Starting phenix.real_space_refine on Mon Jun 16 05:03:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dyw_27784/06_2025/8dyw_27784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dyw_27784/06_2025/8dyw_27784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dyw_27784/06_2025/8dyw_27784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dyw_27784/06_2025/8dyw_27784.map" model { file = "/net/cci-nas-00/data/ceres_data/8dyw_27784/06_2025/8dyw_27784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dyw_27784/06_2025/8dyw_27784.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.150 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 70 5.16 5 C 11574 2.51 5 N 3287 2.21 5 O 3563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18494 Number of models: 1 Model: "" Number of chains: 21 Chain: "I" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 564 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 20, 'TRANS': 59} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "H" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "B" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "D" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "F" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "N" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "M" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "P" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "O" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "R" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "Q" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "T" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "S" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "V" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "U" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "X" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "W" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Time building chain proxies: 11.37, per 1000 atoms: 0.61 Number of scatterers: 18494 At special positions: 0 Unit cell: (120.75, 115, 188.6, 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 70 16.00 O 3563 8.00 N 3287 7.00 C 11574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.71 Conformation dependent library (CDL) restraints added in 2.4 seconds 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4300 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 55 sheets defined 7.0% alpha, 38.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.709A pdb=" N THR H 87 " --> pdb=" O ASP H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.935A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.737A pdb=" N GLU A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.864A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.196A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.582A pdb=" N THR E 87 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.888A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.502A pdb=" N THR M 87 " --> pdb=" O ASP M 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.919A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.722A pdb=" N GLU O 64 " --> pdb=" O ASP O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'Q' and resid 61 through 64 removed outlier: 3.601A pdb=" N GLU Q 64 " --> pdb=" O ASP Q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 61 through 64' Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.514A pdb=" N THR Q 87 " --> pdb=" O ASP Q 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.748A pdb=" N PHE T 83 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 61 through 64 Processing helix chain 'S' and resid 83 through 87 removed outlier: 3.600A pdb=" N THR S 87 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 79 through 83 removed outlier: 4.085A pdb=" N PHE V 83 " --> pdb=" O PRO V 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 61 through 64 removed outlier: 3.544A pdb=" N GLU U 64 " --> pdb=" O ASP U 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 61 through 64' Processing helix chain 'U' and resid 83 through 87 Processing helix chain 'W' and resid 61 through 64 removed outlier: 3.525A pdb=" N GLU W 64 " --> pdb=" O ASP W 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 61 through 64' Processing helix chain 'W' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.630A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.587A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.587A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR L 97 " --> pdb=" O HIS L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 4 removed outlier: 3.622A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.067A pdb=" N GLY H 10 " --> pdb=" O ILE H 110 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 18 through 21 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.558A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 5.807A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 48 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 97 " --> pdb=" O HIS B 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 removed outlier: 5.807A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 48 " --> pdb=" O TRP B 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.513A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 78 " --> pdb=" O CYS A 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.958A pdb=" N MET A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.949A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.539A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.898A pdb=" N THR D 97 " --> pdb=" O HIS D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 3 through 4 Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.867A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 18 through 21 Processing sheet with id=AB9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.634A pdb=" N VAL F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.588A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.781A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.356A pdb=" N GLY E 10 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS E 35 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 18 through 21 Processing sheet with id=AC5, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.706A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.515A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.515A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS N 90 " --> pdb=" O THR N 97 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR N 97 " --> pdb=" O HIS N 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 3 through 4 removed outlier: 3.665A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.067A pdb=" N GLY M 10 " --> pdb=" O ILE M 110 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 18 through 21 Processing sheet with id=AD2, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.956A pdb=" N GLU P 70 " --> pdb=" O SER P 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.547A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.797A pdb=" N THR P 97 " --> pdb=" O HIS P 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.711A pdb=" N GLN O 3 " --> pdb=" O SER O 25 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL O 5 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU O 78 " --> pdb=" O CYS O 22 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.338A pdb=" N GLY O 10 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS O 35 " --> pdb=" O ALA O 93 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 4 through 7 removed outlier: 3.655A pdb=" N GLU R 70 " --> pdb=" O SER R 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.747A pdb=" N GLU R 105 " --> pdb=" O LEU R 11 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.747A pdb=" N GLU R 105 " --> pdb=" O LEU R 11 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR R 97 " --> pdb=" O HIS R 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 3 through 4 removed outlier: 3.893A pdb=" N GLN Q 3 " --> pdb=" O SER Q 25 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER Q 25 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.808A pdb=" N MET Q 34 " --> pdb=" O VAL Q 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 18 through 21 removed outlier: 3.780A pdb=" N THR Q 77 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP Q 72 " --> pdb=" O THR Q 77 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 4 through 7 removed outlier: 3.617A pdb=" N VAL T 19 " --> pdb=" O ILE T 75 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 10 through 13 removed outlier: 3.682A pdb=" N GLU T 105 " --> pdb=" O LEU T 11 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 10 through 13 removed outlier: 3.682A pdb=" N GLU T 105 " --> pdb=" O LEU T 11 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR T 97 " --> pdb=" O HIS T 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 3 through 4 removed outlier: 4.039A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.995A pdb=" N GLY S 10 " --> pdb=" O ILE S 110 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET S 34 " --> pdb=" O VAL S 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 18 through 21 Processing sheet with id=AF1, first strand: chain 'V' and resid 4 through 7 removed outlier: 3.514A pdb=" N CYS V 23 " --> pdb=" O PHE V 71 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE V 71 " --> pdb=" O CYS V 23 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.589A pdb=" N GLU V 105 " --> pdb=" O LEU V 11 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU V 33 " --> pdb=" O TYR V 49 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR V 49 " --> pdb=" O LEU V 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.589A pdb=" N GLU V 105 " --> pdb=" O LEU V 11 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR V 97 " --> pdb=" O HIS V 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.509A pdb=" N GLY U 10 " --> pdb=" O LEU U 108 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS U 35 " --> pdb=" O ALA U 93 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET U 34 " --> pdb=" O VAL U 50 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 18 through 21 removed outlier: 3.564A pdb=" N THR U 77 " --> pdb=" O ASP U 72 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP U 72 " --> pdb=" O THR U 77 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 4 through 5 removed outlier: 3.644A pdb=" N GLU X 70 " --> pdb=" O SER X 67 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.858A pdb=" N LEU X 33 " --> pdb=" O TYR X 49 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR X 49 " --> pdb=" O LEU X 33 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP X 35 " --> pdb=" O LEU X 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 3 through 4 Processing sheet with id=AF9, first strand: chain 'W' and resid 10 through 12 removed outlier: 3.609A pdb=" N ALA W 88 " --> pdb=" O VAL W 109 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN W 39 " --> pdb=" O ILE W 89 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N MET W 34 " --> pdb=" O VAL W 50 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL W 50 " --> pdb=" O MET W 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP W 36 " --> pdb=" O VAL W 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 18 through 21 648 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.20 Time building geometry restraints manager: 5.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 1 1.12 - 1.30: 2984 1.30 - 1.47: 8276 1.47 - 1.65: 7562 1.65 - 1.83: 100 Bond restraints: 18923 Sorted by residual: bond pdb=" CB PRO A 41 " pdb=" CG PRO A 41 " ideal model delta sigma weight residual 1.492 0.945 0.547 5.00e-02 4.00e+02 1.20e+02 bond pdb=" CG PRO A 41 " pdb=" CD PRO A 41 " ideal model delta sigma weight residual 1.503 1.167 0.336 3.40e-02 8.65e+02 9.79e+01 bond pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 1.471 1.502 -0.032 1.32e-02 5.74e+03 5.74e+00 bond pdb=" CB PRO T 44 " pdb=" CG PRO T 44 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.27e+00 bond pdb=" CA PRO A 41 " pdb=" CB PRO A 41 " ideal model delta sigma weight residual 1.534 1.562 -0.029 1.40e-02 5.10e+03 4.17e+00 ... (remaining 18918 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.75: 25666 9.75 - 19.50: 4 19.50 - 29.24: 1 29.24 - 38.99: 1 38.99 - 48.74: 1 Bond angle restraints: 25673 Sorted by residual: angle pdb=" N PRO A 41 " pdb=" CD PRO A 41 " pdb=" CG PRO A 41 " ideal model delta sigma weight residual 103.20 76.87 26.33 1.50e+00 4.44e-01 3.08e+02 angle pdb=" CA PRO A 41 " pdb=" CB PRO A 41 " pdb=" CG PRO A 41 " ideal model delta sigma weight residual 104.50 72.71 31.79 1.90e+00 2.77e-01 2.80e+02 angle pdb=" CB PRO A 41 " pdb=" CG PRO A 41 " pdb=" CD PRO A 41 " ideal model delta sigma weight residual 106.10 154.84 -48.74 3.20e+00 9.77e-02 2.32e+02 angle pdb=" CA PRO A 41 " pdb=" N PRO A 41 " pdb=" CD PRO A 41 " ideal model delta sigma weight residual 112.00 100.00 12.00 1.40e+00 5.10e-01 7.35e+01 angle pdb=" C GLN F 38 " pdb=" N LYS F 39 " pdb=" CA LYS F 39 " ideal model delta sigma weight residual 120.68 112.78 7.90 1.52e+00 4.33e-01 2.70e+01 ... (remaining 25668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9878 17.96 - 35.93: 973 35.93 - 53.89: 215 53.89 - 71.85: 39 71.85 - 89.82: 16 Dihedral angle restraints: 11121 sinusoidal: 4352 harmonic: 6769 Sorted by residual: dihedral pdb=" CB CYS W 22 " pdb=" SG CYS W 22 " pdb=" SG CYS W 92 " pdb=" CB CYS W 92 " ideal model delta sinusoidal sigma weight residual -86.00 -1.67 -84.33 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" N PRO A 41 " pdb=" CG PRO A 41 " pdb=" CD PRO A 41 " pdb=" CB PRO A 41 " ideal model delta sinusoidal sigma weight residual 30.00 114.23 -84.23 1 1.50e+01 4.44e-03 3.84e+01 dihedral pdb=" CB CYS V 23 " pdb=" SG CYS V 23 " pdb=" SG CYS V 88 " pdb=" CB CYS V 88 " ideal model delta sinusoidal sigma weight residual 93.00 49.94 43.06 1 1.00e+01 1.00e-02 2.59e+01 ... (remaining 11118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2259 0.052 - 0.105: 391 0.105 - 0.157: 98 0.157 - 0.209: 2 0.209 - 0.262: 2 Chirality restraints: 2752 Sorted by residual: chirality pdb=" CB ILE U 89 " pdb=" CA ILE U 89 " pdb=" CG1 ILE U 89 " pdb=" CG2 ILE U 89 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CG LEU P 11 " pdb=" CB LEU P 11 " pdb=" CD1 LEU P 11 " pdb=" CD2 LEU P 11 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE C 89 " pdb=" CA ILE C 89 " pdb=" CG1 ILE C 89 " pdb=" CG2 ILE C 89 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 2749 not shown) Planarity restraints: 3329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 79 " 0.066 5.00e-02 4.00e+02 9.92e-02 1.58e+01 pdb=" N PRO D 80 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN N 79 " 0.063 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO N 80 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO N 80 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO N 80 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA T 43 " -0.059 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO T 44 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO T 44 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO T 44 " -0.047 5.00e-02 4.00e+02 ... (remaining 3326 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 456 2.68 - 3.23: 17566 3.23 - 3.79: 29240 3.79 - 4.34: 40137 4.34 - 4.90: 66657 Nonbonded interactions: 154056 Sorted by model distance: nonbonded pdb=" O ASP X 82 " pdb=" OH TYR X 86 " model vdw 2.122 3.040 nonbonded pdb=" OE1 GLN B 6 " pdb=" OG1 THR B 102 " model vdw 2.127 3.040 nonbonded pdb=" OE2 GLU U 6 " pdb=" N GLY U 106 " model vdw 2.139 3.120 nonbonded pdb=" OE1 GLN D 6 " pdb=" OG1 THR D 102 " model vdw 2.166 3.040 nonbonded pdb=" N GLU U 6 " pdb=" OE1 GLU U 6 " model vdw 2.167 3.120 ... (remaining 154051 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' } 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' } 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 group one per residue 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: 0.860 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: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 45.380 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.120 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.006 0.547 18943 Z= 0.185 Angle : 0.848 48.738 25713 Z= 0.446 Chirality : 0.044 0.262 2752 Planarity : 0.005 0.099 3329 Dihedral : 15.005 89.817 6761 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.65 % Favored : 95.92 % Rotamer: Outliers : 0.30 % Allowed : 17.18 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.23 (0.16), residues: 1150 loop : -0.08 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP W 36 HIS 0.004 0.001 HIS X 90 PHE 0.022 0.002 PHE X 71 TYR 0.030 0.001 TYR T 91 ARG 0.016 0.001 ARG H 105 Details of bonding type rmsd hydrogen bonds : bond 0.27452 ( 609) hydrogen bonds : angle 10.65822 ( 1524) SS BOND : bond 0.00261 ( 20) SS BOND : angle 1.26198 ( 40) covalent geometry : bond 0.00568 (18923) covalent geometry : angle 0.84672 (25673) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 253 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 70 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6645 (mm-30) REVERT: R 78 LEU cc_start: 0.8990 (tt) cc_final: 0.8724 (mp) REVERT: V 70 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8076 (mp0) outliers start: 6 outliers final: 5 residues processed: 256 average time/residue: 0.3683 time to fit residues: 134.7639 Evaluate side-chains 234 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 229 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain X residue 50 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 40.0000 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 207 optimal weight: 40.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN A 1 GLN F 3 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 38 GLN R 89 GLN T 89 GLN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.095220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.071816 restraints weight = 51195.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.070748 restraints weight = 54136.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.071415 restraints weight = 52713.648| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18943 Z= 0.178 Angle : 0.626 8.492 25713 Z= 0.330 Chirality : 0.045 0.239 2752 Planarity : 0.005 0.077 3329 Dihedral : 5.065 59.453 2642 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.78 % Favored : 95.79 % Rotamer: Outliers : 2.45 % Allowed : 14.54 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.40 (0.16), residues: 1160 loop : -0.08 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 35 HIS 0.003 0.001 HIS O 35 PHE 0.019 0.002 PHE H 29 TYR 0.022 0.001 TYR X 87 ARG 0.007 0.001 ARG H 105 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 609) hydrogen bonds : angle 7.22346 ( 1524) SS BOND : bond 0.00493 ( 20) SS BOND : angle 1.49121 ( 40) covalent geometry : bond 0.00416 (18923) covalent geometry : angle 0.62372 (25673) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 261 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7617 (pp30) REVERT: D 4 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8042 (mmm) REVERT: R 18 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7711 (ttp80) REVERT: Q 100 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8788 (m-80) REVERT: T 81 ASP cc_start: 0.7997 (t0) cc_final: 0.7661 (t0) REVERT: S 95 ASP cc_start: 0.7268 (t70) cc_final: 0.6951 (t0) REVERT: S 111 VAL cc_start: 0.7377 (OUTLIER) cc_final: 0.6995 (p) REVERT: V 86 TYR cc_start: 0.7531 (m-10) cc_final: 0.7256 (m-10) REVERT: U 79 TYR cc_start: 0.7210 (m-80) cc_final: 0.6934 (m-80) REVERT: U 108 LEU cc_start: 0.8501 (tt) cc_final: 0.8137 (mp) REVERT: X 98 PHE cc_start: 0.4630 (OUTLIER) cc_final: 0.4215 (m-10) outliers start: 49 outliers final: 22 residues processed: 292 average time/residue: 0.3885 time to fit residues: 165.0523 Evaluate side-chains 248 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 82 MET Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain W residue 80 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 131 optimal weight: 3.9990 chunk 220 optimal weight: 50.0000 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 30.0000 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN B 6 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 89 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN ** T 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN ** X 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.096380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.067661 restraints weight = 49617.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.066877 restraints weight = 32266.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067809 restraints weight = 26393.575| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18943 Z= 0.149 Angle : 0.586 8.268 25713 Z= 0.308 Chirality : 0.044 0.218 2752 Planarity : 0.004 0.058 3329 Dihedral : 4.423 17.573 2629 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.26 % Favored : 96.31 % Rotamer: Outliers : 2.80 % Allowed : 15.23 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.37 (0.16), residues: 1120 loop : -0.15 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 103 HIS 0.004 0.001 HIS O 35 PHE 0.019 0.002 PHE O 29 TYR 0.015 0.001 TYR X 87 ARG 0.006 0.001 ARG W 105 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 609) hydrogen bonds : angle 6.69281 ( 1524) SS BOND : bond 0.00496 ( 20) SS BOND : angle 1.37064 ( 40) covalent geometry : bond 0.00346 (18923) covalent geometry : angle 0.58425 (25673) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 266 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 81 ASP cc_start: 0.8518 (t0) cc_final: 0.7870 (m-30) REVERT: A 16 ARG cc_start: 0.7093 (ttp80) cc_final: 0.6825 (ttp80) REVERT: A 28 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7662 (t) REVERT: D 27 GLN cc_start: 0.8936 (pm20) cc_final: 0.8548 (pm20) REVERT: C 110 ILE cc_start: 0.9146 (mm) cc_final: 0.8915 (tp) REVERT: F 33 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8278 (mt) REVERT: F 89 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8532 (tm-30) REVERT: M 79 TYR cc_start: 0.8656 (m-80) cc_final: 0.8200 (m-80) REVERT: R 18 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7765 (ttp80) REVERT: Q 72 ASP cc_start: 0.7543 (p0) cc_final: 0.7306 (p0) REVERT: Q 100 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.9047 (m-80) REVERT: T 49 TYR cc_start: 0.8607 (p90) cc_final: 0.8095 (p90) REVERT: S 83 ARG cc_start: 0.8083 (ptp-170) cc_final: 0.7428 (ptp90) REVERT: S 95 ASP cc_start: 0.7318 (t70) cc_final: 0.7007 (t0) REVERT: V 70 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8303 (mm-30) REVERT: V 86 TYR cc_start: 0.8097 (m-10) cc_final: 0.7736 (m-10) REVERT: U 108 LEU cc_start: 0.8936 (tt) cc_final: 0.8494 (mp) REVERT: X 86 TYR cc_start: 0.5942 (m-80) cc_final: 0.5677 (m-80) REVERT: X 87 TYR cc_start: 0.6458 (m-80) cc_final: 0.6091 (m-80) REVERT: X 92 ASN cc_start: 0.8891 (t0) cc_final: 0.8367 (m-40) REVERT: X 98 PHE cc_start: 0.5168 (OUTLIER) cc_final: 0.4744 (m-10) outliers start: 56 outliers final: 25 residues processed: 308 average time/residue: 0.3674 time to fit residues: 162.1634 Evaluate side-chains 263 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 70 GLU Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 98 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 82 optimal weight: 1.9990 chunk 204 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 170 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 39 ASN L 3 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN R 6 GLN T 89 GLN V 79 GLN ** X 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.094542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.065938 restraints weight = 50684.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.065763 restraints weight = 31747.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.065924 restraints weight = 24505.040| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18943 Z= 0.153 Angle : 0.580 7.283 25713 Z= 0.303 Chirality : 0.044 0.194 2752 Planarity : 0.004 0.053 3329 Dihedral : 4.332 19.240 2629 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.65 % Favored : 95.92 % Rotamer: Outliers : 3.35 % Allowed : 15.28 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.51 (0.16), residues: 1100 loop : -0.24 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 35 HIS 0.006 0.001 HIS F 90 PHE 0.021 0.002 PHE X 71 TYR 0.013 0.001 TYR X 87 ARG 0.007 0.000 ARG C 16 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 609) hydrogen bonds : angle 6.33656 ( 1524) SS BOND : bond 0.00473 ( 20) SS BOND : angle 1.44443 ( 40) covalent geometry : bond 0.00360 (18923) covalent geometry : angle 0.57756 (25673) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 253 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 78 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8508 (mp) REVERT: L 81 ASP cc_start: 0.8740 (t0) cc_final: 0.8523 (t0) REVERT: B 24 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.7036 (mtm-85) REVERT: A 16 ARG cc_start: 0.6996 (ttp80) cc_final: 0.6721 (ttp80) REVERT: D 4 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7925 (mmm) REVERT: D 6 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.5625 (pp30) REVERT: D 27 GLN cc_start: 0.9068 (pm20) cc_final: 0.8636 (pm20) REVERT: C 71 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8625 (ptm160) REVERT: M 71 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7549 (ttm-80) REVERT: M 79 TYR cc_start: 0.8658 (m-80) cc_final: 0.8231 (m-80) REVERT: R 18 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7642 (ttp80) REVERT: Q 100 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8871 (m-80) REVERT: T 33 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7186 (mp) REVERT: T 89 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8115 (tm-30) REVERT: T 105 GLU cc_start: 0.3547 (tp30) cc_final: 0.3136 (tp30) REVERT: S 95 ASP cc_start: 0.7333 (t70) cc_final: 0.7029 (t0) REVERT: V 3 GLN cc_start: 0.8612 (pm20) cc_final: 0.8166 (pp30) REVERT: V 50 GLN cc_start: 0.9245 (mm-40) cc_final: 0.8634 (tp-100) REVERT: V 86 TYR cc_start: 0.8043 (m-10) cc_final: 0.7695 (m-10) REVERT: U 108 LEU cc_start: 0.8861 (tt) cc_final: 0.8486 (mp) REVERT: X 86 TYR cc_start: 0.6108 (m-80) cc_final: 0.5730 (m-80) REVERT: X 92 ASN cc_start: 0.8728 (t0) cc_final: 0.8230 (m-40) REVERT: X 94 TYR cc_start: 0.7160 (m-80) cc_final: 0.6602 (m-80) REVERT: X 98 PHE cc_start: 0.5233 (OUTLIER) cc_final: 0.4748 (m-10) REVERT: X 107 LYS cc_start: -0.0503 (pptt) cc_final: -0.1029 (pttp) REVERT: W 6 GLU cc_start: 0.3331 (mp0) cc_final: 0.1712 (tp30) outliers start: 67 outliers final: 34 residues processed: 298 average time/residue: 0.3761 time to fit residues: 160.5569 Evaluate side-chains 268 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 70 GLU Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 35 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 180 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 209 optimal weight: 50.0000 chunk 214 optimal weight: 40.0000 chunk 157 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 63 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN M 31 ASN R 6 GLN R 27 GLN T 89 GLN ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.103343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.079268 restraints weight = 53110.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.079103 restraints weight = 50155.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.079456 restraints weight = 52909.101| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18943 Z= 0.208 Angle : 0.599 8.890 25713 Z= 0.315 Chirality : 0.044 0.175 2752 Planarity : 0.004 0.051 3329 Dihedral : 4.454 20.373 2629 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.95 % Favored : 95.62 % Rotamer: Outliers : 3.35 % Allowed : 16.28 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.56 (0.17), residues: 1020 loop : -0.23 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 35 HIS 0.005 0.001 HIS C 35 PHE 0.021 0.002 PHE S 67 TYR 0.016 0.002 TYR R 49 ARG 0.008 0.001 ARG Q 105 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 609) hydrogen bonds : angle 6.29451 ( 1524) SS BOND : bond 0.00505 ( 20) SS BOND : angle 1.46162 ( 40) covalent geometry : bond 0.00488 (18923) covalent geometry : angle 0.59638 (25673) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 229 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 81 ASP cc_start: 0.8802 (t0) cc_final: 0.8534 (t0) REVERT: B 78 LEU cc_start: 0.9331 (tp) cc_final: 0.8962 (tt) REVERT: D 4 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8024 (mmm) REVERT: D 6 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.5865 (pp30) REVERT: D 18 ARG cc_start: 0.7932 (tpp80) cc_final: 0.7575 (mmm-85) REVERT: D 27 GLN cc_start: 0.9164 (pm20) cc_final: 0.8737 (pm20) REVERT: M 71 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7683 (ttm-80) REVERT: O 28 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7935 (t) REVERT: R 18 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7713 (ttp80) REVERT: Q 79 TYR cc_start: 0.8026 (m-80) cc_final: 0.7516 (m-80) REVERT: Q 100 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8690 (m-80) REVERT: T 33 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7613 (mp) REVERT: T 105 GLU cc_start: 0.3074 (tp30) cc_final: 0.2648 (tp30) REVERT: S 95 ASP cc_start: 0.7330 (t70) cc_final: 0.7077 (t0) REVERT: V 50 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8418 (tp-100) REVERT: V 86 TYR cc_start: 0.7376 (m-10) cc_final: 0.7113 (m-10) REVERT: U 108 LEU cc_start: 0.8681 (tt) cc_final: 0.8423 (mp) REVERT: X 86 TYR cc_start: 0.5857 (m-80) cc_final: 0.5586 (m-80) REVERT: X 92 ASN cc_start: 0.8312 (t0) cc_final: 0.8044 (m-40) REVERT: X 94 TYR cc_start: 0.6802 (m-80) cc_final: 0.6404 (m-80) REVERT: X 98 PHE cc_start: 0.5086 (OUTLIER) cc_final: 0.4514 (m-10) REVERT: W 6 GLU cc_start: 0.3679 (mp0) cc_final: 0.2111 (tp30) outliers start: 67 outliers final: 41 residues processed: 279 average time/residue: 0.3763 time to fit residues: 150.9997 Evaluate side-chains 266 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 90 HIS Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 70 GLU Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 35 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 32 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 157 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN N 6 GLN N 38 GLN M 39 GLN R 27 GLN T 89 GLN S 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.092314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.064868 restraints weight = 52834.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.064658 restraints weight = 31792.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065631 restraints weight = 25579.470| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18943 Z= 0.102 Angle : 0.575 9.835 25713 Z= 0.295 Chirality : 0.044 0.337 2752 Planarity : 0.004 0.050 3329 Dihedral : 4.171 19.760 2629 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.43 % Allowed : 2.92 % Favored : 96.65 % Rotamer: Outliers : 2.70 % Allowed : 17.13 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.66 (0.17), residues: 1020 loop : -0.17 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP W 103 HIS 0.004 0.001 HIS S 35 PHE 0.022 0.001 PHE X 71 TYR 0.024 0.001 TYR S 91 ARG 0.010 0.000 ARG H 105 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 609) hydrogen bonds : angle 5.87014 ( 1524) SS BOND : bond 0.00443 ( 20) SS BOND : angle 1.21549 ( 40) covalent geometry : bond 0.00239 (18923) covalent geometry : angle 0.57304 (25673) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 268 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 81 ASP cc_start: 0.8842 (t0) cc_final: 0.8542 (t0) REVERT: H 59 TYR cc_start: 0.9059 (m-80) cc_final: 0.8776 (m-80) REVERT: B 78 LEU cc_start: 0.9122 (tp) cc_final: 0.8431 (tt) REVERT: D 6 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6316 (pt0) REVERT: D 27 GLN cc_start: 0.9044 (pm20) cc_final: 0.8675 (pm20) REVERT: M 34 MET cc_start: 0.8431 (mmm) cc_final: 0.8208 (mmt) REVERT: M 79 TYR cc_start: 0.8621 (m-80) cc_final: 0.8271 (m-80) REVERT: O 28 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7504 (t) REVERT: Q 79 TYR cc_start: 0.7963 (m-80) cc_final: 0.7476 (m-80) REVERT: Q 100 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8831 (m-80) REVERT: T 33 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7058 (mp) REVERT: T 49 TYR cc_start: 0.8585 (p90) cc_final: 0.8161 (p90) REVERT: T 105 GLU cc_start: 0.3163 (tp30) cc_final: 0.2722 (tp30) REVERT: S 95 ASP cc_start: 0.7212 (t70) cc_final: 0.6850 (t0) REVERT: V 50 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8687 (tp-100) REVERT: V 86 TYR cc_start: 0.7966 (m-10) cc_final: 0.7673 (m-10) REVERT: U 13 GLN cc_start: 0.8846 (mp10) cc_final: 0.8434 (mm-40) REVERT: U 85 GLU cc_start: 0.8888 (pm20) cc_final: 0.8642 (pm20) REVERT: U 108 LEU cc_start: 0.8970 (tt) cc_final: 0.8666 (mp) REVERT: X 86 TYR cc_start: 0.6338 (m-80) cc_final: 0.5992 (m-80) REVERT: X 87 TYR cc_start: 0.6462 (m-80) cc_final: 0.6223 (m-80) REVERT: X 92 ASN cc_start: 0.8631 (t0) cc_final: 0.8182 (m-40) REVERT: X 94 TYR cc_start: 0.7583 (m-80) cc_final: 0.7068 (m-80) REVERT: X 98 PHE cc_start: 0.5036 (OUTLIER) cc_final: 0.4771 (m-10) outliers start: 54 outliers final: 31 residues processed: 307 average time/residue: 0.3667 time to fit residues: 161.9308 Evaluate side-chains 266 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 70 GLU Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 61 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 50.0000 chunk 53 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 overall best weight: 6.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN B 6 GLN B 89 GLN A 31 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 38 GLN T 89 GLN V 38 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.095711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.067882 restraints weight = 48234.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.068738 restraints weight = 37861.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069206 restraints weight = 27796.105| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 18943 Z= 0.338 Angle : 0.691 10.214 25713 Z= 0.364 Chirality : 0.046 0.274 2752 Planarity : 0.005 0.054 3329 Dihedral : 4.742 20.681 2629 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.28 % Favored : 94.29 % Rotamer: Outliers : 3.60 % Allowed : 16.78 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.29 (0.17), residues: 1040 loop : -0.29 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP X 35 HIS 0.006 0.001 HIS O 35 PHE 0.027 0.002 PHE O 29 TYR 0.024 0.002 TYR F 87 ARG 0.010 0.001 ARG M 26 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 609) hydrogen bonds : angle 6.36041 ( 1524) SS BOND : bond 0.00623 ( 20) SS BOND : angle 1.93256 ( 40) covalent geometry : bond 0.00789 (18923) covalent geometry : angle 0.68768 (25673) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 222 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 81 ASP cc_start: 0.8655 (t0) cc_final: 0.7826 (m-30) REVERT: B 89 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6839 (pp30) REVERT: A 89 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8709 (tp) REVERT: A 100 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8644 (m-80) REVERT: D 4 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7951 (tpp) REVERT: D 6 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.5919 (pp30) REVERT: D 18 ARG cc_start: 0.8042 (tpp80) cc_final: 0.7662 (mmm-85) REVERT: D 27 GLN cc_start: 0.9162 (pm20) cc_final: 0.8730 (pm20) REVERT: F 105 GLU cc_start: 0.6727 (tp30) cc_final: 0.6448 (tp30) REVERT: E 6 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8289 (pm20) REVERT: E 82 MET cc_start: 0.8612 (mmt) cc_final: 0.8143 (mmt) REVERT: M 71 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7621 (ttm-80) REVERT: O 28 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7889 (t) REVERT: R 18 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7484 (ttp80) REVERT: Q 72 ASP cc_start: 0.7264 (p0) cc_final: 0.7036 (p0) REVERT: Q 79 TYR cc_start: 0.7966 (m-80) cc_final: 0.7622 (m-80) REVERT: Q 100 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8752 (m-80) REVERT: T 89 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: S 95 ASP cc_start: 0.7477 (t70) cc_final: 0.7226 (t0) REVERT: V 4 MET cc_start: 0.7707 (mmm) cc_final: 0.7163 (mmm) REVERT: V 50 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8430 (tp-100) REVERT: V 86 TYR cc_start: 0.7556 (m-10) cc_final: 0.7253 (m-10) REVERT: U 108 LEU cc_start: 0.8663 (tt) cc_final: 0.8437 (mp) REVERT: X 50 GLN cc_start: 0.8152 (mm110) cc_final: 0.7944 (mm-40) REVERT: X 86 TYR cc_start: 0.5915 (m-80) cc_final: 0.5684 (m-80) REVERT: X 87 TYR cc_start: 0.5806 (m-80) cc_final: 0.5514 (m-80) REVERT: X 92 ASN cc_start: 0.8318 (t0) cc_final: 0.7991 (m-40) REVERT: X 94 TYR cc_start: 0.7048 (m-80) cc_final: 0.6720 (m-80) REVERT: X 98 PHE cc_start: 0.4849 (OUTLIER) cc_final: 0.4200 (m-80) REVERT: W 6 GLU cc_start: 0.3175 (mp0) cc_final: 0.1794 (tp30) outliers start: 72 outliers final: 37 residues processed: 279 average time/residue: 0.3541 time to fit residues: 143.9233 Evaluate side-chains 248 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain V residue 88 CYS Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain W residue 35 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 64 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 41 optimal weight: 30.0000 chunk 198 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 97 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN B 6 GLN B 89 GLN A 31 ASN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.090716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.064077 restraints weight = 52782.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.063102 restraints weight = 29996.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063544 restraints weight = 26808.156| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18943 Z= 0.128 Angle : 0.606 9.638 25713 Z= 0.313 Chirality : 0.044 0.246 2752 Planarity : 0.004 0.049 3329 Dihedral : 4.373 21.998 2629 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.44 % Favored : 96.13 % Rotamer: Outliers : 2.20 % Allowed : 18.28 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.50 (0.17), residues: 1020 loop : -0.29 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 35 HIS 0.005 0.001 HIS E 35 PHE 0.022 0.001 PHE X 71 TYR 0.014 0.001 TYR S 91 ARG 0.008 0.001 ARG W 30 Details of bonding type rmsd hydrogen bonds : bond 0.02921 ( 609) hydrogen bonds : angle 5.97776 ( 1524) SS BOND : bond 0.00405 ( 20) SS BOND : angle 1.28431 ( 40) covalent geometry : bond 0.00304 (18923) covalent geometry : angle 0.60411 (25673) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 81 ASP cc_start: 0.8765 (t0) cc_final: 0.8303 (t0) REVERT: B 18 ARG cc_start: 0.8820 (ttp80) cc_final: 0.8570 (ttp80) REVERT: D 6 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.5583 (pp30) REVERT: D 18 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7550 (mmm-85) REVERT: D 27 GLN cc_start: 0.9111 (pm20) cc_final: 0.8723 (pm20) REVERT: F 105 GLU cc_start: 0.6630 (tp30) cc_final: 0.6329 (tp30) REVERT: E 28 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7979 (p) REVERT: E 82 MET cc_start: 0.8478 (mmt) cc_final: 0.7993 (mmt) REVERT: M 34 MET cc_start: 0.8428 (mmm) cc_final: 0.8184 (mmt) REVERT: M 71 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7576 (ttm-80) REVERT: M 79 TYR cc_start: 0.8693 (m-80) cc_final: 0.8282 (m-80) REVERT: O 28 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7776 (t) REVERT: Q 72 ASP cc_start: 0.7197 (p0) cc_final: 0.6949 (p0) REVERT: Q 79 TYR cc_start: 0.8010 (m-80) cc_final: 0.7715 (m-80) REVERT: Q 100 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8851 (m-80) REVERT: S 79 TYR cc_start: 0.7557 (m-80) cc_final: 0.6958 (m-10) REVERT: S 95 ASP cc_start: 0.7518 (t70) cc_final: 0.7196 (t0) REVERT: V 4 MET cc_start: 0.7905 (mmm) cc_final: 0.7319 (mmm) REVERT: V 50 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8641 (tp40) REVERT: V 86 TYR cc_start: 0.7885 (m-10) cc_final: 0.7605 (m-10) REVERT: U 108 LEU cc_start: 0.8940 (tt) cc_final: 0.8667 (mp) REVERT: X 21 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6276 (tp) REVERT: X 50 GLN cc_start: 0.8260 (mm110) cc_final: 0.8040 (mm-40) REVERT: X 86 TYR cc_start: 0.6377 (m-80) cc_final: 0.6125 (m-80) REVERT: X 87 TYR cc_start: 0.6277 (m-80) cc_final: 0.5908 (m-80) REVERT: X 94 TYR cc_start: 0.7527 (m-80) cc_final: 0.6988 (m-80) REVERT: X 98 PHE cc_start: 0.5614 (OUTLIER) cc_final: 0.5242 (m-80) REVERT: W 6 GLU cc_start: 0.3643 (mp0) cc_final: 0.2029 (tp30) outliers start: 44 outliers final: 26 residues processed: 259 average time/residue: 0.3554 time to fit residues: 134.8604 Evaluate side-chains 244 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain V residue 88 CYS Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain W residue 35 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 163 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 191 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 142 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 196 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN T 89 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.091860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.067213 restraints weight = 51598.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.066480 restraints weight = 49751.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.066507 restraints weight = 57965.546| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 18943 Z= 0.296 Angle : 0.680 9.424 25713 Z= 0.356 Chirality : 0.046 0.251 2752 Planarity : 0.004 0.053 3329 Dihedral : 4.718 19.966 2629 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.24 % Favored : 94.33 % Rotamer: Outliers : 2.75 % Allowed : 18.18 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.38 (0.17), residues: 960 loop : -0.43 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP X 35 HIS 0.006 0.001 HIS X 90 PHE 0.026 0.002 PHE W 58 TYR 0.021 0.002 TYR F 87 ARG 0.006 0.001 ARG R 18 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 609) hydrogen bonds : angle 6.28482 ( 1524) SS BOND : bond 0.00555 ( 20) SS BOND : angle 1.78987 ( 40) covalent geometry : bond 0.00694 (18923) covalent geometry : angle 0.67721 (25673) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 200 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 81 ASP cc_start: 0.8626 (t0) cc_final: 0.8205 (t0) REVERT: B 6 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7410 (pp30) REVERT: A 89 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8770 (tp) REVERT: D 6 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.5817 (pp30) REVERT: D 18 ARG cc_start: 0.8216 (tpp80) cc_final: 0.7703 (mmm-85) REVERT: D 27 GLN cc_start: 0.9194 (pm20) cc_final: 0.8754 (pm20) REVERT: C 89 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.9035 (tp) REVERT: F 105 GLU cc_start: 0.6724 (tp30) cc_final: 0.6438 (tp30) REVERT: E 6 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: E 82 MET cc_start: 0.8569 (mmt) cc_final: 0.8176 (mmt) REVERT: M 34 MET cc_start: 0.8508 (mmm) cc_final: 0.8236 (mmt) REVERT: M 71 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.7506 (ttm-80) REVERT: O 28 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.7951 (t) REVERT: Q 72 ASP cc_start: 0.7312 (p0) cc_final: 0.7038 (p0) REVERT: Q 79 TYR cc_start: 0.7969 (m-80) cc_final: 0.7632 (m-80) REVERT: Q 100 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8643 (m-80) REVERT: T 18 ARG cc_start: 0.8480 (tpp80) cc_final: 0.8168 (tpp80) REVERT: S 95 ASP cc_start: 0.7712 (t70) cc_final: 0.7476 (t0) REVERT: V 4 MET cc_start: 0.7856 (mmm) cc_final: 0.7141 (mmm) REVERT: V 50 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8442 (tp-100) REVERT: V 86 TYR cc_start: 0.7614 (m-10) cc_final: 0.7296 (m-10) REVERT: U 61 ASP cc_start: 0.8554 (p0) cc_final: 0.8251 (p0) REVERT: X 21 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.6202 (tp) REVERT: X 50 GLN cc_start: 0.8277 (mm110) cc_final: 0.8076 (mm-40) REVERT: X 86 TYR cc_start: 0.5974 (m-80) cc_final: 0.5575 (m-80) REVERT: X 94 TYR cc_start: 0.7207 (m-80) cc_final: 0.6938 (m-80) REVERT: X 98 PHE cc_start: 0.5115 (OUTLIER) cc_final: 0.4426 (m-80) outliers start: 55 outliers final: 36 residues processed: 243 average time/residue: 0.3581 time to fit residues: 125.6571 Evaluate side-chains 240 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain V residue 88 CYS Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain W residue 35 HIS Chi-restraints excluded: chain W residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 170 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 98 optimal weight: 0.1980 chunk 190 optimal weight: 50.0000 chunk 210 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 194 optimal weight: 40.0000 chunk 227 optimal weight: 5.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.091692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.067194 restraints weight = 51727.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.066092 restraints weight = 48849.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.066314 restraints weight = 55173.104| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 18943 Z= 0.263 Angle : 0.676 9.377 25713 Z= 0.352 Chirality : 0.045 0.295 2752 Planarity : 0.004 0.053 3329 Dihedral : 4.735 19.544 2629 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.51 % Favored : 95.06 % Rotamer: Outliers : 2.50 % Allowed : 18.48 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.32 (0.17), residues: 950 loop : -0.52 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP X 35 HIS 0.006 0.001 HIS C 35 PHE 0.022 0.002 PHE O 29 TYR 0.019 0.002 TYR R 49 ARG 0.011 0.001 ARG R 56 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 609) hydrogen bonds : angle 6.26412 ( 1524) SS BOND : bond 0.00563 ( 20) SS BOND : angle 1.80327 ( 40) covalent geometry : bond 0.00619 (18923) covalent geometry : angle 0.67305 (25673) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 81 ASP cc_start: 0.8676 (t0) cc_final: 0.8255 (t0) REVERT: B 18 ARG cc_start: 0.8842 (ttp80) cc_final: 0.8572 (ttp80) REVERT: A 89 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8772 (tp) REVERT: D 6 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.5786 (pp30) REVERT: D 18 ARG cc_start: 0.8117 (tpp80) cc_final: 0.7689 (mmm-85) REVERT: D 27 GLN cc_start: 0.9203 (pm20) cc_final: 0.8750 (pm20) REVERT: C 89 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9032 (tp) REVERT: F 105 GLU cc_start: 0.6660 (tp30) cc_final: 0.6377 (tp30) REVERT: E 6 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8266 (pm20) REVERT: E 82 MET cc_start: 0.8546 (mmt) cc_final: 0.8196 (mmt) REVERT: M 34 MET cc_start: 0.8539 (mmm) cc_final: 0.8268 (mmt) REVERT: M 71 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.7545 (ttm-80) REVERT: O 28 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7930 (t) REVERT: Q 72 ASP cc_start: 0.7362 (p0) cc_final: 0.6979 (p0) REVERT: Q 79 TYR cc_start: 0.8054 (m-80) cc_final: 0.7665 (m-80) REVERT: Q 100 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8637 (m-80) REVERT: S 95 ASP cc_start: 0.7729 (t70) cc_final: 0.7476 (t0) REVERT: V 4 MET cc_start: 0.7852 (mmm) cc_final: 0.7312 (mmm) REVERT: V 50 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8474 (tp-100) REVERT: V 86 TYR cc_start: 0.7681 (m-10) cc_final: 0.7352 (m-10) REVERT: X 50 GLN cc_start: 0.8278 (mm110) cc_final: 0.8077 (mm-40) REVERT: X 94 TYR cc_start: 0.7361 (m-80) cc_final: 0.7072 (m-80) REVERT: X 98 PHE cc_start: 0.5361 (OUTLIER) cc_final: 0.4648 (m-80) outliers start: 50 outliers final: 37 residues processed: 237 average time/residue: 0.3597 time to fit residues: 123.9431 Evaluate side-chains 239 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain V residue 88 CYS Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain W residue 35 HIS Chi-restraints excluded: chain W residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 226 optimal weight: 30.0000 chunk 122 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 186 optimal weight: 50.0000 chunk 147 optimal weight: 9.9990 chunk 24 optimal weight: 0.0570 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 89 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.090521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066975 restraints weight = 52511.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.067141 restraints weight = 48964.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067411 restraints weight = 51285.740| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18943 Z= 0.131 Angle : 0.624 10.001 25713 Z= 0.319 Chirality : 0.044 0.258 2752 Planarity : 0.004 0.049 3329 Dihedral : 4.403 22.493 2629 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.57 % Favored : 96.01 % Rotamer: Outliers : 2.10 % Allowed : 18.78 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.41 (0.17), residues: 950 loop : -0.44 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 35 HIS 0.010 0.001 HIS C 35 PHE 0.020 0.002 PHE X 71 TYR 0.014 0.001 TYR W 91 ARG 0.008 0.000 ARG R 56 Details of bonding type rmsd hydrogen bonds : bond 0.02897 ( 609) hydrogen bonds : angle 5.91727 ( 1524) SS BOND : bond 0.00431 ( 20) SS BOND : angle 1.40876 ( 40) covalent geometry : bond 0.00313 (18923) covalent geometry : angle 0.62184 (25673) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5471.49 seconds wall clock time: 96 minutes 13.14 seconds (5773.14 seconds total)