Starting phenix.real_space_refine on Tue Jun 17 06:43:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dyx_27785/06_2025/8dyx_27785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dyx_27785/06_2025/8dyx_27785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dyx_27785/06_2025/8dyx_27785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dyx_27785/06_2025/8dyx_27785.map" model { file = "/net/cci-nas-00/data/ceres_data/8dyx_27785/06_2025/8dyx_27785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dyx_27785/06_2025/8dyx_27785.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 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 66 5.16 5 C 12566 2.51 5 N 3464 2.21 5 O 3934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20030 Number of models: 1 Model: "" Number of chains: 23 Chain: "I" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 637 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 23, 'TRANS': 66} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "A" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "C" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "M" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "O" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "P" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "Q" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "R" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "S" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "T" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "U" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "V" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "W" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "X" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "Y" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "Z" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Time building chain proxies: 11.31, per 1000 atoms: 0.56 Number of scatterers: 20030 At special positions: 0 Unit cell: (131.84, 121.54, 159.65, 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 66 16.00 O 3934 8.00 N 3464 7.00 C 12566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 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=2.04 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=2.03 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 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.69 Conformation dependent library (CDL) restraints added in 2.3 seconds 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 66 sheets defined 6.2% alpha, 47.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.696A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.536A pdb=" N ASN A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.872A pdb=" N GLU B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.784A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.987A pdb=" N GLU F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.543A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.602A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 removed outlier: 4.121A pdb=" N GLU P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.539A pdb=" N ASN Q 31 " --> pdb=" O THR Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.686A pdb=" N ASP R 82 " --> pdb=" O GLN R 79 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU R 83 " --> pdb=" O ALA R 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 79 through 83' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 83 through 87 Processing helix chain 'T' and resid 79 through 83 removed outlier: 4.118A pdb=" N GLU T 83 " --> pdb=" O ALA T 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 83 through 87 Processing helix chain 'V' and resid 79 through 83 removed outlier: 3.865A pdb=" N GLU V 83 " --> pdb=" O ALA V 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 32 Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'X' and resid 79 through 83 removed outlier: 3.681A pdb=" N GLU X 83 " --> pdb=" O ALA X 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 32 Processing helix chain 'Y' and resid 83 through 87 removed outlier: 3.502A pdb=" N THR Y 87 " --> pdb=" O VAL Y 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 83 removed outlier: 3.782A pdb=" N GLU Z 83 " --> pdb=" O ALA Z 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.203A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.203A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA H 96 " --> pdb=" O GLY H 100D" (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLY H 100D" --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.435A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA7, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.599A pdb=" N THR A 77 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.091A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N MET A 34 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.091A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS A 92 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TRP A 103 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARG A 94 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.494A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 9 through 13 Processing sheet with id=AB3, first strand: chain 'B' and resid 19 through 24 Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.548A pdb=" N THR C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.913A pdb=" N MET C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.939A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.596A pdb=" N THR D 105 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 13 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.596A pdb=" N THR D 105 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 13 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.585A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.277A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.277A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA E 96 " --> pdb=" O GLY E 100D" (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLY E 100D" --> pdb=" O ALA E 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 9 through 13 removed outlier: 6.719A pdb=" N VAL F 11 " --> pdb=" O THR F 105 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 9 through 13 removed outlier: 6.719A pdb=" N VAL F 11 " --> pdb=" O THR F 105 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AC7, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.503A pdb=" N SER M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.764A pdb=" N MET M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.769A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 9 through 13 removed outlier: 3.747A pdb=" N ALA N 84 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 9 through 13 removed outlier: 3.747A pdb=" N ALA N 84 " --> pdb=" O LEU N 104 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AD4, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.437A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET O 34 " --> pdb=" O ILE O 50 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.437A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS O 92 " --> pdb=" O TRP O 103 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TRP O 103 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP O 101 " --> pdb=" O ARG O 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 9 through 13 removed outlier: 5.854A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 9 through 13 Processing sheet with id=AD9, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AE1, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.234A pdb=" N GLY Q 10 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET Q 34 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.234A pdb=" N GLY Q 10 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR Q 102 " --> pdb=" O ARG Q 94 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA Q 96 " --> pdb=" O GLY Q 100D" (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLY Q 100D" --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 9 through 13 removed outlier: 5.715A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 9 through 13 Processing sheet with id=AE6, first strand: chain 'R' and resid 18 through 24 Processing sheet with id=AE7, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.562A pdb=" N GLY S 10 " --> pdb=" O LEU S 108 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET S 34 " --> pdb=" O ILE S 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.562A pdb=" N GLY S 10 " --> pdb=" O LEU S 108 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR S 102 " --> pdb=" O ARG S 94 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA S 96 " --> pdb=" O GLY S 100D" (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLY S 100D" --> pdb=" O ALA S 96 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 9 through 13 removed outlier: 6.436A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 9 through 13 Processing sheet with id=AF3, first strand: chain 'T' and resid 19 through 24 Processing sheet with id=AF4, first strand: chain 'U' and resid 3 through 7 removed outlier: 3.540A pdb=" N SER U 70 " --> pdb=" O TYR U 79 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.546A pdb=" N GLY U 10 " --> pdb=" O LEU U 108 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA U 93 " --> pdb=" O HIS U 35 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET U 34 " --> pdb=" O ILE U 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.546A pdb=" N GLY U 10 " --> pdb=" O LEU U 108 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR U 102 " --> pdb=" O ARG U 94 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA U 96 " --> pdb=" O GLY U 100D" (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLY U 100D" --> pdb=" O ALA U 96 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 9 through 13 removed outlier: 5.836A pdb=" N GLN V 37 " --> pdb=" O LEU V 46 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU V 46 " --> pdb=" O GLN V 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 9 through 13 Processing sheet with id=AF9, first strand: chain 'V' and resid 18 through 24 Processing sheet with id=AG1, first strand: chain 'W' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'W' and resid 10 through 12 removed outlier: 3.755A pdb=" N GLY W 10 " --> pdb=" O LEU W 108 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N MET W 34 " --> pdb=" O ILE W 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE W 50 " --> pdb=" O MET W 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP W 36 " --> pdb=" O VAL W 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 10 through 12 removed outlier: 3.755A pdb=" N GLY W 10 " --> pdb=" O LEU W 108 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS W 92 " --> pdb=" O TRP W 103 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TRP W 103 " --> pdb=" O CYS W 92 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG W 94 " --> pdb=" O ASP W 101 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 9 through 13 removed outlier: 6.644A pdb=" N TRP X 35 " --> pdb=" O LEU X 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 9 through 13 Processing sheet with id=AG6, first strand: chain 'X' and resid 19 through 24 Processing sheet with id=AG7, first strand: chain 'Y' and resid 3 through 7 removed outlier: 3.632A pdb=" N THR Y 77 " --> pdb=" O ASP Y 72 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 10 through 12 removed outlier: 6.101A pdb=" N GLY Y 10 " --> pdb=" O THR Y 110 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA Y 93 " --> pdb=" O HIS Y 35 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N MET Y 34 " --> pdb=" O ILE Y 50 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 96 through 97 Processing sheet with id=AH1, first strand: chain 'Z' and resid 9 through 13 removed outlier: 6.623A pdb=" N VAL Z 11 " --> pdb=" O THR Z 105 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP Z 35 " --> pdb=" O LEU Z 47 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 9 through 13 removed outlier: 6.623A pdb=" N VAL Z 11 " --> pdb=" O THR Z 105 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 19 through 24 832 hydrogen bonds defined for protein. 1890 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: 6.98 Time building geometry restraints manager: 5.61 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: 6582 1.34 - 1.46: 5469 1.46 - 1.58: 8397 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 20536 Sorted by residual: bond pdb=" CA ASP H 101 " pdb=" C ASP H 101 " ideal model delta sigma weight residual 1.521 1.534 -0.013 1.36e-02 5.41e+03 9.17e-01 bond pdb=" N TYR U 98 " pdb=" CA TYR U 98 " ideal model delta sigma weight residual 1.468 1.456 0.012 1.24e-02 6.50e+03 9.04e-01 bond pdb=" CA ASN I 177 " pdb=" C ASN I 177 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.08e-02 8.57e+03 7.48e-01 bond pdb=" N ASN I 183 " pdb=" CA ASN I 183 " ideal model delta sigma weight residual 1.465 1.456 0.009 1.05e-02 9.07e+03 7.06e-01 bond pdb=" CB GLN C 3 " pdb=" CG GLN C 3 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.84e-01 ... (remaining 20531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 27423 1.71 - 3.42: 508 3.42 - 5.13: 42 5.13 - 6.84: 6 6.84 - 8.54: 1 Bond angle restraints: 27980 Sorted by residual: angle pdb=" C ASP H 101 " pdb=" CA ASP H 101 " pdb=" CB ASP H 101 " ideal model delta sigma weight residual 109.24 114.21 -4.97 1.75e+00 3.27e-01 8.08e+00 angle pdb=" C GLY P 50 " pdb=" N ASN P 51 " pdb=" CA ASN P 51 " ideal model delta sigma weight residual 121.54 126.87 -5.33 1.91e+00 2.74e-01 7.78e+00 angle pdb=" C GLY V 50 " pdb=" N ASN V 51 " pdb=" CA ASN V 51 " ideal model delta sigma weight residual 121.54 126.83 -5.29 1.91e+00 2.74e-01 7.66e+00 angle pdb=" C GLY L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.42e+00 angle pdb=" C GLY N 50 " pdb=" N ASN N 51 " pdb=" CA ASN N 51 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.42e+00 ... (remaining 27975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 10854 17.86 - 35.72: 725 35.72 - 53.59: 201 53.59 - 71.45: 25 71.45 - 89.31: 33 Dihedral angle restraints: 11838 sinusoidal: 4408 harmonic: 7430 Sorted by residual: dihedral pdb=" CB CYS Z 23 " pdb=" SG CYS Z 23 " pdb=" SG CYS Z 88 " pdb=" CB CYS Z 88 " ideal model delta sinusoidal sigma weight residual 93.00 55.97 37.03 1 1.00e+01 1.00e-02 1.94e+01 dihedral pdb=" CB CYS Y 22 " pdb=" SG CYS Y 22 " pdb=" SG CYS Y 92 " pdb=" CB CYS Y 92 " ideal model delta sinusoidal sigma weight residual 93.00 59.65 33.35 1 1.00e+01 1.00e-02 1.58e+01 dihedral pdb=" CB CYS X 23 " pdb=" SG CYS X 23 " pdb=" SG CYS X 88 " pdb=" CB CYS X 88 " ideal model delta sinusoidal sigma weight residual 93.00 59.70 33.30 1 1.00e+01 1.00e-02 1.58e+01 ... (remaining 11835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1791 0.028 - 0.056: 836 0.056 - 0.084: 128 0.084 - 0.112: 152 0.112 - 0.140: 68 Chirality restraints: 2975 Sorted by residual: chirality pdb=" CA ASP H 101 " pdb=" N ASP H 101 " pdb=" C ASP H 101 " pdb=" CB ASP H 101 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE E 50 " pdb=" N ILE E 50 " pdb=" C ILE E 50 " pdb=" CB ILE E 50 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE Y 50 " pdb=" N ILE Y 50 " pdb=" C ILE Y 50 " pdb=" CB ILE Y 50 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 2972 not shown) Planarity restraints: 3655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 7 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO R 8 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 8 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 8 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP I 111 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.14e+00 pdb=" CG ASP I 111 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP I 111 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP I 111 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG N 54 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO N 55 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO N 55 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO N 55 " -0.023 5.00e-02 4.00e+02 ... (remaining 3652 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 635 2.71 - 3.25: 17730 3.25 - 3.80: 31494 3.80 - 4.35: 42344 4.35 - 4.90: 73408 Nonbonded interactions: 165611 Sorted by model distance: nonbonded pdb=" NH2 ARG M 16 " pdb=" O THR T 18 " model vdw 2.157 3.120 nonbonded pdb=" OG1 THR S 24 " pdb=" O ASN S 76 " model vdw 2.197 3.040 nonbonded pdb=" N GLU E 85 " pdb=" OE1 GLU E 85 " model vdw 2.201 3.120 nonbonded pdb=" O PRO P 7 " pdb=" OG1 THR P 102 " model vdw 2.223 3.040 nonbonded pdb=" OG SER V 27A" pdb=" OD1 ASP V 92 " model vdw 2.236 3.040 ... (remaining 165606 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'H' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } 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: 0.010 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 45.840 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.130 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:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20558 Z= 0.135 Angle : 0.568 8.545 28024 Z= 0.324 Chirality : 0.040 0.140 2975 Planarity : 0.004 0.055 3655 Dihedral : 13.780 89.309 7148 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.24 % Allowed : 12.05 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.69 (0.15), residues: 1100 loop : -0.61 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 103 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE B 98 TYR 0.014 0.001 TYR U 52A ARG 0.005 0.000 ARG T 93 Details of bonding type rmsd hydrogen bonds : bond 0.24789 ( 733) hydrogen bonds : angle 9.60414 ( 1890) SS BOND : bond 0.00301 ( 22) SS BOND : angle 0.88042 ( 44) covalent geometry : bond 0.00269 (20536) covalent geometry : angle 0.56771 (27980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 332 time to evaluate : 2.033 Fit side-chains revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8695 (tt) cc_final: 0.8415 (tp) REVERT: C 56 ARG cc_start: 0.8011 (mmt90) cc_final: 0.7580 (mpp80) REVERT: M 3 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7649 (mm110) REVERT: M 108 LEU cc_start: 0.8969 (tt) cc_final: 0.8720 (tp) REVERT: N 45 LYS cc_start: 0.9014 (ttpt) cc_final: 0.8738 (tttp) REVERT: T 24 THR cc_start: 0.8366 (m) cc_final: 0.8102 (p) REVERT: U 56 ARG cc_start: 0.8402 (mmt-90) cc_final: 0.8128 (ttm-80) REVERT: V 79 GLN cc_start: 0.7866 (tt0) cc_final: 0.7534 (mm-40) outliers start: 5 outliers final: 2 residues processed: 333 average time/residue: 1.2361 time to fit residues: 467.3186 Evaluate side-chains 313 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 311 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain V residue 65 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 205 optimal weight: 20.0000 chunk 79 optimal weight: 0.0170 chunk 124 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 237 optimal weight: 9.9990 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 185 ASN H 3 GLN E 1 GLN N 79 GLN Q 105 GLN R 79 GLN W 76 ASN X 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.173291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.115325 restraints weight = 25089.730| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.42 r_work: 0.3058 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20558 Z= 0.175 Angle : 0.594 6.979 28024 Z= 0.320 Chirality : 0.043 0.145 2975 Planarity : 0.005 0.041 3655 Dihedral : 4.262 22.482 2940 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.74 % Allowed : 12.90 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.56 (0.15), residues: 1133 loop : -0.68 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 103 HIS 0.005 0.002 HIS H 35 PHE 0.012 0.002 PHE U 29 TYR 0.017 0.001 TYR S 90 ARG 0.006 0.000 ARG H 16 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 733) hydrogen bonds : angle 6.45179 ( 1890) SS BOND : bond 0.00564 ( 22) SS BOND : angle 1.37488 ( 44) covalent geometry : bond 0.00403 (20536) covalent geometry : angle 0.59196 (27980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 332 time to evaluate : 2.148 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.9277 (mmm) cc_final: 0.9075 (mmm) REVERT: H 84 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8323 (t) REVERT: A 50 ILE cc_start: 0.8777 (tt) cc_final: 0.8357 (tp) REVERT: C 6 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: C 81 GLN cc_start: 0.8511 (tp40) cc_final: 0.8305 (tp40) REVERT: C 105 GLN cc_start: 0.7121 (pt0) cc_final: 0.6643 (pt0) REVERT: D 32 ASP cc_start: 0.8466 (m-30) cc_final: 0.8218 (m-30) REVERT: F 45 LYS cc_start: 0.9190 (ttpt) cc_final: 0.8953 (pttp) REVERT: F 83 GLU cc_start: 0.8068 (tt0) cc_final: 0.7868 (mt-10) REVERT: M 108 LEU cc_start: 0.9029 (tt) cc_final: 0.8822 (tp) REVERT: N 45 LYS cc_start: 0.9120 (ttpt) cc_final: 0.8867 (tttp) REVERT: O 3 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: O 46 GLU cc_start: 0.8725 (tt0) cc_final: 0.8513 (tt0) REVERT: O 105 GLN cc_start: 0.8381 (pt0) cc_final: 0.8103 (pm20) REVERT: O 110 THR cc_start: 0.9084 (t) cc_final: 0.8817 (p) REVERT: P 81 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: Q 43 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8026 (mppt) REVERT: R 45 LYS cc_start: 0.8656 (mttm) cc_final: 0.8304 (ptmm) REVERT: T 24 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8285 (p) REVERT: U 56 ARG cc_start: 0.8503 (mmt-90) cc_final: 0.8212 (ttm-80) REVERT: V 66 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7046 (ptpt) REVERT: V 79 GLN cc_start: 0.7535 (tt0) cc_final: 0.7292 (mm-40) REVERT: W 94 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7759 (ttm170) REVERT: X 37 GLN cc_start: 0.6928 (tm130) cc_final: 0.6724 (tm-30) REVERT: Y 82 MET cc_start: 0.5807 (mpm) cc_final: 0.2582 (ptp) outliers start: 58 outliers final: 31 residues processed: 354 average time/residue: 1.2038 time to fit residues: 484.6478 Evaluate side-chains 349 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 310 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 72 ASP Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 0.9990 chunk 181 optimal weight: 7.9990 chunk 50 optimal weight: 30.0000 chunk 3 optimal weight: 0.2980 chunk 52 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 40 optimal weight: 30.0000 chunk 177 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 113 ASN H 1 GLN E 57 ASN M 3 GLN Q 105 GLN V 53 ASN W 76 ASN X 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.171500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.110216 restraints weight = 24998.502| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.34 r_work: 0.2982 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20558 Z= 0.207 Angle : 0.604 6.520 28024 Z= 0.323 Chirality : 0.044 0.150 2975 Planarity : 0.005 0.039 3655 Dihedral : 4.433 19.142 2938 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.78 % Allowed : 13.27 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.33 (0.14), residues: 1133 loop : -0.88 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 103 HIS 0.006 0.002 HIS S 35 PHE 0.013 0.002 PHE C 29 TYR 0.021 0.002 TYR S 90 ARG 0.004 0.000 ARG V 54 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 733) hydrogen bonds : angle 5.79256 ( 1890) SS BOND : bond 0.00585 ( 22) SS BOND : angle 1.50855 ( 44) covalent geometry : bond 0.00487 (20536) covalent geometry : angle 0.60134 (27980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 318 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.9283 (mmm) cc_final: 0.9063 (mmm) REVERT: A 50 ILE cc_start: 0.8657 (tt) cc_final: 0.8233 (tp) REVERT: C 6 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7084 (mt-10) REVERT: C 105 GLN cc_start: 0.7131 (pt0) cc_final: 0.6657 (pt0) REVERT: D 32 ASP cc_start: 0.8609 (m-30) cc_final: 0.8304 (m-30) REVERT: O 3 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: O 46 GLU cc_start: 0.8760 (tt0) cc_final: 0.8543 (tt0) REVERT: O 105 GLN cc_start: 0.8403 (pt0) cc_final: 0.8093 (pm20) REVERT: P 17 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7519 (pt0) REVERT: P 81 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: R 45 LYS cc_start: 0.8717 (mttm) cc_final: 0.8449 (ptmm) REVERT: T 24 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8278 (p) REVERT: U 56 ARG cc_start: 0.8463 (mmt-90) cc_final: 0.8176 (ttm-80) REVERT: U 105 GLN cc_start: 0.8432 (pt0) cc_final: 0.7883 (mm110) REVERT: V 66 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7288 (ptpp) REVERT: V 79 GLN cc_start: 0.7456 (tt0) cc_final: 0.7070 (mm-40) REVERT: W 94 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7710 (ttm170) REVERT: X 37 GLN cc_start: 0.6835 (tm130) cc_final: 0.6574 (tm-30) REVERT: Y 82 MET cc_start: 0.5631 (mpm) cc_final: 0.2792 (ptt) outliers start: 80 outliers final: 45 residues processed: 355 average time/residue: 1.1948 time to fit residues: 482.7316 Evaluate side-chains 359 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 307 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 50 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 79 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 3 optimal weight: 0.0970 chunk 169 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 3 GLN P 79 GLN Q 105 GLN V 51 ASN X 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.170006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108886 restraints weight = 25042.743| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.02 r_work: 0.3012 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20558 Z= 0.181 Angle : 0.578 7.212 28024 Z= 0.309 Chirality : 0.043 0.139 2975 Planarity : 0.004 0.040 3655 Dihedral : 4.376 19.876 2938 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.26 % Allowed : 14.55 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 2607 helix: None (None), residues: 0 sheet: 0.26 (0.14), residues: 1133 loop : -0.96 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 103 HIS 0.005 0.001 HIS H 35 PHE 0.011 0.002 PHE U 29 TYR 0.016 0.002 TYR U 79 ARG 0.003 0.000 ARG S 16 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 733) hydrogen bonds : angle 5.54390 ( 1890) SS BOND : bond 0.00543 ( 22) SS BOND : angle 1.34003 ( 44) covalent geometry : bond 0.00425 (20536) covalent geometry : angle 0.57612 (27980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 310 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.9231 (mmm) cc_final: 0.8997 (mmm) REVERT: H 82 MET cc_start: 0.9031 (mtp) cc_final: 0.8575 (mtp) REVERT: L 79 GLN cc_start: 0.7604 (mp10) cc_final: 0.7365 (mp10) REVERT: A 50 ILE cc_start: 0.8673 (tt) cc_final: 0.8244 (tp) REVERT: A 82 SER cc_start: 0.3786 (OUTLIER) cc_final: 0.3544 (m) REVERT: C 6 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: D 32 ASP cc_start: 0.8605 (m-30) cc_final: 0.8281 (m-30) REVERT: O 3 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7694 (mp10) REVERT: O 46 GLU cc_start: 0.8672 (tt0) cc_final: 0.8449 (tt0) REVERT: O 105 GLN cc_start: 0.8424 (pt0) cc_final: 0.8115 (pm20) REVERT: P 17 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7680 (pm20) REVERT: R 45 LYS cc_start: 0.8716 (mttm) cc_final: 0.8510 (pttp) REVERT: T 24 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8282 (p) REVERT: U 56 ARG cc_start: 0.8474 (mmt-90) cc_final: 0.8165 (ttm-80) REVERT: U 105 GLN cc_start: 0.8391 (pt0) cc_final: 0.7888 (mm110) REVERT: V 66 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7229 (ptpp) REVERT: V 79 GLN cc_start: 0.7424 (tt0) cc_final: 0.7139 (mm-40) REVERT: W 94 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7715 (ttm170) REVERT: X 37 GLN cc_start: 0.6811 (tm130) cc_final: 0.6343 (tm-30) REVERT: X 89 GLN cc_start: 0.8446 (tm130) cc_final: 0.8040 (tm130) REVERT: Y 82 MET cc_start: 0.5480 (mpm) cc_final: 0.2790 (ptt) outliers start: 69 outliers final: 45 residues processed: 338 average time/residue: 1.2864 time to fit residues: 499.1334 Evaluate side-chains 350 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 298 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 34 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 224 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 229 optimal weight: 9.9990 chunk 255 optimal weight: 0.4980 chunk 239 optimal weight: 30.0000 chunk 245 optimal weight: 20.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 ASN E 81 GLN M 3 GLN P 79 GLN Q 81 GLN Q 105 GLN V 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.171565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.108852 restraints weight = 25079.708| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.31 r_work: 0.3059 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20558 Z= 0.150 Angle : 0.557 7.174 28024 Z= 0.297 Chirality : 0.042 0.137 2975 Planarity : 0.004 0.039 3655 Dihedral : 4.295 19.996 2938 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.50 % Allowed : 14.55 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.28 (0.14), residues: 1133 loop : -0.96 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 47 HIS 0.005 0.001 HIS H 35 PHE 0.009 0.001 PHE U 29 TYR 0.014 0.001 TYR U 79 ARG 0.003 0.000 ARG X 93 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 733) hydrogen bonds : angle 5.39446 ( 1890) SS BOND : bond 0.00516 ( 22) SS BOND : angle 1.20931 ( 44) covalent geometry : bond 0.00349 (20536) covalent geometry : angle 0.55575 (27980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 316 time to evaluate : 2.298 Fit side-chains revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8746 (tt) cc_final: 0.8317 (tp) REVERT: A 82 SER cc_start: 0.3902 (OUTLIER) cc_final: 0.3656 (m) REVERT: C 6 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7063 (mt-10) REVERT: D 32 ASP cc_start: 0.8630 (m-30) cc_final: 0.8291 (m-30) REVERT: O 3 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: O 46 GLU cc_start: 0.8674 (tt0) cc_final: 0.8458 (tt0) REVERT: O 105 GLN cc_start: 0.8485 (pt0) cc_final: 0.8182 (pm20) REVERT: P 27 ASN cc_start: 0.9369 (OUTLIER) cc_final: 0.9043 (p0) REVERT: P 81 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: T 24 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8164 (p) REVERT: U 56 ARG cc_start: 0.8547 (mmt-90) cc_final: 0.8259 (ttm-80) REVERT: U 105 GLN cc_start: 0.8325 (pt0) cc_final: 0.7849 (mm110) REVERT: V 66 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7179 (ptpp) REVERT: V 79 GLN cc_start: 0.7380 (tt0) cc_final: 0.7098 (mm-40) REVERT: W 94 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7781 (ttm170) REVERT: X 37 GLN cc_start: 0.6793 (tm130) cc_final: 0.6393 (tm-30) REVERT: X 89 GLN cc_start: 0.8503 (tm130) cc_final: 0.8086 (tm130) REVERT: Y 34 MET cc_start: 0.5918 (ppp) cc_final: 0.5647 (ptt) REVERT: Y 82 MET cc_start: 0.5340 (mpm) cc_final: 0.2726 (ptt) outliers start: 74 outliers final: 53 residues processed: 352 average time/residue: 1.2024 time to fit residues: 483.7293 Evaluate side-chains 364 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 303 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 50 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 212 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 75 optimal weight: 0.0970 chunk 46 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN M 1 GLN M 3 GLN P 79 GLN Q 39 GLN Q 105 GLN V 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.107148 restraints weight = 24984.352| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.12 r_work: 0.3050 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20558 Z= 0.219 Angle : 0.612 7.951 28024 Z= 0.326 Chirality : 0.044 0.156 2975 Planarity : 0.005 0.038 3655 Dihedral : 4.473 20.444 2938 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.68 % Allowed : 14.88 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.20 (0.14), residues: 1133 loop : -1.07 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP U 103 HIS 0.007 0.002 HIS H 35 PHE 0.012 0.002 PHE U 29 TYR 0.015 0.002 TYR M 91 ARG 0.011 0.001 ARG E 16 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 733) hydrogen bonds : angle 5.42769 ( 1890) SS BOND : bond 0.00592 ( 22) SS BOND : angle 1.52027 ( 44) covalent geometry : bond 0.00518 (20536) covalent geometry : angle 0.60914 (27980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 306 time to evaluate : 2.025 Fit side-chains revert: symmetry clash REVERT: H 82 MET cc_start: 0.9013 (mtp) cc_final: 0.8538 (mtp) REVERT: A 50 ILE cc_start: 0.8731 (tt) cc_final: 0.8291 (OUTLIER) REVERT: A 82 SER cc_start: 0.4321 (OUTLIER) cc_final: 0.4062 (m) REVERT: C 6 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7047 (mt-10) REVERT: D 32 ASP cc_start: 0.8718 (m-30) cc_final: 0.8349 (m-30) REVERT: O 3 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: O 46 GLU cc_start: 0.8628 (tt0) cc_final: 0.8392 (tt0) REVERT: O 105 GLN cc_start: 0.8450 (pt0) cc_final: 0.8155 (pm20) REVERT: P 27 ASN cc_start: 0.9377 (OUTLIER) cc_final: 0.9043 (p0) REVERT: P 81 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: Q 16 ARG cc_start: 0.8365 (ptp-110) cc_final: 0.8086 (ptp-110) REVERT: T 24 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8309 (p) REVERT: U 56 ARG cc_start: 0.8500 (mmt-90) cc_final: 0.8193 (ttm-80) REVERT: U 105 GLN cc_start: 0.8304 (pt0) cc_final: 0.7877 (mm-40) REVERT: V 66 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7280 (ptpp) REVERT: V 79 GLN cc_start: 0.7388 (tt0) cc_final: 0.7102 (mm-40) REVERT: W 94 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7579 (ttm170) REVERT: W 101 ASP cc_start: 0.7543 (p0) cc_final: 0.7342 (p0) REVERT: X 37 GLN cc_start: 0.6778 (tm130) cc_final: 0.6397 (tm-30) REVERT: X 89 GLN cc_start: 0.8515 (tm130) cc_final: 0.8086 (tm130) REVERT: Y 34 MET cc_start: 0.5759 (ppp) cc_final: 0.5406 (ptt) REVERT: Y 82 MET cc_start: 0.5037 (mpm) cc_final: 0.2654 (ptt) outliers start: 78 outliers final: 62 residues processed: 343 average time/residue: 1.2156 time to fit residues: 474.3328 Evaluate side-chains 369 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 300 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain M residue 1 GLN Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 50 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 166 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 59 optimal weight: 0.0970 chunk 148 optimal weight: 10.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN E 57 ASN M 3 GLN P 17 GLN P 79 GLN Q 105 GLN V 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.172018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112525 restraints weight = 25084.884| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.43 r_work: 0.3041 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20558 Z= 0.127 Angle : 0.556 7.953 28024 Z= 0.296 Chirality : 0.042 0.160 2975 Planarity : 0.004 0.041 3655 Dihedral : 4.301 20.518 2938 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.26 % Allowed : 15.78 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.26 (0.14), residues: 1133 loop : -1.01 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.004 0.001 HIS H 35 PHE 0.008 0.001 PHE C 29 TYR 0.016 0.001 TYR U 52A ARG 0.004 0.000 ARG E 16 Details of bonding type rmsd hydrogen bonds : bond 0.02802 ( 733) hydrogen bonds : angle 5.24756 ( 1890) SS BOND : bond 0.00470 ( 22) SS BOND : angle 1.06442 ( 44) covalent geometry : bond 0.00295 (20536) covalent geometry : angle 0.55464 (27980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 315 time to evaluate : 2.183 Fit side-chains revert: symmetry clash REVERT: H 82 MET cc_start: 0.9016 (mtp) cc_final: 0.8591 (mtp) REVERT: A 20 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5366 (mp) REVERT: A 50 ILE cc_start: 0.8788 (tt) cc_final: 0.8341 (tp) REVERT: A 82 SER cc_start: 0.4570 (OUTLIER) cc_final: 0.4264 (m) REVERT: C 6 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7147 (mt-10) REVERT: D 32 ASP cc_start: 0.8733 (m-30) cc_final: 0.8376 (m-30) REVERT: E 75 LYS cc_start: 0.8888 (pttp) cc_final: 0.8634 (ptmm) REVERT: O 3 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: O 46 GLU cc_start: 0.8744 (tt0) cc_final: 0.8521 (tt0) REVERT: O 105 GLN cc_start: 0.8554 (pt0) cc_final: 0.8246 (pm20) REVERT: P 17 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7610 (pm20) REVERT: P 81 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: Q 16 ARG cc_start: 0.8363 (ptp-110) cc_final: 0.7979 (ptp-110) REVERT: T 24 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8203 (p) REVERT: T 72 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.8129 (p) REVERT: U 105 GLN cc_start: 0.8283 (pt0) cc_final: 0.7857 (mm110) REVERT: V 66 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7227 (ptpp) REVERT: V 79 GLN cc_start: 0.7503 (tt0) cc_final: 0.7244 (mm-40) REVERT: W 94 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7697 (ttm170) REVERT: X 37 GLN cc_start: 0.6699 (tm130) cc_final: 0.6342 (tm-30) REVERT: X 89 GLN cc_start: 0.8586 (tm130) cc_final: 0.8185 (tm130) REVERT: Y 34 MET cc_start: 0.5823 (ppp) cc_final: 0.5569 (ptt) REVERT: Y 82 MET cc_start: 0.5079 (mpm) cc_final: 0.2734 (ptt) outliers start: 69 outliers final: 49 residues processed: 351 average time/residue: 1.1771 time to fit residues: 472.2273 Evaluate side-chains 362 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 303 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 50 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 31 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 140 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 259 optimal weight: 30.0000 chunk 37 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 206 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN E 57 ASN M 3 GLN P 79 GLN Q 105 GLN S 81 GLN W 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.171634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109428 restraints weight = 25146.180| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.09 r_work: 0.3086 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20558 Z= 0.141 Angle : 0.561 7.447 28024 Z= 0.297 Chirality : 0.042 0.167 2975 Planarity : 0.004 0.040 3655 Dihedral : 4.264 20.171 2938 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.31 % Allowed : 16.06 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.26 (0.14), residues: 1133 loop : -1.01 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 47 HIS 0.004 0.001 HIS H 35 PHE 0.009 0.001 PHE C 29 TYR 0.017 0.001 TYR U 52A ARG 0.004 0.000 ARG X 93 Details of bonding type rmsd hydrogen bonds : bond 0.02812 ( 733) hydrogen bonds : angle 5.18134 ( 1890) SS BOND : bond 0.00492 ( 22) SS BOND : angle 1.14848 ( 44) covalent geometry : bond 0.00330 (20536) covalent geometry : angle 0.55942 (27980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 309 time to evaluate : 2.019 Fit side-chains revert: symmetry clash REVERT: H 82 MET cc_start: 0.9018 (mtp) cc_final: 0.8612 (mtp) REVERT: L 79 GLN cc_start: 0.7664 (mp10) cc_final: 0.7369 (mp10) REVERT: L 94 ARG cc_start: 0.8761 (mtm-85) cc_final: 0.8534 (mtt180) REVERT: A 20 LEU cc_start: 0.5604 (OUTLIER) cc_final: 0.5211 (mp) REVERT: A 50 ILE cc_start: 0.8691 (tt) cc_final: 0.8251 (tp) REVERT: A 82 SER cc_start: 0.4523 (OUTLIER) cc_final: 0.4164 (m) REVERT: C 6 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7085 (mt-10) REVERT: D 32 ASP cc_start: 0.8693 (m-30) cc_final: 0.8329 (m-30) REVERT: E 75 LYS cc_start: 0.8883 (pttp) cc_final: 0.8663 (ptmm) REVERT: O 3 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: O 46 GLU cc_start: 0.8636 (tt0) cc_final: 0.8400 (tt0) REVERT: O 105 GLN cc_start: 0.8467 (pt0) cc_final: 0.8164 (pm20) REVERT: P 81 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: Q 16 ARG cc_start: 0.8314 (ptp-110) cc_final: 0.7909 (ptp-110) REVERT: T 24 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8227 (p) REVERT: T 72 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8054 (p) REVERT: U 105 GLN cc_start: 0.8242 (pt0) cc_final: 0.7848 (mm110) REVERT: V 66 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7224 (ptpp) REVERT: V 79 GLN cc_start: 0.7514 (tt0) cc_final: 0.7255 (mm-40) REVERT: W 94 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7585 (ttm170) REVERT: X 37 GLN cc_start: 0.6728 (tm130) cc_final: 0.6286 (tm-30) REVERT: X 89 GLN cc_start: 0.8501 (tm130) cc_final: 0.8073 (tm130) REVERT: Y 34 MET cc_start: 0.5584 (ppp) cc_final: 0.5291 (ptt) REVERT: Y 82 MET cc_start: 0.4937 (mpm) cc_final: 0.2632 (ptt) outliers start: 70 outliers final: 49 residues processed: 344 average time/residue: 1.1852 time to fit residues: 464.8399 Evaluate side-chains 360 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 302 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 50 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 208 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 114 optimal weight: 30.0000 chunk 115 optimal weight: 2.9990 chunk 260 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN M 3 GLN P 79 GLN Q 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.170681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.108802 restraints weight = 24828.678| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.42 r_work: 0.2939 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20558 Z= 0.208 Angle : 0.621 7.641 28024 Z= 0.330 Chirality : 0.044 0.178 2975 Planarity : 0.005 0.038 3655 Dihedral : 4.492 20.927 2938 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.93 % Allowed : 16.77 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 2607 helix: None (None), residues: 0 sheet: 0.22 (0.15), residues: 1056 loop : -1.13 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 47 HIS 0.007 0.002 HIS H 35 PHE 0.011 0.002 PHE U 29 TYR 0.019 0.002 TYR U 52A ARG 0.008 0.000 ARG X 93 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 733) hydrogen bonds : angle 5.31867 ( 1890) SS BOND : bond 0.00587 ( 22) SS BOND : angle 1.50476 ( 44) covalent geometry : bond 0.00490 (20536) covalent geometry : angle 0.61843 (27980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 307 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 82 MET cc_start: 0.9116 (mtp) cc_final: 0.8716 (mtp) REVERT: A 20 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.5135 (mp) REVERT: A 50 ILE cc_start: 0.8597 (tt) cc_final: 0.8156 (OUTLIER) REVERT: A 82 SER cc_start: 0.4328 (OUTLIER) cc_final: 0.3941 (m) REVERT: A 99 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.6631 (m-30) REVERT: C 6 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7037 (mt-10) REVERT: C 76 ASN cc_start: 0.8853 (m-40) cc_final: 0.8629 (m-40) REVERT: D 32 ASP cc_start: 0.8700 (m-30) cc_final: 0.8278 (m-30) REVERT: E 75 LYS cc_start: 0.8928 (pttp) cc_final: 0.8641 (ptmm) REVERT: O 3 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: O 46 GLU cc_start: 0.8753 (tt0) cc_final: 0.8527 (tt0) REVERT: O 105 GLN cc_start: 0.8524 (pt0) cc_final: 0.8187 (pm20) REVERT: Q 16 ARG cc_start: 0.8443 (ptp-110) cc_final: 0.7994 (ptp-110) REVERT: T 24 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8326 (p) REVERT: T 72 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.8069 (p) REVERT: U 105 GLN cc_start: 0.8364 (pt0) cc_final: 0.7870 (mm-40) REVERT: V 66 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7204 (ptpp) REVERT: V 79 GLN cc_start: 0.7477 (tt0) cc_final: 0.7213 (mm-40) REVERT: W 94 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7401 (ttm170) REVERT: W 101 ASP cc_start: 0.7356 (p0) cc_final: 0.7152 (p0) REVERT: X 37 GLN cc_start: 0.6633 (tm130) cc_final: 0.6264 (tm-30) REVERT: X 89 GLN cc_start: 0.8404 (tm130) cc_final: 0.7913 (tm130) outliers start: 62 outliers final: 48 residues processed: 341 average time/residue: 1.2491 time to fit residues: 484.7043 Evaluate side-chains 356 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 300 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 92 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 164 optimal weight: 0.0060 chunk 121 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN E 57 ASN M 3 GLN P 79 GLN Q 105 GLN X 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.174444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.112778 restraints weight = 24905.290| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.27 r_work: 0.3001 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20558 Z= 0.117 Angle : 0.558 7.714 28024 Z= 0.295 Chirality : 0.042 0.209 2975 Planarity : 0.004 0.042 3655 Dihedral : 4.231 24.057 2938 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.36 % Allowed : 17.71 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.35 (0.14), residues: 1122 loop : -1.02 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 47 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE C 29 TYR 0.017 0.001 TYR U 52A ARG 0.009 0.000 ARG X 93 Details of bonding type rmsd hydrogen bonds : bond 0.02637 ( 733) hydrogen bonds : angle 5.04069 ( 1890) SS BOND : bond 0.00437 ( 22) SS BOND : angle 0.92313 ( 44) covalent geometry : bond 0.00270 (20536) covalent geometry : angle 0.55733 (27980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 327 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 82 MET cc_start: 0.9062 (mtp) cc_final: 0.8692 (mtp) REVERT: A 20 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.5109 (mp) REVERT: A 50 ILE cc_start: 0.8627 (tt) cc_final: 0.8187 (tp) REVERT: A 82 SER cc_start: 0.4169 (OUTLIER) cc_final: 0.3820 (m) REVERT: A 99 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6491 (m-30) REVERT: C 38 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8176 (ptt180) REVERT: D 32 ASP cc_start: 0.8709 (m-30) cc_final: 0.8342 (m-30) REVERT: M 3 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7304 (mm-40) REVERT: O 3 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7640 (tm-30) REVERT: O 46 GLU cc_start: 0.8701 (tt0) cc_final: 0.8484 (tt0) REVERT: O 105 GLN cc_start: 0.8517 (pt0) cc_final: 0.8195 (pm20) REVERT: Q 16 ARG cc_start: 0.8311 (ptp-110) cc_final: 0.8030 (ptp-110) REVERT: T 24 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8229 (p) REVERT: T 93 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8461 (ttp-170) REVERT: V 66 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7201 (ptpp) REVERT: V 79 GLN cc_start: 0.7452 (tt0) cc_final: 0.7202 (mm-40) REVERT: W 94 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7475 (ttm170) REVERT: X 37 GLN cc_start: 0.6708 (tm130) cc_final: 0.6230 (tm-30) REVERT: X 89 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8004 (tm130) outliers start: 50 outliers final: 38 residues processed: 355 average time/residue: 1.2327 time to fit residues: 498.3160 Evaluate side-chains 361 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 315 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 252 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 40 optimal weight: 30.0000 chunk 123 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN P 17 GLN P 79 GLN Q 105 GLN S 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.174369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.112362 restraints weight = 24994.547| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.59 r_work: 0.2962 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 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 0.040 20558 Z= 0.119 Angle : 0.563 9.162 28024 Z= 0.296 Chirality : 0.042 0.218 2975 Planarity : 0.004 0.040 3655 Dihedral : 4.161 24.104 2938 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.31 % Allowed : 18.09 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.38 (0.14), residues: 1188 loop : -0.94 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 47 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE C 29 TYR 0.017 0.001 TYR U 52A ARG 0.009 0.000 ARG X 93 Details of bonding type rmsd hydrogen bonds : bond 0.02639 ( 733) hydrogen bonds : angle 4.97434 ( 1890) SS BOND : bond 0.00464 ( 22) SS BOND : angle 1.03597 ( 44) covalent geometry : bond 0.00275 (20536) covalent geometry : angle 0.56190 (27980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16815.77 seconds wall clock time: 286 minutes 26.10 seconds (17186.10 seconds total)