Starting phenix.real_space_refine on Sun Aug 24 11:47:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dyx_27785/08_2025/8dyx_27785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dyx_27785/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dyx_27785/08_2025/8dyx_27785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dyx_27785/08_2025/8dyx_27785.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dyx_27785/08_2025/8dyx_27785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dyx_27785/08_2025/8dyx_27785.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.09, per 1000 atoms: 0.25 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: 1.69 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.16 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: 4.30 Time building geometry restraints manager: 2.25 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: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.460 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.990 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (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 ARG 0.005 0.000 ARG T 93 TYR 0.014 0.001 TYR U 52A PHE 0.009 0.001 PHE B 98 TRP 0.009 0.001 TRP Q 103 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00269 (20536) covalent geometry : angle 0.56771 (27980) SS BOND : bond 0.00301 ( 22) SS BOND : angle 0.88042 ( 44) hydrogen bonds : bond 0.24789 ( 733) hydrogen bonds : angle 9.60414 ( 1890) *********************** 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 : 0.828 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: D 52 ILE cc_start: 0.8377 (mt) cc_final: 0.8109 (mm) 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: 0.6542 time to fit residues: 245.9665 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 : 0.742 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 179 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 = 0.4018 r_free = 0.4018 target = 0.173497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.114538 restraints weight = 25106.205| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.59 r_work: 0.3066 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0981 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= 0.165 Angle : 0.586 6.130 28024 Z= 0.316 Chirality : 0.043 0.147 2975 Planarity : 0.005 0.041 3655 Dihedral : 4.226 22.227 2940 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.79 % Allowed : 12.75 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.56 (0.15), residues: 1133 loop : -0.66 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 16 TYR 0.016 0.001 TYR S 90 PHE 0.011 0.002 PHE C 29 TRP 0.009 0.001 TRP U 103 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00379 (20536) covalent geometry : angle 0.58356 (27980) SS BOND : bond 0.00534 ( 22) SS BOND : angle 1.34507 ( 44) hydrogen bonds : bond 0.04446 ( 733) hydrogen bonds : angle 6.46181 ( 1890) *********************** 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 393 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 334 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.9279 (mmm) cc_final: 0.9072 (mmm) REVERT: H 84 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8321 (t) REVERT: A 50 ILE cc_start: 0.8803 (tt) cc_final: 0.8387 (tp) REVERT: C 6 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7300 (mt-10) REVERT: C 81 GLN cc_start: 0.8523 (tp40) cc_final: 0.8322 (tp40) REVERT: C 105 GLN cc_start: 0.7125 (pt0) cc_final: 0.6642 (pt0) REVERT: D 32 ASP cc_start: 0.8463 (m-30) cc_final: 0.8212 (m-30) REVERT: F 83 GLU cc_start: 0.8084 (tt0) cc_final: 0.7883 (mt-10) REVERT: M 108 LEU cc_start: 0.9038 (tt) cc_final: 0.8821 (tp) REVERT: N 45 LYS cc_start: 0.9124 (ttpt) cc_final: 0.8887 (tttp) REVERT: O 3 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: O 46 GLU cc_start: 0.8752 (tt0) cc_final: 0.8550 (tt0) REVERT: O 105 GLN cc_start: 0.8396 (pt0) cc_final: 0.8127 (pm20) REVERT: O 110 THR cc_start: 0.9093 (t) cc_final: 0.8821 (p) REVERT: P 81 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: R 45 LYS cc_start: 0.8668 (mttm) cc_final: 0.8311 (ptmm) REVERT: T 24 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8294 (p) REVERT: U 56 ARG cc_start: 0.8513 (mmt-90) cc_final: 0.8226 (ttm-80) REVERT: V 66 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7044 (ptpt) REVERT: V 79 GLN cc_start: 0.7610 (tt0) cc_final: 0.7358 (mm-40) REVERT: W 94 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7814 (ttm170) REVERT: X 37 GLN cc_start: 0.6947 (tm130) cc_final: 0.6746 (tm-30) REVERT: Y 82 MET cc_start: 0.5839 (mpm) cc_final: 0.2635 (ptp) outliers start: 59 outliers final: 32 residues processed: 356 average time/residue: 0.6286 time to fit residues: 253.6353 Evaluate side-chains 353 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 314 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 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 66 LYS 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 67 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 52 optimal weight: 0.0370 chunk 235 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 overall best weight: 3.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 179 ASN I 185 ASN H 1 GLN E 57 ASN M 3 GLN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 GLN V 53 ASN W 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.171543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.112133 restraints weight = 25221.205| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.46 r_work: 0.2959 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1362 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= 0.217 Angle : 0.609 6.524 28024 Z= 0.326 Chirality : 0.044 0.141 2975 Planarity : 0.005 0.038 3655 Dihedral : 4.423 19.088 2938 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.59 % Allowed : 13.32 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.35 (0.14), residues: 1133 loop : -0.87 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 71 TYR 0.020 0.002 TYR S 90 PHE 0.014 0.002 PHE U 29 TRP 0.011 0.002 TRP U 103 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00512 (20536) covalent geometry : angle 0.60675 (27980) SS BOND : bond 0.00591 ( 22) SS BOND : angle 1.53593 ( 44) hydrogen bonds : bond 0.03679 ( 733) hydrogen bonds : angle 5.86550 ( 1890) *********************** 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 391 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 315 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.9308 (mmm) cc_final: 0.9090 (mmm) REVERT: A 50 ILE cc_start: 0.8731 (tt) cc_final: 0.8306 (tp) REVERT: C 6 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: C 105 GLN cc_start: 0.7143 (pt0) cc_final: 0.6646 (pt0) REVERT: D 32 ASP cc_start: 0.8607 (m-30) cc_final: 0.8306 (m-30) REVERT: F 45 LYS cc_start: 0.9265 (ttpt) cc_final: 0.9062 (pttp) REVERT: O 3 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7740 (mp10) REVERT: O 46 GLU cc_start: 0.8826 (tt0) cc_final: 0.8619 (tt0) REVERT: O 105 GLN cc_start: 0.8464 (pt0) cc_final: 0.8148 (pm20) REVERT: P 17 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7544 (pt0) REVERT: P 81 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: Q 43 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8016 (mppt) REVERT: R 45 LYS cc_start: 0.8759 (mttm) cc_final: 0.8489 (ptmm) REVERT: R 83 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7163 (mt-10) REVERT: S 85 GLU cc_start: 0.7819 (mp0) cc_final: 0.7601 (tp30) REVERT: T 24 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8277 (p) REVERT: U 56 ARG cc_start: 0.8516 (mmt-90) cc_final: 0.8232 (ttm-80) REVERT: U 105 GLN cc_start: 0.8425 (pt0) cc_final: 0.7887 (mm-40) REVERT: V 66 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7195 (ptpp) REVERT: V 79 GLN cc_start: 0.7483 (tt0) cc_final: 0.7097 (mm-40) REVERT: W 94 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7696 (ttm170) REVERT: X 37 GLN cc_start: 0.6859 (tm130) cc_final: 0.6589 (tm-30) REVERT: Y 82 MET cc_start: 0.5377 (mpm) cc_final: 0.2708 (ptt) outliers start: 76 outliers final: 46 residues processed: 349 average time/residue: 0.6382 time to fit residues: 251.9511 Evaluate side-chains 358 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 304 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 25 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 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 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 43 LYS 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 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 213 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 185 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 113 ASN M 3 GLN Q 81 GLN Q 105 GLN V 51 ASN X 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.171130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110214 restraints weight = 24959.486| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.01 r_work: 0.3022 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20558 Z= 0.156 Angle : 0.560 7.791 28024 Z= 0.299 Chirality : 0.042 0.136 2975 Planarity : 0.004 0.040 3655 Dihedral : 4.297 19.602 2938 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.12 % Allowed : 14.27 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.37 (0.14), residues: 1122 loop : -0.91 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 16 TYR 0.016 0.001 TYR U 79 PHE 0.011 0.001 PHE C 29 TRP 0.009 0.001 TRP U 103 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00363 (20536) covalent geometry : angle 0.55804 (27980) SS BOND : bond 0.00503 ( 22) SS BOND : angle 1.20550 ( 44) hydrogen bonds : bond 0.03083 ( 733) hydrogen bonds : angle 5.51262 ( 1890) *********************** 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 386 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 320 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8679 (tt) cc_final: 0.8262 (tp) REVERT: A 79 TYR cc_start: 0.7357 (m-80) cc_final: 0.7129 (m-80) REVERT: C 6 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: D 32 ASP cc_start: 0.8602 (m-30) cc_final: 0.8266 (m-30) REVERT: O 3 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: O 46 GLU cc_start: 0.8670 (tt0) cc_final: 0.8453 (tt0) REVERT: O 105 GLN cc_start: 0.8383 (pt0) cc_final: 0.8086 (pm20) REVERT: P 17 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: T 24 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8156 (p) REVERT: U 56 ARG cc_start: 0.8477 (mmt-90) cc_final: 0.8169 (ttm-80) REVERT: U 105 GLN cc_start: 0.8374 (pt0) cc_final: 0.7884 (mm110) REVERT: V 66 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7173 (ptpp) REVERT: V 79 GLN cc_start: 0.7456 (tt0) cc_final: 0.7122 (mm-40) REVERT: W 94 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7790 (ttm170) REVERT: X 37 GLN cc_start: 0.6849 (tm130) cc_final: 0.6392 (tm-30) REVERT: X 89 GLN cc_start: 0.8413 (tm130) cc_final: 0.7918 (tm130) REVERT: Y 82 MET cc_start: 0.5099 (mpm) cc_final: 0.2616 (ptt) outliers start: 66 outliers final: 40 residues processed: 348 average time/residue: 0.6446 time to fit residues: 253.6998 Evaluate side-chains 349 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 303 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 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 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 74 SER 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 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 82 LEU 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 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 134 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 0.0770 chunk 225 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 241 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 overall best weight: 3.9544 ------------------------------------------------------------------------------- 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 1 GLN M 3 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 = 0.3970 r_free = 0.3970 target = 0.169399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.109381 restraints weight = 25138.196| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.54 r_work: 0.3019 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20558 Z= 0.260 Angle : 0.643 8.333 28024 Z= 0.343 Chirality : 0.045 0.143 2975 Planarity : 0.005 0.040 3655 Dihedral : 4.591 20.850 2938 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.73 % Allowed : 14.64 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.15), residues: 2607 helix: None (None), residues: 0 sheet: 0.18 (0.14), residues: 1133 loop : -1.11 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 16 TYR 0.021 0.002 TYR S 90 PHE 0.014 0.002 PHE U 29 TRP 0.011 0.002 TRP U 103 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00618 (20536) covalent geometry : angle 0.64036 (27980) SS BOND : bond 0.00629 ( 22) SS BOND : angle 1.67862 ( 44) hydrogen bonds : bond 0.03453 ( 733) hydrogen bonds : angle 5.61319 ( 1890) *********************** 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: 79 poor density : 311 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: H 82 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8801 (mtp) REVERT: A 50 ILE cc_start: 0.8668 (tt) cc_final: 0.8207 (OUTLIER) REVERT: C 6 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6964 (mt-10) REVERT: D 32 ASP cc_start: 0.8775 (m-30) cc_final: 0.8393 (m-30) REVERT: O 3 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7731 (mp10) REVERT: O 46 GLU cc_start: 0.8762 (tt0) cc_final: 0.8526 (tt0) REVERT: O 105 GLN cc_start: 0.8494 (pt0) cc_final: 0.8156 (pm20) REVERT: P 17 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7692 (pm20) REVERT: P 27 ASN cc_start: 0.9391 (OUTLIER) cc_final: 0.9037 (p0) REVERT: P 81 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: Q 43 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8014 (mppt) REVERT: T 24 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8296 (p) REVERT: U 56 ARG cc_start: 0.8509 (mmt-90) cc_final: 0.8173 (ttm-80) REVERT: U 105 GLN cc_start: 0.8427 (pt0) cc_final: 0.7916 (mm-40) REVERT: V 66 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7169 (ptpp) REVERT: V 79 GLN cc_start: 0.7388 (tt0) cc_final: 0.7085 (mm-40) REVERT: X 37 GLN cc_start: 0.6793 (tm130) cc_final: 0.6422 (tm-30) REVERT: X 89 GLN cc_start: 0.8463 (tm130) cc_final: 0.7987 (tm130) REVERT: Y 82 MET cc_start: 0.4927 (mpm) cc_final: 0.2630 (ptt) outliers start: 79 outliers final: 54 residues processed: 347 average time/residue: 0.6360 time to fit residues: 249.9614 Evaluate side-chains 364 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 302 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 82 MET 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 B residue 12 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 C residue 105 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 SER 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 M residue 1 GLN 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 P residue 5 THR Chi-restraints excluded: chain P residue 17 GLN 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 43 LYS Chi-restraints excluded: chain Q residue 50 ILE 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 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 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 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 230 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 237 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 242 optimal weight: 20.0000 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 ASN M 3 GLN P 79 GLN Q 105 GLN V 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.169597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.108039 restraints weight = 24876.835| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.29 r_work: 0.2932 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20558 Z= 0.267 Angle : 0.652 7.774 28024 Z= 0.348 Chirality : 0.045 0.156 2975 Planarity : 0.005 0.041 3655 Dihedral : 4.688 21.521 2938 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.87 % Allowed : 15.35 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.15), residues: 2607 helix: None (None), residues: 0 sheet: -0.01 (0.14), residues: 1111 loop : -1.21 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 16 TYR 0.020 0.002 TYR U 79 PHE 0.013 0.002 PHE U 29 TRP 0.011 0.002 TRP U 103 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00631 (20536) covalent geometry : angle 0.64927 (27980) SS BOND : bond 0.00617 ( 22) SS BOND : angle 1.65517 ( 44) hydrogen bonds : bond 0.03465 ( 733) hydrogen bonds : angle 5.59786 ( 1890) *********************** 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 393 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 311 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5334 (mp) REVERT: A 50 ILE cc_start: 0.8629 (tt) cc_final: 0.8185 (OUTLIER) REVERT: A 82 SER cc_start: 0.4347 (OUTLIER) cc_final: 0.4077 (m) REVERT: C 6 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6986 (mt-10) REVERT: D 32 ASP cc_start: 0.8691 (m-30) cc_final: 0.8301 (m-30) REVERT: O 3 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: O 105 GLN cc_start: 0.8459 (pt0) cc_final: 0.8137 (pm20) REVERT: P 27 ASN cc_start: 0.9391 (OUTLIER) cc_final: 0.9040 (p0) REVERT: P 81 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: Q 16 ARG cc_start: 0.8444 (ptp-110) cc_final: 0.8114 (ptp-110) REVERT: Q 43 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.7926 (mppt) REVERT: T 24 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8316 (p) REVERT: U 56 ARG cc_start: 0.8482 (mmt-90) cc_final: 0.8139 (ttm-80) REVERT: U 105 GLN cc_start: 0.8389 (pt0) cc_final: 0.7891 (mm-40) REVERT: U 110 THR cc_start: 0.7823 (m) cc_final: 0.7475 (p) REVERT: V 66 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7254 (ptpp) REVERT: V 79 GLN cc_start: 0.7434 (tt0) cc_final: 0.7105 (mm-40) REVERT: X 37 GLN cc_start: 0.6763 (tm130) cc_final: 0.6301 (tm-30) REVERT: X 89 GLN cc_start: 0.8363 (tm130) cc_final: 0.7872 (tm130) outliers start: 82 outliers final: 57 residues processed: 351 average time/residue: 0.6319 time to fit residues: 251.4324 Evaluate side-chains 369 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 304 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 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 12 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 C residue 105 GLN Chi-restraints excluded: chain D residue 103 LYS 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 52 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 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 43 LYS Chi-restraints excluded: chain Q residue 50 ILE 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 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 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 68 optimal weight: 10.0000 chunk 218 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 242 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 48 optimal weight: 0.4980 chunk 205 optimal weight: 20.0000 chunk 191 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 113 ASN ** 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 ** W 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 89 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.171713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109346 restraints weight = 24976.917| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.29 r_work: 0.2968 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20558 Z= 0.197 Angle : 0.606 7.749 28024 Z= 0.324 Chirality : 0.043 0.159 2975 Planarity : 0.004 0.042 3655 Dihedral : 4.552 21.546 2938 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.64 % Allowed : 16.11 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.15), residues: 2607 helix: None (None), residues: 0 sheet: 0.15 (0.15), residues: 1056 loop : -1.23 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 16 TYR 0.019 0.002 TYR U 79 PHE 0.010 0.002 PHE U 29 TRP 0.010 0.001 TRP M 36 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00463 (20536) covalent geometry : angle 0.60471 (27980) SS BOND : bond 0.00557 ( 22) SS BOND : angle 1.29907 ( 44) hydrogen bonds : bond 0.03140 ( 733) hydrogen bonds : angle 5.44153 ( 1890) *********************** 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 400 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 323 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 82 MET cc_start: 0.9059 (mtp) cc_final: 0.8651 (mtp) REVERT: A 50 ILE cc_start: 0.8681 (tt) cc_final: 0.8236 (OUTLIER) REVERT: A 82 SER cc_start: 0.4156 (OUTLIER) cc_final: 0.3809 (m) REVERT: A 99 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6785 (m-30) REVERT: C 6 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: C 38 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8221 (ptt180) REVERT: C 70 SER cc_start: 0.8475 (p) cc_final: 0.8257 (t) REVERT: D 32 ASP cc_start: 0.8656 (m-30) cc_final: 0.8282 (m-30) REVERT: F 105 THR cc_start: 0.8475 (m) cc_final: 0.8240 (p) REVERT: O 3 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7706 (mp10) REVERT: O 105 GLN cc_start: 0.8481 (pt0) cc_final: 0.8172 (pm20) REVERT: P 17 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: P 27 ASN cc_start: 0.9386 (OUTLIER) cc_final: 0.9052 (p0) REVERT: P 81 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: Q 16 ARG cc_start: 0.8406 (ptp-110) cc_final: 0.7988 (ptp-110) REVERT: T 24 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8312 (p) REVERT: T 72 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.8136 (p) REVERT: U 105 GLN cc_start: 0.8381 (pt0) cc_final: 0.7941 (mm-40) REVERT: U 110 THR cc_start: 0.7774 (m) cc_final: 0.7448 (p) REVERT: V 66 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7263 (ptpp) REVERT: V 79 GLN cc_start: 0.7483 (tt0) cc_final: 0.7209 (mm-40) REVERT: W 17 SER cc_start: 0.6966 (p) cc_final: 0.6347 (t) REVERT: X 37 GLN cc_start: 0.6796 (tm130) cc_final: 0.6336 (tm-30) REVERT: X 89 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8053 (tm130) REVERT: Y 34 MET cc_start: 0.5653 (ppp) cc_final: 0.5256 (ptt) outliers start: 77 outliers final: 54 residues processed: 360 average time/residue: 0.5909 time to fit residues: 242.1027 Evaluate side-chains 371 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 307 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 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 12 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 19 ARG 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 D residue 103 LYS 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 52 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 P residue 5 THR Chi-restraints excluded: chain P residue 17 GLN 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 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 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 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 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 228 optimal weight: 20.0000 chunk 177 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 171 optimal weight: 0.0050 chunk 151 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- 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 V 51 ASN W 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.173079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113830 restraints weight = 25052.343| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.49 r_work: 0.3064 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20558 Z= 0.132 Angle : 0.566 7.888 28024 Z= 0.302 Chirality : 0.042 0.150 2975 Planarity : 0.004 0.042 3655 Dihedral : 4.372 21.158 2938 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.12 % Allowed : 16.82 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.15), residues: 2607 helix: None (None), residues: 0 sheet: 0.22 (0.15), residues: 1056 loop : -1.12 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 93 TYR 0.017 0.001 TYR U 52A PHE 0.009 0.001 PHE C 29 TRP 0.015 0.001 TRP A 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00305 (20536) covalent geometry : angle 0.56545 (27980) SS BOND : bond 0.00485 ( 22) SS BOND : angle 1.02234 ( 44) hydrogen bonds : bond 0.02828 ( 733) hydrogen bonds : angle 5.25455 ( 1890) *********************** 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 387 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 321 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 82 MET cc_start: 0.9040 (mtp) cc_final: 0.8656 (mtp) REVERT: L 94 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8459 (mtt180) REVERT: A 50 ILE cc_start: 0.8676 (tt) cc_final: 0.8235 (tp) REVERT: A 82 SER cc_start: 0.4128 (OUTLIER) cc_final: 0.3784 (m) REVERT: C 6 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: C 38 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8209 (ptt180) REVERT: C 70 SER cc_start: 0.8464 (p) cc_final: 0.8255 (t) REVERT: C 76 ASN cc_start: 0.8864 (m-40) cc_final: 0.8576 (m-40) REVERT: D 32 ASP cc_start: 0.8697 (m-30) cc_final: 0.8345 (m-30) REVERT: E 75 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8573 (ptmm) REVERT: F 105 THR cc_start: 0.8480 (m) cc_final: 0.8260 (p) REVERT: O 3 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: O 105 GLN cc_start: 0.8489 (pt0) cc_final: 0.8164 (pm20) REVERT: P 17 GLN cc_start: 0.7914 (pm20) cc_final: 0.7705 (pm20) REVERT: P 81 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: Q 16 ARG cc_start: 0.8335 (ptp-110) cc_final: 0.8034 (ptp-110) REVERT: Q 43 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.7937 (mppt) REVERT: T 24 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8322 (p) REVERT: T 72 SER cc_start: 0.8379 (OUTLIER) cc_final: 0.8114 (p) REVERT: U 105 GLN cc_start: 0.8336 (pt0) cc_final: 0.7929 (mm110) REVERT: V 66 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7291 (ptpp) REVERT: V 79 GLN cc_start: 0.7491 (tt0) cc_final: 0.7244 (mm-40) REVERT: W 17 SER cc_start: 0.6861 (p) cc_final: 0.6293 (t) REVERT: X 37 GLN cc_start: 0.6799 (tm130) cc_final: 0.6358 (tm-30) REVERT: X 89 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8092 (tm130) REVERT: Y 34 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.5508 (ptt) outliers start: 66 outliers final: 45 residues processed: 354 average time/residue: 0.6236 time to fit residues: 250.4664 Evaluate side-chains 367 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 311 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 42 THR Chi-restraints excluded: chain L residue 51 ASN 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 D residue 103 LYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 LYS 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 82 MET 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 50 ILE 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 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 X residue 63 SER Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 34 MET 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 57 optimal weight: 0.9990 chunk 8 optimal weight: 30.0000 chunk 175 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 255 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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** C 3 GLN 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 = 0.4015 r_free = 0.4015 target = 0.172681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.110067 restraints weight = 24809.196| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.49 r_work: 0.2948 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20558 Z= 0.155 Angle : 0.585 7.421 28024 Z= 0.310 Chirality : 0.043 0.164 2975 Planarity : 0.004 0.040 3655 Dihedral : 4.354 20.576 2938 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.16 % Allowed : 17.01 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.22 (0.15), residues: 1056 loop : -1.12 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 93 TYR 0.018 0.001 TYR U 52A PHE 0.010 0.001 PHE C 29 TRP 0.020 0.001 TRP A 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00364 (20536) covalent geometry : angle 0.58341 (27980) SS BOND : bond 0.00519 ( 22) SS BOND : angle 1.19903 ( 44) hydrogen bonds : bond 0.02894 ( 733) hydrogen bonds : angle 5.20995 ( 1890) *********************** 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 385 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 318 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: H 82 MET cc_start: 0.9109 (mtp) cc_final: 0.8735 (mtp) REVERT: A 20 LEU cc_start: 0.5574 (OUTLIER) cc_final: 0.5159 (mp) REVERT: A 50 ILE cc_start: 0.8625 (tt) cc_final: 0.8178 (tp) REVERT: A 82 SER cc_start: 0.4193 (OUTLIER) cc_final: 0.3829 (m) REVERT: C 6 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7053 (mt-10) REVERT: C 70 SER cc_start: 0.8476 (p) cc_final: 0.8267 (t) REVERT: C 76 ASN cc_start: 0.8843 (m-40) cc_final: 0.8578 (m-40) REVERT: D 32 ASP cc_start: 0.8717 (m-30) cc_final: 0.8346 (m-30) REVERT: E 75 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8600 (ptmm) REVERT: F 105 THR cc_start: 0.8426 (m) cc_final: 0.8194 (p) REVERT: O 3 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7632 (tt0) REVERT: O 105 GLN cc_start: 0.8525 (pt0) cc_final: 0.8197 (pm20) REVERT: P 17 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7662 (pm20) REVERT: P 81 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: Q 16 ARG cc_start: 0.8350 (ptp-110) cc_final: 0.8035 (ptp-110) REVERT: Q 43 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.7912 (mppt) REVERT: T 24 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8325 (p) REVERT: T 72 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.8076 (p) REVERT: U 105 GLN cc_start: 0.8412 (pt0) cc_final: 0.7936 (mm110) REVERT: V 66 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7218 (ptpp) REVERT: V 79 GLN cc_start: 0.7380 (tt0) cc_final: 0.7134 (mm-40) REVERT: W 17 SER cc_start: 0.6768 (p) cc_final: 0.6248 (t) REVERT: X 37 GLN cc_start: 0.6652 (tm130) cc_final: 0.6204 (tm-30) REVERT: X 89 GLN cc_start: 0.8435 (tm-30) cc_final: 0.7978 (tm130) REVERT: Y 34 MET cc_start: 0.5724 (OUTLIER) cc_final: 0.5509 (ptt) REVERT: Y 82 MET cc_start: 0.4846 (mpm) cc_final: 0.2709 (ptt) outliers start: 67 outliers final: 50 residues processed: 350 average time/residue: 0.6092 time to fit residues: 242.2096 Evaluate side-chains 370 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 308 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 75 LYS 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 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 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 43 LYS 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 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 24 THR Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 34 MET 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 161 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 241 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 S 81 GLN V 51 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.172547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112878 restraints weight = 24881.156| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.52 r_work: 0.3051 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2186 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= 0.111 Angle : 0.559 7.556 28024 Z= 0.297 Chirality : 0.042 0.161 2975 Planarity : 0.004 0.042 3655 Dihedral : 4.247 21.118 2938 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.41 % Allowed : 18.14 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.28 (0.15), residues: 1056 loop : -1.06 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 93 TYR 0.018 0.001 TYR U 52A PHE 0.008 0.001 PHE C 29 TRP 0.028 0.001 TRP A 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00252 (20536) covalent geometry : angle 0.55830 (27980) SS BOND : bond 0.00448 ( 22) SS BOND : angle 0.91557 ( 44) hydrogen bonds : bond 0.02686 ( 733) hydrogen bonds : angle 5.07724 ( 1890) ********************** 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 373 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 322 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: H 82 MET cc_start: 0.9027 (mtp) cc_final: 0.8715 (mtp) REVERT: A 50 ILE cc_start: 0.8720 (tt) cc_final: 0.8266 (tp) REVERT: A 82 SER cc_start: 0.4143 (OUTLIER) cc_final: 0.3780 (m) REVERT: C 38 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8280 (ptt180) REVERT: D 32 ASP cc_start: 0.8740 (m-30) cc_final: 0.8415 (m-30) REVERT: F 105 THR cc_start: 0.8500 (m) cc_final: 0.8275 (p) REVERT: O 3 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: O 46 GLU cc_start: 0.8729 (tt0) cc_final: 0.8513 (tt0) REVERT: O 105 GLN cc_start: 0.8588 (pt0) cc_final: 0.8236 (pm20) REVERT: P 17 GLN cc_start: 0.7989 (pm20) cc_final: 0.7618 (pm20) REVERT: Q 16 ARG cc_start: 0.8257 (ptp-110) cc_final: 0.8008 (ptp-110) REVERT: Q 43 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.7988 (mppt) REVERT: T 24 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8317 (p) REVERT: U 105 GLN cc_start: 0.8361 (pt0) cc_final: 0.7951 (mm110) REVERT: V 66 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7243 (ptpp) REVERT: V 79 GLN cc_start: 0.7488 (tt0) cc_final: 0.7262 (mm-40) REVERT: W 17 SER cc_start: 0.6892 (p) cc_final: 0.6303 (t) REVERT: X 37 GLN cc_start: 0.6683 (tm130) cc_final: 0.6340 (tm-30) REVERT: X 89 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8233 (tm130) REVERT: Y 82 MET cc_start: 0.4725 (mpm) cc_final: 0.2602 (ptt) outliers start: 51 outliers final: 39 residues processed: 346 average time/residue: 0.6086 time to fit residues: 238.7140 Evaluate side-chains 359 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 314 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 A residue 20 LEU 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 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 N residue 103 LYS Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain Q residue 43 LYS 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 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 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 24 THR Chi-restraints excluded: chain W residue 70 SER 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 160 optimal weight: 0.0870 chunk 259 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN M 3 GLN P 79 GLN Q 105 GLN V 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.169660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.112583 restraints weight = 25164.539| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.41 r_work: 0.3037 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20558 Z= 0.231 Angle : 0.643 9.213 28024 Z= 0.341 Chirality : 0.045 0.218 2975 Planarity : 0.005 0.041 3655 Dihedral : 4.532 21.033 2938 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.88 % Allowed : 18.04 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.20 (0.15), residues: 1056 loop : -1.18 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 93 TYR 0.020 0.002 TYR U 52A PHE 0.012 0.002 PHE C 29 TRP 0.036 0.002 TRP A 47 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00549 (20536) covalent geometry : angle 0.64064 (27980) SS BOND : bond 0.00603 ( 22) SS BOND : angle 1.57387 ( 44) hydrogen bonds : bond 0.03176 ( 733) hydrogen bonds : angle 5.29061 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8859.34 seconds wall clock time: 151 minutes 28.80 seconds (9088.80 seconds total)