERT: T 4 MET cc_start: 0.6730 (mmt) cc_final: 0.4592 (mmt) REVERT: T 55 GLN cc_start: 0.0565 (OUTLIER) cc_final: 0.0072 (pm20) REVERT: T 100 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: V 3 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8356 (tp40) REVERT: V 4 MET cc_start: 0.4136 (mmt) cc_final: -0.2362 (tpp) REVERT: V 6 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7753 (mm-40) REVERT: V 55 GLN cc_start: 0.1142 (OUTLIER) cc_final: 0.0645 (pm20) REVERT: V 100 GLN cc_start: 0.8472 (mm110) cc_final: 0.8010 (mp10) REVERT: X 3 GLN cc_start: 0.8667 (tp-100) cc_final: 0.8178 (tm-30) REVERT: X 4 MET cc_start: 0.4310 (mmt) cc_final: 0.0866 (mpt) REVERT: X 6 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8232 (mm-40) REVERT: X 55 GLN cc_start: 0.1595 (OUTLIER) cc_final: 0.1169 (pm20) REVERT: X 100 GLN cc_start: 0.8379 (mm110) cc_final: 0.7894 (mp10) outliers start: 74 outliers final: 40 residues processed: 353 average time/residue: 0.7355 time to fit residues: 292.5021 Evaluate side-chains 336 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 286 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 98 SER Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 45 LYS Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 100 ARG Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 55 GLN Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 55 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 194 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 290 optimal weight: 2.9990 chunk 233 optimal weight: 20.0000 chunk 138 optimal weight: 0.0570 chunk 237 optimal weight: 30.0000 chunk 207 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS C 56 HIS ** D 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS F 551 GLN ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN T 42 GLN ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 GLN V 55 GLN ** X 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN X 55 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.128381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.069246 restraints weight = 51502.941| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 4.41 r_work: 0.2595 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.259 23952 Z= 0.236 Angle : 0.674 11.658 32601 Z= 0.343 Chirality : 0.045 0.248 3588 Planarity : 0.007 0.280 4140 Dihedral : 6.860 60.737 3602 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.07 % Favored : 95.82 % Rotamer: Outliers : 2.83 % Allowed : 21.23 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.16), residues: 2970 helix: 1.19 (0.41), residues: 171 sheet: 0.69 (0.16), residues: 1089 loop : -0.22 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.057 0.001 ARG K 97 TYR 0.017 0.001 TYR T 92 PHE 0.014 0.001 PHE K 78 TRP 0.015 0.001 TRP H 96 HIS 0.002 0.001 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00570 (23904) covalent geometry : angle 0.67222 (32496) SS BOND : bond 0.00344 ( 30) SS BOND : angle 0.57401 ( 60) hydrogen bonds : bond 0.03218 ( 902) hydrogen bonds : angle 5.03484 ( 2448) Misc. bond : bond 0.02209 ( 3) link_ALPHA1-3 : bond 0.00563 ( 3) link_ALPHA1-3 : angle 1.75698 ( 9) link_ALPHA1-6 : bond 0.00429 ( 3) link_ALPHA1-6 : angle 1.77963 ( 9) link_BETA1-4 : bond 0.00295 ( 6) link_BETA1-4 : angle 1.36297 ( 18) link_NAG-ASN : bond 0.00258 ( 3) link_NAG-ASN : angle 1.85625 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 289 time to evaluate : 0.891 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: A 54 LYS cc_start: 0.9422 (ttpp) cc_final: 0.9222 (ttpp) REVERT: A 55 ASP cc_start: 0.8336 (m-30) cc_final: 0.7974 (m-30) REVERT: A 136 ARG cc_start: 0.8858 (tpp80) cc_final: 0.8360 (tpt90) REVERT: B 523 GLN cc_start: 0.8388 (tp-100) cc_final: 0.8038 (tp-100) REVERT: B 540 GLU cc_start: 0.8767 (pm20) cc_final: 0.8410 (pm20) REVERT: C 55 ASP cc_start: 0.8205 (m-30) cc_final: 0.7957 (m-30) REVERT: C 100 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8753 (mm-30) REVERT: C 136 ARG cc_start: 0.8708 (tpt-90) cc_final: 0.8380 (tpt90) REVERT: C 219 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8519 (mm-30) REVERT: D 540 GLU cc_start: 0.8802 (pm20) cc_final: 0.8384 (pm20) REVERT: E 44 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8526 (tt0) REVERT: E 100 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8661 (mp0) REVERT: E 136 ARG cc_start: 0.8714 (tpt-90) cc_final: 0.8384 (tpt90) REVERT: F 540 GLU cc_start: 0.8810 (pm20) cc_final: 0.8472 (pm20) REVERT: G 3 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7385 (tm-30) REVERT: G 64 GLU cc_start: 0.8455 (pm20) cc_final: 0.8050 (pm20) REVERT: G 72 ASP cc_start: 0.8009 (t0) cc_final: 0.7101 (t0) REVERT: G 75 LYS cc_start: 0.9539 (mttt) cc_final: 0.9167 (pttt) REVERT: G 89 VAL cc_start: 0.8725 (t) cc_final: 0.8428 (p) REVERT: H 27 ASN cc_start: 0.8984 (t0) cc_final: 0.8404 (t0) REVERT: H 29 ASP cc_start: 0.9324 (m-30) cc_final: 0.9015 (m-30) REVERT: I 13 LYS cc_start: 0.8374 (mppt) cc_final: 0.7744 (mppt) REVERT: I 16 GLN cc_start: 0.8492 (mm110) cc_final: 0.8162 (mt0) REVERT: I 75 LYS cc_start: 0.9538 (mttt) cc_final: 0.9311 (mttp) REVERT: I 89 VAL cc_start: 0.8734 (t) cc_final: 0.8399 (p) REVERT: J 66 ASP cc_start: 0.8422 (t0) cc_final: 0.8001 (t0) REVERT: K 72 ASP cc_start: 0.8092 (t0) cc_final: 0.7270 (t0) REVERT: K 75 LYS cc_start: 0.9499 (mttt) cc_final: 0.9178 (pttt) REVERT: K 89 VAL cc_start: 0.8779 (t) cc_final: 0.8557 (p) REVERT: L 27 ASN cc_start: 0.9107 (t0) cc_final: 0.8845 (t0) REVERT: L 33 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8902 (mm) REVERT: L 45 GLN cc_start: 0.8546 (mm110) cc_final: 0.8295 (mm110) REVERT: M 10 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7088 (tm-30) REVERT: M 105 LYS cc_start: 0.9645 (mmtp) cc_final: 0.9293 (mmmt) REVERT: N 79 GLN cc_start: 0.8042 (mt0) cc_final: 0.7644 (mp10) REVERT: O 1 GLN cc_start: 0.8708 (pm20) cc_final: 0.8467 (pp30) REVERT: O 43 GLN cc_start: 0.8938 (mp10) cc_final: 0.8434 (mp10) REVERT: O 46 GLU cc_start: 0.8756 (pt0) cc_final: 0.8394 (pt0) REVERT: O 105 LYS cc_start: 0.9576 (mmtm) cc_final: 0.9282 (mmmt) REVERT: P 79 GLN cc_start: 0.8053 (mt0) cc_final: 0.7702 (mp10) REVERT: Q 43 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8731 (mp10) REVERT: Q 105 LYS cc_start: 0.9558 (mmtm) cc_final: 0.9204 (mmmt) REVERT: R 79 GLN cc_start: 0.8130 (mt0) cc_final: 0.7779 (mp10) REVERT: T 3 GLN cc_start: 0.8728 (tp-100) cc_final: 0.8132 (pp30) REVERT: T 4 MET cc_start: 0.6056 (mmt) cc_final: 0.4152 (mmt) REVERT: T 55 GLN cc_start: -0.0303 (OUTLIER) cc_final: -0.0683 (pm20) REVERT: T 90 GLN cc_start: 0.2113 (tm-30) cc_final: 0.1803 (tp40) REVERT: T 100 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: V 3 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8317 (tp40) REVERT: V 4 MET cc_start: 0.3119 (mmt) cc_final: -0.3438 (tpp) REVERT: V 6 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7381 (mm-40) REVERT: V 55 GLN cc_start: 0.0587 (OUTLIER) cc_final: 0.0178 (pm20) REVERT: V 100 GLN cc_start: 0.8496 (mm110) cc_final: 0.7994 (mp10) REVERT: W 100 MET cc_start: -0.3641 (pmm) cc_final: -0.4403 (ptt) REVERT: X 3 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8132 (tm-30) REVERT: X 4 MET cc_start: 0.3461 (mmt) cc_final: -0.0217 (mpt) REVERT: X 6 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7976 (mm-40) REVERT: X 55 GLN cc_start: 0.1064 (OUTLIER) cc_final: 0.0677 (pm20) REVERT: X 100 GLN cc_start: 0.8379 (mm110) cc_final: 0.7873 (mp10) outliers start: 71 outliers final: 45 residues processed: 347 average time/residue: 0.7485 time to fit residues: 292.5724 Evaluate side-chains 341 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 286 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 584 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 98 SER Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 45 LYS Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 100 ARG Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 55 GLN Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 55 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 226 optimal weight: 1.9990 chunk 260 optimal weight: 0.0670 chunk 30 optimal weight: 0.0970 chunk 265 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 269 optimal weight: 50.0000 chunk 219 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS C 56 HIS ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS F 551 GLN ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN T 42 GLN T 55 GLN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 GLN V 55 GLN W 50 ASN ** X 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN X 55 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.129071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.069260 restraints weight = 51740.179| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 4.38 r_work: 0.2609 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.290 23952 Z= 0.176 Angle : 0.669 13.466 32601 Z= 0.339 Chirality : 0.044 0.242 3588 Planarity : 0.007 0.266 4140 Dihedral : 6.679 58.189 3602 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.77 % Favored : 96.13 % Rotamer: Outliers : 2.55 % Allowed : 21.59 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.16), residues: 2970 helix: 1.10 (0.41), residues: 174 sheet: 0.71 (0.16), residues: 1068 loop : -0.22 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.074 0.001 ARG K 97 TYR 0.012 0.001 TYR K 91 PHE 0.013 0.001 PHE K 78 TRP 0.013 0.001 TRP H 96 HIS 0.002 0.001 HIS U 35 Details of bonding type rmsd covalent geometry : bond 0.00448 (23904) covalent geometry : angle 0.66748 (32496) SS BOND : bond 0.00311 ( 30) SS BOND : angle 0.54446 ( 60) hydrogen bonds : bond 0.03049 ( 902) hydrogen bonds : angle 4.99156 ( 2448) Misc. bond : bond 0.02324 ( 3) link_ALPHA1-3 : bond 0.00580 ( 3) link_ALPHA1-3 : angle 1.57620 ( 9) link_ALPHA1-6 : bond 0.00572 ( 3) link_ALPHA1-6 : angle 1.74606 ( 9) link_BETA1-4 : bond 0.00209 ( 6) link_BETA1-4 : angle 1.19970 ( 18) link_NAG-ASN : bond 0.00047 ( 3) link_NAG-ASN : angle 1.61002 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 289 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.9461 (ttpp) cc_final: 0.9257 (ttpp) REVERT: A 55 ASP cc_start: 0.8332 (m-30) cc_final: 0.7934 (m-30) REVERT: A 136 ARG cc_start: 0.8848 (tpp80) cc_final: 0.8356 (tpt90) REVERT: B 523 GLN cc_start: 0.8386 (tp-100) cc_final: 0.8027 (tp-100) REVERT: B 540 GLU cc_start: 0.8724 (pm20) cc_final: 0.8367 (pm20) REVERT: C 55 ASP cc_start: 0.8158 (m-30) cc_final: 0.7883 (m-30) REVERT: C 100 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8782 (mm-30) REVERT: C 136 ARG cc_start: 0.8705 (tpt-90) cc_final: 0.8355 (tpt90) REVERT: C 219 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8464 (mm-30) REVERT: D 540 GLU cc_start: 0.8774 (pm20) cc_final: 0.8379 (pm20) REVERT: E 44 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: E 100 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8701 (mp0) REVERT: E 136 ARG cc_start: 0.8717 (tpt-90) cc_final: 0.8370 (tpt90) REVERT: F 540 GLU cc_start: 0.8798 (pm20) cc_final: 0.8514 (pm20) REVERT: F 551 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8569 (mp10) REVERT: G 3 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7382 (tm-30) REVERT: G 64 GLU cc_start: 0.8480 (pm20) cc_final: 0.8069 (pm20) REVERT: G 72 ASP cc_start: 0.8059 (t0) cc_final: 0.7125 (t0) REVERT: G 75 LYS cc_start: 0.9546 (mttt) cc_final: 0.9160 (pttt) REVERT: G 89 VAL cc_start: 0.8809 (t) cc_final: 0.8530 (p) REVERT: H 27 ASN cc_start: 0.8977 (t0) cc_final: 0.8399 (t0) REVERT: H 29 ASP cc_start: 0.9326 (m-30) cc_final: 0.9014 (m-30) REVERT: I 13 LYS cc_start: 0.8395 (mppt) cc_final: 0.7754 (mppt) REVERT: I 16 GLN cc_start: 0.8533 (mm110) cc_final: 0.8209 (mt0) REVERT: I 75 LYS cc_start: 0.9537 (mttt) cc_final: 0.9330 (mttp) REVERT: I 89 VAL cc_start: 0.8789 (t) cc_final: 0.8467 (p) REVERT: J 66 ASP cc_start: 0.8430 (t0) cc_final: 0.8016 (t0) REVERT: K 3 GLN cc_start: 0.7568 (tm-30) cc_final: 0.7349 (tm130) REVERT: K 72 ASP cc_start: 0.8145 (t0) cc_final: 0.7304 (t0) REVERT: K 75 LYS cc_start: 0.9511 (mttt) cc_final: 0.9197 (pttt) REVERT: K 89 VAL cc_start: 0.8859 (t) cc_final: 0.8646 (p) REVERT: L 27 ASN cc_start: 0.9118 (t0) cc_final: 0.8872 (t0) REVERT: L 33 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8898 (mm) REVERT: L 45 GLN cc_start: 0.8572 (mm110) cc_final: 0.8320 (mm110) REVERT: M 105 LYS cc_start: 0.9599 (mmtp) cc_final: 0.9243 (mmmt) REVERT: N 79 GLN cc_start: 0.7964 (mt0) cc_final: 0.7534 (mp10) REVERT: O 1 GLN cc_start: 0.8716 (pm20) cc_final: 0.8505 (pp30) REVERT: O 43 GLN cc_start: 0.8923 (mp10) cc_final: 0.8461 (mp10) REVERT: O 46 GLU cc_start: 0.8763 (pt0) cc_final: 0.8305 (pt0) REVERT: O 105 LYS cc_start: 0.9559 (mmtm) cc_final: 0.9269 (mmmt) REVERT: P 79 GLN cc_start: 0.7944 (mt0) cc_final: 0.7603 (mp10) REVERT: Q 43 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8751 (mp10) REVERT: Q 105 LYS cc_start: 0.9518 (mmtm) cc_final: 0.9180 (mmmt) REVERT: R 79 GLN cc_start: 0.8081 (mt0) cc_final: 0.7743 (mp10) REVERT: T 3 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8174 (pp30) REVERT: T 4 MET cc_start: 0.6665 (mmt) cc_final: 0.4459 (ttm) REVERT: T 55 GLN cc_start: 0.0465 (OUTLIER) cc_final: -0.0090 (pm20) REVERT: T 100 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7995 (mp10) REVERT: V 3 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8351 (pp30) REVERT: V 4 MET cc_start: 0.4068 (mmt) cc_final: 0.0841 (mpt) REVERT: V 6 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7875 (mm-40) REVERT: V 55 GLN cc_start: 0.0543 (OUTLIER) cc_final: 0.0066 (pm20) REVERT: V 100 GLN cc_start: 0.8484 (mm110) cc_final: 0.7851 (mp10) REVERT: W 100 MET cc_start: -0.3659 (pmm) cc_final: -0.4342 (ptt) REVERT: X 3 GLN cc_start: 0.8715 (tp-100) cc_final: 0.8268 (pp30) REVERT: X 4 MET cc_start: 0.4335 (mmt) cc_final: 0.1642 (mpt) REVERT: X 6 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8304 (mm-40) REVERT: X 55 GLN cc_start: 0.1274 (OUTLIER) cc_final: 0.0776 (pm20) REVERT: X 100 GLN cc_start: 0.8416 (mm110) cc_final: 0.7932 (mp10) outliers start: 64 outliers final: 40 residues processed: 339 average time/residue: 0.7345 time to fit residues: 279.9798 Evaluate side-chains 340 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 289 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 551 GLN Chi-restraints excluded: chain F residue 584 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 98 SER Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 45 LYS Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 100 ARG Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 55 GLN Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 55 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 209 optimal weight: 0.0570 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 261 optimal weight: 0.0870 chunk 195 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS F 551 GLN ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN T 42 GLN ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 GLN V 55 GLN ** X 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN X 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.130122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.071296 restraints weight = 51726.841| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 4.59 r_work: 0.2640 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.259 23952 Z= 0.139 Angle : 0.669 12.976 32601 Z= 0.340 Chirality : 0.043 0.240 3588 Planarity : 0.008 0.251 4140 Dihedral : 6.393 54.314 3602 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.99 % Rotamer: Outliers : 2.03 % Allowed : 22.26 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2970 helix: 0.96 (0.40), residues: 174 sheet: 0.75 (0.16), residues: 1062 loop : -0.17 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.071 0.001 ARG I 97 TYR 0.010 0.001 TYR I 91 PHE 0.011 0.001 PHE K 78 TRP 0.012 0.001 TRP O 47 HIS 0.006 0.000 HIS F 549 Details of bonding type rmsd covalent geometry : bond 0.00379 (23904) covalent geometry : angle 0.66808 (32496) SS BOND : bond 0.00257 ( 30) SS BOND : angle 0.51105 ( 60) hydrogen bonds : bond 0.02881 ( 902) hydrogen bonds : angle 4.96671 ( 2448) Misc. bond : bond 0.02881 ( 3) link_ALPHA1-3 : bond 0.00850 ( 3) link_ALPHA1-3 : angle 1.59052 ( 9) link_ALPHA1-6 : bond 0.00796 ( 3) link_ALPHA1-6 : angle 1.64696 ( 9) link_BETA1-4 : bond 0.00286 ( 6) link_BETA1-4 : angle 1.08242 ( 18) link_NAG-ASN : bond 0.00251 ( 3) link_NAG-ASN : angle 1.30411 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 299 time to evaluate : 0.748 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: A 54 LYS cc_start: 0.9468 (ttpp) cc_final: 0.9251 (ttpp) REVERT: A 55 ASP cc_start: 0.8338 (m-30) cc_final: 0.7880 (m-30) REVERT: A 136 ARG cc_start: 0.8867 (tpp80) cc_final: 0.8342 (tpt90) REVERT: A 224 ASN cc_start: 0.8956 (t0) cc_final: 0.8685 (t0) REVERT: B 523 GLN cc_start: 0.8382 (tp-100) cc_final: 0.8021 (tp-100) REVERT: B 540 GLU cc_start: 0.8739 (pm20) cc_final: 0.8382 (pm20) REVERT: C 55 ASP cc_start: 0.8096 (m-30) cc_final: 0.7789 (m-30) REVERT: C 100 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8782 (mm-30) REVERT: C 136 ARG cc_start: 0.8750 (tpt-90) cc_final: 0.8357 (tpt90) REVERT: C 219 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8424 (mm-30) REVERT: D 540 GLU cc_start: 0.8783 (pm20) cc_final: 0.8433 (pm20) REVERT: E 100 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8731 (mm-30) REVERT: E 136 ARG cc_start: 0.8756 (tpt-90) cc_final: 0.8364 (tpt90) REVERT: F 540 GLU cc_start: 0.8791 (pm20) cc_final: 0.8502 (pm20) REVERT: F 551 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: G 3 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7336 (tm-30) REVERT: G 64 GLU cc_start: 0.8480 (pm20) cc_final: 0.8184 (pm20) REVERT: G 72 ASP cc_start: 0.8096 (t0) cc_final: 0.7170 (t0) REVERT: G 75 LYS cc_start: 0.9554 (mttt) cc_final: 0.9175 (pttt) REVERT: G 89 VAL cc_start: 0.8865 (t) cc_final: 0.8600 (p) REVERT: H 27 ASN cc_start: 0.8946 (t0) cc_final: 0.8373 (t0) REVERT: H 29 ASP cc_start: 0.9324 (m-30) cc_final: 0.9013 (m-30) REVERT: I 13 LYS cc_start: 0.8469 (mppt) cc_final: 0.7813 (mppt) REVERT: I 16 GLN cc_start: 0.8616 (mm110) cc_final: 0.8319 (mt0) REVERT: I 75 LYS cc_start: 0.9541 (mttt) cc_final: 0.9227 (mtmm) REVERT: I 89 VAL cc_start: 0.8841 (t) cc_final: 0.8540 (p) REVERT: J 66 ASP cc_start: 0.8455 (t0) cc_final: 0.8034 (t0) REVERT: K 13 LYS cc_start: 0.8242 (mppt) cc_final: 0.7895 (mmpt) REVERT: K 16 GLN cc_start: 0.8983 (mt0) cc_final: 0.8540 (mm110) REVERT: K 72 ASP cc_start: 0.8141 (t0) cc_final: 0.7358 (t0) REVERT: K 89 VAL cc_start: 0.8894 (t) cc_final: 0.8663 (p) REVERT: L 27 ASN cc_start: 0.9114 (t0) cc_final: 0.8876 (t0) REVERT: L 33 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8917 (mm) REVERT: L 45 GLN cc_start: 0.8571 (mm110) cc_final: 0.8315 (mm110) REVERT: M 10 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7150 (tm-30) REVERT: M 46 GLU cc_start: 0.8583 (pt0) cc_final: 0.8000 (pt0) REVERT: M 105 LYS cc_start: 0.9599 (mmtp) cc_final: 0.9244 (mmmt) REVERT: N 79 GLN cc_start: 0.7972 (mt0) cc_final: 0.7562 (mp10) REVERT: O 10 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7919 (mm-30) REVERT: O 43 GLN cc_start: 0.8913 (mp10) cc_final: 0.8466 (mp10) REVERT: P 79 GLN cc_start: 0.7937 (mt0) cc_final: 0.7617 (mp10) REVERT: Q 43 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8787 (mp10) REVERT: Q 105 LYS cc_start: 0.9536 (mmtm) cc_final: 0.9194 (mmmt) REVERT: R 79 GLN cc_start: 0.8030 (mt0) cc_final: 0.7710 (mp10) REVERT: T 3 GLN cc_start: 0.8824 (tp-100) cc_final: 0.8293 (pp30) REVERT: T 4 MET cc_start: 0.7032 (mmt) cc_final: 0.5157 (ttm) REVERT: T 55 GLN cc_start: 0.1102 (OUTLIER) cc_final: 0.0587 (pm20) REVERT: T 100 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: V 3 GLN cc_start: 0.8810 (tp-100) cc_final: 0.8391 (pp30) REVERT: V 4 MET cc_start: 0.4576 (mmt) cc_final: 0.1446 (mpt) REVERT: V 6 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8061 (mm-40) REVERT: V 55 GLN cc_start: 0.0873 (OUTLIER) cc_final: 0.0316 (pm20) REVERT: V 100 GLN cc_start: 0.8498 (mm110) cc_final: 0.7886 (mp10) REVERT: W 100 MET cc_start: -0.3777 (pmm) cc_final: -0.4396 (ptt) REVERT: X 3 GLN cc_start: 0.8751 (tp-100) cc_final: 0.8260 (tm-30) REVERT: X 4 MET cc_start: 0.4885 (mmt) cc_final: 0.1554 (mpt) REVERT: X 6 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8466 (mm-40) REVERT: X 55 GLN cc_start: 0.1597 (OUTLIER) cc_final: 0.1080 (pm20) REVERT: X 100 GLN cc_start: 0.8420 (mm110) cc_final: 0.7974 (mp10) outliers start: 51 outliers final: 27 residues processed: 334 average time/residue: 0.7458 time to fit residues: 279.9333 Evaluate side-chains 326 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 289 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 551 GLN Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 45 LYS Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 100 ARG Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain T residue 100 GLN Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 42 GLN Chi-restraints excluded: chain V residue 55 GLN Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 55 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 4 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS F 551 GLN ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN T 42 GLN ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 38 GLN ** 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 = 0.4025 r_free = 0.4025 target = 0.129932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.070912 restraints weight = 51590.881| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 4.71 r_work: 0.2641 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.296 23952 Z= 0.239 Angle : 0.879 59.190 32601 Z= 0.481 Chirality : 0.048 0.940 3588 Planarity : 0.008 0.265 4140 Dihedral : 6.397 54.389 3602 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.99 % Rotamer: Outliers : 1.83 % Allowed : 22.54 % Favored : 75.63 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2970 helix: 0.90 (0.40), residues: 174 sheet: 0.77 (0.16), residues: 1062 loop : -0.18 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.001 ARG K 97 TYR 0.010 0.001 TYR I 91 PHE 0.012 0.001 PHE K 78 TRP 0.012 0.001 TRP O 47 HIS 0.004 0.001 HIS F 549 Details of bonding type rmsd covalent geometry : bond 0.00547 (23904) covalent geometry : angle 0.87859 (32496) SS BOND : bond 0.00305 ( 30) SS BOND : angle 0.52950 ( 60) hydrogen bonds : bond 0.02936 ( 902) hydrogen bonds : angle 4.96239 ( 2448) Misc. bond : bond 0.02595 ( 3) link_ALPHA1-3 : bond 0.00982 ( 3) link_ALPHA1-3 : angle 1.67237 ( 9) link_ALPHA1-6 : bond 0.00779 ( 3) link_ALPHA1-6 : angle 1.60387 ( 9) link_BETA1-4 : bond 0.00303 ( 6) link_BETA1-4 : angle 1.09788 ( 18) link_NAG-ASN : bond 0.00267 ( 3) link_NAG-ASN : angle 1.19115 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13644.34 seconds wall clock time: 232 minutes 1.89 seconds (13921.89 seconds total)