Starting phenix.real_space_refine on Sun Aug 24 07:57:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dyw_27784/08_2025/8dyw_27784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dyw_27784/08_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_27784/08_2025/8dyw_27784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dyw_27784/08_2025/8dyw_27784.map" model { file = "/net/cci-nas-00/data/ceres_data/8dyw_27784/08_2025/8dyw_27784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dyw_27784/08_2025/8dyw_27784.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.01, per 1000 atoms: 0.22 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: 1.44 Conformation dependent library (CDL) restraints added in 782.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.69 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: 2.68 Time building geometry restraints manager: 1.94 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.290 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (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 ARG 0.016 0.001 ARG H 105 TYR 0.030 0.001 TYR T 91 PHE 0.022 0.002 PHE X 71 TRP 0.023 0.001 TRP W 36 HIS 0.004 0.001 HIS X 90 Details of bonding type rmsd covalent geometry : bond 0.00568 (18923) covalent geometry : angle 0.84672 (25673) SS BOND : bond 0.00261 ( 20) SS BOND : angle 1.26198 ( 40) hydrogen bonds : bond 0.27452 ( 609) hydrogen bonds : angle 10.65822 ( 1524) *********************** 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 : 0.691 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: 0.1690 time to fit residues: 61.4238 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 : 0.529 ------------------------------------------------------------------------------- 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 216 optimal weight: 40.0000 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- 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 A 1 GLN F 3 GLN R 6 GLN R 38 GLN R 89 GLN T 38 GLN T 89 GLN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.096203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.072839 restraints weight = 50118.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.072441 restraints weight = 51438.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.072791 restraints weight = 50042.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.073304 restraints weight = 28513.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.075789 restraints weight = 24089.507| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 18943 Z= 0.211 Angle : 0.643 8.624 25713 Z= 0.340 Chirality : 0.046 0.241 2752 Planarity : 0.005 0.079 3329 Dihedral : 5.135 59.430 2642 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.91 % Favored : 95.66 % Rotamer: Outliers : 2.55 % Allowed : 14.69 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.37 (0.16), residues: 1160 loop : -0.10 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 105 TYR 0.022 0.002 TYR X 87 PHE 0.022 0.002 PHE H 29 TRP 0.022 0.001 TRP X 35 HIS 0.004 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00496 (18923) covalent geometry : angle 0.64018 (25673) SS BOND : bond 0.00522 ( 20) SS BOND : angle 1.57180 ( 40) hydrogen bonds : bond 0.04173 ( 609) hydrogen bonds : angle 7.32741 ( 1524) *********************** 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 305 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 254 time to evaluate : 0.627 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: 0.8325 (OUTLIER) cc_final: 0.7622 (pp30) REVERT: R 18 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7736 (ttp80) REVERT: Q 100 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8767 (m-80) REVERT: T 81 ASP cc_start: 0.7884 (t0) cc_final: 0.7550 (t0) REVERT: S 95 ASP cc_start: 0.7368 (t70) cc_final: 0.7050 (t0) REVERT: S 111 VAL cc_start: 0.7133 (OUTLIER) cc_final: 0.6789 (p) REVERT: V 50 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8396 (tp40) REVERT: V 86 TYR cc_start: 0.7563 (m-10) cc_final: 0.7277 (m-10) REVERT: U 79 TYR cc_start: 0.7244 (m-80) cc_final: 0.6961 (m-80) REVERT: U 108 LEU cc_start: 0.8585 (tt) cc_final: 0.8164 (mp) REVERT: X 92 ASN cc_start: 0.8672 (t0) cc_final: 0.8263 (m-40) REVERT: X 98 PHE cc_start: 0.4505 (OUTLIER) cc_final: 0.4072 (m-10) outliers start: 51 outliers final: 22 residues processed: 286 average time/residue: 0.1656 time to fit residues: 68.3030 Evaluate side-chains 243 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 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 207 optimal weight: 50.0000 chunk 70 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 214 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 A 31 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN R 6 GLN T 89 GLN ** X 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 82AASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.103185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.075139 restraints weight = 52903.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.075450 restraints weight = 27897.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.075727 restraints weight = 22191.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.076170 restraints weight = 20207.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.076188 restraints weight = 18311.674| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18943 Z= 0.177 Angle : 0.599 8.256 25713 Z= 0.316 Chirality : 0.044 0.219 2752 Planarity : 0.004 0.057 3329 Dihedral : 4.549 17.676 2629 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.35 % Favored : 96.22 % Rotamer: Outliers : 2.90 % Allowed : 15.03 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.32 (0.16), residues: 1120 loop : -0.22 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 56 TYR 0.015 0.001 TYR X 87 PHE 0.019 0.002 PHE O 29 TRP 0.012 0.001 TRP X 35 HIS 0.004 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00416 (18923) covalent geometry : angle 0.59684 (25673) SS BOND : bond 0.00523 ( 20) SS BOND : angle 1.46035 ( 40) hydrogen bonds : bond 0.03613 ( 609) hydrogen bonds : angle 6.77916 ( 1524) *********************** 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 303 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 245 time to evaluate : 0.785 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: 0.8569 (t0) cc_final: 0.7979 (m-30) REVERT: B 78 LEU cc_start: 0.9194 (tp) cc_final: 0.8815 (tt) REVERT: A 16 ARG cc_start: 0.6927 (ttp80) cc_final: 0.6610 (ttp80) REVERT: D 27 GLN cc_start: 0.9068 (pm20) cc_final: 0.8600 (pm20) REVERT: C 110 ILE cc_start: 0.9116 (mm) cc_final: 0.8870 (tp) REVERT: R 18 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7560 (ttp80) REVERT: Q 100 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8896 (m-80) REVERT: S 83 ARG cc_start: 0.8396 (ptp-170) cc_final: 0.8016 (ptp90) REVERT: S 85 GLU cc_start: 0.8580 (mp0) cc_final: 0.8152 (mp0) REVERT: S 95 ASP cc_start: 0.7278 (t70) cc_final: 0.6972 (t0) REVERT: V 50 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8573 (tp40) REVERT: V 86 TYR cc_start: 0.8045 (m-10) cc_final: 0.7644 (m-10) REVERT: U 82 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7571 (ttm) REVERT: U 108 LEU cc_start: 0.8913 (tt) cc_final: 0.8478 (mp) REVERT: X 87 TYR cc_start: 0.6183 (m-80) cc_final: 0.5830 (m-80) REVERT: X 92 ASN cc_start: 0.8782 (t0) cc_final: 0.8314 (m-40) REVERT: X 98 PHE cc_start: 0.5058 (OUTLIER) cc_final: 0.4428 (m-10) outliers start: 58 outliers final: 27 residues processed: 288 average time/residue: 0.1787 time to fit residues: 72.9083 Evaluate side-chains 248 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain B residue 90 HIS 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 78 LEU 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 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 58 VAL 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 U residue 82 MET 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 87 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 chunk 178 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 ASN L 3 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 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** ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN R 6 GLN T 89 GLN V 38 GLN ** X 90 HIS ** 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 = 0.3751 r_free = 0.3751 target = 0.102332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.078908 restraints weight = 53518.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.079040 restraints weight = 52041.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079443 restraints weight = 50879.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080509 restraints weight = 28089.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.081368 restraints weight = 22493.701| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 18943 Z= 0.253 Angle : 0.628 8.715 25713 Z= 0.333 Chirality : 0.045 0.209 2752 Planarity : 0.004 0.055 3329 Dihedral : 4.693 19.858 2629 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.47 % Favored : 95.10 % Rotamer: Outliers : 3.50 % Allowed : 15.08 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.38 (0.16), residues: 1100 loop : -0.41 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 105 TYR 0.019 0.002 TYR T 49 PHE 0.023 0.002 PHE O 29 TRP 0.020 0.002 TRP X 35 HIS 0.005 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00591 (18923) covalent geometry : angle 0.62487 (25673) SS BOND : bond 0.00606 ( 20) SS BOND : angle 1.69569 ( 40) hydrogen bonds : bond 0.03497 ( 609) hydrogen bonds : angle 6.61724 ( 1524) *********************** 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 293 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 223 time to evaluate : 0.524 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: 0.8658 (t0) cc_final: 0.8402 (t0) REVERT: H 91 TYR cc_start: 0.8412 (m-80) cc_final: 0.8190 (m-80) REVERT: B 6 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7642 (pp30) REVERT: B 78 LEU cc_start: 0.9288 (tp) cc_final: 0.8902 (tt) REVERT: D 6 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.5955 (pp30) REVERT: D 18 ARG cc_start: 0.7729 (tpp80) cc_final: 0.7502 (mmm-85) REVERT: D 27 GLN cc_start: 0.9123 (pm20) cc_final: 0.8671 (pm20) REVERT: C 71 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.7443 (ttm-80) REVERT: C 110 ILE cc_start: 0.9157 (mm) cc_final: 0.8949 (tp) REVERT: E 6 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: R 18 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7800 (ttp80) REVERT: Q 100 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8746 (m-80) REVERT: T 33 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7737 (mp) REVERT: T 89 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8312 (tm-30) REVERT: S 82 MET cc_start: 0.8096 (mmm) cc_final: 0.7711 (mmm) REVERT: S 95 ASP cc_start: 0.7454 (t70) cc_final: 0.7231 (t0) REVERT: V 86 TYR cc_start: 0.7423 (m-10) cc_final: 0.7104 (m-10) REVERT: U 108 LEU cc_start: 0.8618 (tt) cc_final: 0.8324 (mp) REVERT: X 92 ASN cc_start: 0.8411 (t0) cc_final: 0.8090 (m-40) REVERT: X 94 TYR cc_start: 0.6790 (m-80) cc_final: 0.6495 (m-80) REVERT: X 98 PHE cc_start: 0.4434 (OUTLIER) cc_final: 0.3608 (m-10) REVERT: W 6 GLU cc_start: 0.2973 (mp0) cc_final: 0.1397 (tp30) outliers start: 70 outliers final: 35 residues processed: 272 average time/residue: 0.1658 time to fit residues: 64.5796 Evaluate side-chains 251 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 90 HIS 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 11 VAL Chi-restraints excluded: chain C residue 71 ARG 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 39 LYS 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 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 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 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 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 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 98 PHE 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 218 optimal weight: 20.0000 chunk 220 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 208 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 203 optimal weight: 40.0000 chunk 20 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 6 GLN F 89 GLN R 6 GLN T 89 GLN ** X 90 HIS ** 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 = 0.3768 r_free = 0.3768 target = 0.103721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.079891 restraints weight = 52591.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079459 restraints weight = 50702.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.079747 restraints weight = 55408.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.081482 restraints weight = 29210.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.081595 restraints weight = 21925.906| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18943 Z= 0.177 Angle : 0.590 8.845 25713 Z= 0.311 Chirality : 0.044 0.178 2752 Planarity : 0.004 0.051 3329 Dihedral : 4.531 18.590 2629 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.82 % Favored : 95.75 % Rotamer: Outliers : 3.50 % Allowed : 15.78 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.51 (0.17), residues: 1020 loop : -0.31 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 56 TYR 0.013 0.001 TYR T 49 PHE 0.015 0.002 PHE O 29 TRP 0.013 0.001 TRP X 35 HIS 0.005 0.001 HIS T 90 Details of bonding type rmsd covalent geometry : bond 0.00414 (18923) covalent geometry : angle 0.58751 (25673) SS BOND : bond 0.00514 ( 20) SS BOND : angle 1.42824 ( 40) hydrogen bonds : bond 0.03199 ( 609) hydrogen bonds : angle 6.33509 ( 1524) *********************** 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 300 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 230 time to evaluate : 0.595 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: L 81 ASP cc_start: 0.8692 (t0) cc_final: 0.8442 (t0) REVERT: H 91 TYR cc_start: 0.8355 (m-80) cc_final: 0.8039 (m-80) REVERT: B 78 LEU cc_start: 0.9251 (tp) cc_final: 0.8696 (tt) REVERT: D 6 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.5850 (pp30) REVERT: D 27 GLN cc_start: 0.9140 (pm20) cc_final: 0.8713 (pm20) REVERT: C 71 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8795 (ptm160) REVERT: F 89 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8469 (tm-30) REVERT: O 28 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7956 (t) REVERT: R 18 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7724 (ttp80) REVERT: Q 72 ASP cc_start: 0.7346 (p0) cc_final: 0.7089 (p0) REVERT: Q 79 TYR cc_start: 0.8055 (m-80) cc_final: 0.7681 (m-80) REVERT: Q 100 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8704 (m-80) REVERT: T 33 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7692 (mp) REVERT: S 82 MET cc_start: 0.7999 (mmm) cc_final: 0.7766 (mmm) REVERT: S 95 ASP cc_start: 0.7335 (t70) cc_final: 0.7040 (t0) REVERT: V 4 MET cc_start: 0.7961 (tpp) cc_final: 0.7690 (tpp) REVERT: V 50 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8583 (tp-100) REVERT: V 86 TYR cc_start: 0.7526 (m-10) cc_final: 0.7212 (m-10) REVERT: U 108 LEU cc_start: 0.8724 (tt) cc_final: 0.8439 (mp) REVERT: X 92 ASN cc_start: 0.8440 (t0) cc_final: 0.8089 (m-40) REVERT: X 94 TYR cc_start: 0.6935 (m-80) cc_final: 0.6597 (m-80) REVERT: X 98 PHE cc_start: 0.5023 (OUTLIER) cc_final: 0.4314 (m-10) REVERT: W 6 GLU cc_start: 0.3716 (mp0) cc_final: 0.2153 (tp30) outliers start: 70 outliers final: 39 residues processed: 282 average time/residue: 0.1497 time to fit residues: 60.9281 Evaluate side-chains 258 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 90 HIS 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 B residue 90 HIS Chi-restraints excluded: chain B residue 107 LYS 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 11 VAL Chi-restraints excluded: chain C residue 71 ARG 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 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 39 LYS Chi-restraints excluded: chain N residue 58 VAL 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 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 100 PHE Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 58 VAL 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 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 82 MET 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 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 139 optimal weight: 7.9990 chunk 189 optimal weight: 30.0000 chunk 80 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 199 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN L 89 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 89 GLN T 89 GLN ** X 90 HIS ** 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 = 0.3751 r_free = 0.3751 target = 0.102743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.074558 restraints weight = 52842.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.074667 restraints weight = 33714.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.075177 restraints weight = 24640.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.075604 restraints weight = 22847.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.075701 restraints weight = 20417.072| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 18943 Z= 0.236 Angle : 0.624 9.035 25713 Z= 0.329 Chirality : 0.045 0.326 2752 Planarity : 0.004 0.051 3329 Dihedral : 4.630 20.387 2629 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.55 % Favored : 95.02 % Rotamer: Outliers : 3.90 % Allowed : 15.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.46 (0.17), residues: 1020 loop : -0.38 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 18 TYR 0.022 0.002 TYR S 91 PHE 0.022 0.002 PHE X 71 TRP 0.013 0.001 TRP E 47 HIS 0.009 0.001 HIS F 90 Details of bonding type rmsd covalent geometry : bond 0.00556 (18923) covalent geometry : angle 0.62143 (25673) SS BOND : bond 0.00555 ( 20) SS BOND : angle 1.59369 ( 40) hydrogen bonds : bond 0.03284 ( 609) hydrogen bonds : angle 6.32672 ( 1524) *********************** 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 299 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 221 time to evaluate : 0.734 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: 0.8807 (t0) cc_final: 0.8519 (t0) REVERT: H 91 TYR cc_start: 0.8497 (m-80) cc_final: 0.8167 (m-80) REVERT: A 89 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8818 (tp) REVERT: D 6 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.5850 (pp30) REVERT: D 18 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.8085 (mmm-85) REVERT: D 27 GLN cc_start: 0.9140 (pm20) cc_final: 0.8712 (pm20) REVERT: C 71 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.7411 (ttm-80) REVERT: F 2 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.7899 (tt) REVERT: E 6 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: R 18 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7789 (ttp80) REVERT: Q 72 ASP cc_start: 0.7232 (p0) cc_final: 0.6998 (p0) REVERT: Q 79 TYR cc_start: 0.7980 (m-80) cc_final: 0.7658 (m-80) REVERT: Q 100 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8892 (m-80) REVERT: T 33 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7587 (mp) REVERT: T 89 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: S 95 ASP cc_start: 0.7453 (t70) cc_final: 0.7181 (t0) REVERT: V 2 ILE cc_start: 0.8237 (mp) cc_final: 0.7873 (mp) REVERT: V 4 MET cc_start: 0.8154 (tpp) cc_final: 0.7813 (tpp) REVERT: V 50 GLN cc_start: 0.9257 (mm-40) cc_final: 0.8785 (tp-100) REVERT: V 86 TYR cc_start: 0.7910 (m-10) cc_final: 0.7559 (m-10) REVERT: U 108 LEU cc_start: 0.8938 (tt) cc_final: 0.8591 (mp) REVERT: X 87 TYR cc_start: 0.6046 (m-80) cc_final: 0.5813 (m-80) REVERT: X 92 ASN cc_start: 0.8701 (t0) cc_final: 0.8226 (m-40) REVERT: X 94 TYR cc_start: 0.7465 (m-80) cc_final: 0.7012 (m-80) REVERT: X 98 PHE cc_start: 0.5153 (OUTLIER) cc_final: 0.4487 (m-10) REVERT: W 6 GLU cc_start: 0.4039 (mp0) cc_final: 0.2401 (tp30) REVERT: W 31 ASN cc_start: 0.5891 (p0) cc_final: 0.5450 (p0) outliers start: 78 outliers final: 48 residues processed: 277 average time/residue: 0.1524 time to fit residues: 60.9919 Evaluate side-chains 266 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 L residue 106 ILE Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain B residue 11 LEU 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 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 C residue 71 ARG 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 E residue 100 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 58 VAL 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 47 LEU Chi-restraints excluded: chain P residue 90 HIS 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 50 VAL 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 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 S residue 105 ARG 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 82 MET 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 35 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 205 optimal weight: 40.0000 chunk 106 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 207 optimal weight: 50.0000 chunk 124 optimal weight: 6.9990 chunk 218 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 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** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN T 89 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 HIS ** 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 = 0.3741 r_free = 0.3741 target = 0.102260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.074025 restraints weight = 53267.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.073880 restraints weight = 36328.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.074478 restraints weight = 26127.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.074926 restraints weight = 23770.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.075268 restraints weight = 21600.344| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 18943 Z= 0.261 Angle : 0.645 10.510 25713 Z= 0.339 Chirality : 0.045 0.274 2752 Planarity : 0.004 0.051 3329 Dihedral : 4.732 21.205 2629 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.73 % Favored : 94.85 % Rotamer: Outliers : 3.70 % Allowed : 17.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.45 (0.17), residues: 1010 loop : -0.48 (0.18), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 56 TYR 0.018 0.002 TYR T 49 PHE 0.019 0.002 PHE O 29 TRP 0.023 0.001 TRP X 35 HIS 0.006 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00610 (18923) covalent geometry : angle 0.64223 (25673) SS BOND : bond 0.00558 ( 20) SS BOND : angle 1.61608 ( 40) hydrogen bonds : bond 0.03320 ( 609) hydrogen bonds : angle 6.38808 ( 1524) *********************** 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 290 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 216 time to evaluate : 0.648 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: 0.8822 (t0) cc_final: 0.8517 (t0) REVERT: H 91 TYR cc_start: 0.8509 (m-80) cc_final: 0.8112 (m-80) REVERT: A 89 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8817 (tp) REVERT: D 6 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.5876 (pp30) REVERT: D 27 GLN cc_start: 0.9141 (pm20) cc_final: 0.8713 (pm20) REVERT: C 71 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.7345 (ttm-80) REVERT: C 89 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9096 (tp) REVERT: F 105 GLU cc_start: 0.6635 (tp30) cc_final: 0.6323 (tp30) REVERT: E 6 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8393 (pm20) REVERT: E 28 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7995 (p) REVERT: E 95 ASP cc_start: 0.9087 (t0) cc_final: 0.8838 (t0) REVERT: M 71 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.7564 (ttm-80) REVERT: O 28 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8133 (t) REVERT: R 18 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7804 (ttp80) REVERT: Q 72 ASP cc_start: 0.7315 (p0) cc_final: 0.7080 (p0) REVERT: Q 79 TYR cc_start: 0.7979 (m-80) cc_final: 0.7689 (m-80) REVERT: Q 100 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8818 (m-80) REVERT: T 18 ARG cc_start: 0.8551 (tpp80) cc_final: 0.8158 (tpp80) REVERT: T 33 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7663 (mp) REVERT: T 89 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8041 (tm-30) REVERT: S 29 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8244 (t80) REVERT: S 95 ASP cc_start: 0.7475 (t70) cc_final: 0.7218 (t0) REVERT: V 2 ILE cc_start: 0.8241 (mp) cc_final: 0.7885 (mp) REVERT: V 4 MET cc_start: 0.8164 (tpp) cc_final: 0.7834 (tpp) REVERT: V 27 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: V 50 GLN cc_start: 0.9261 (mm-40) cc_final: 0.8708 (tp-100) REVERT: U 61 ASP cc_start: 0.8438 (p0) cc_final: 0.8027 (p0) REVERT: U 108 LEU cc_start: 0.8944 (tt) cc_final: 0.8625 (mp) REVERT: X 87 TYR cc_start: 0.6011 (m-80) cc_final: 0.5732 (m-80) REVERT: X 94 TYR cc_start: 0.7641 (m-80) cc_final: 0.7215 (m-80) REVERT: X 98 PHE cc_start: 0.5265 (OUTLIER) cc_final: 0.4503 (m-80) REVERT: W 6 GLU cc_start: 0.3761 (mp0) cc_final: 0.2138 (tp30) outliers start: 74 outliers final: 50 residues processed: 270 average time/residue: 0.1624 time to fit residues: 62.6561 Evaluate side-chains 270 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 206 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 L residue 106 ILE Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 90 HIS 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 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 C residue 71 ARG Chi-restraints excluded: chain C residue 89 ILE 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 28 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 72 THR 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 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 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 50 VAL 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 89 GLN 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 29 PHE Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain V residue 27 GLN 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 X residue 104 LEU 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 180 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 167 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 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 T 89 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 HIS ** 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 = 0.3733 r_free = 0.3733 target = 0.089637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.062792 restraints weight = 52573.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.062193 restraints weight = 29952.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062400 restraints weight = 26882.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.062785 restraints weight = 23307.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.062863 restraints weight = 21458.573| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18943 Z= 0.155 Angle : 0.615 9.299 25713 Z= 0.319 Chirality : 0.044 0.252 2752 Planarity : 0.004 0.049 3329 Dihedral : 4.494 20.990 2629 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.87 % Favored : 95.70 % Rotamer: Outliers : 3.45 % Allowed : 17.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.54 (0.17), residues: 1000 loop : -0.35 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 56 TYR 0.016 0.001 TYR S 91 PHE 0.022 0.002 PHE X 71 TRP 0.019 0.001 TRP X 35 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00368 (18923) covalent geometry : angle 0.61303 (25673) SS BOND : bond 0.00459 ( 20) SS BOND : angle 1.29728 ( 40) hydrogen bonds : bond 0.03035 ( 609) hydrogen bonds : angle 6.13999 ( 1524) *********************** 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 288 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 219 time to evaluate : 0.713 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: 0.8908 (t0) cc_final: 0.8636 (t0) REVERT: H 91 TYR cc_start: 0.8332 (m-80) cc_final: 0.7898 (m-80) REVERT: B 18 ARG cc_start: 0.8901 (ttp80) cc_final: 0.8663 (ttp80) REVERT: D 6 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.5671 (pp30) REVERT: D 27 GLN cc_start: 0.9148 (pm20) cc_final: 0.8721 (pm20) REVERT: C 71 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8761 (ptm160) REVERT: C 89 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9067 (tp) REVERT: F 3 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7639 (pp30) REVERT: F 105 GLU cc_start: 0.6703 (tp30) cc_final: 0.6370 (tp30) REVERT: E 6 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8380 (pm20) REVERT: E 28 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7858 (p) REVERT: M 71 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7542 (ttm-80) REVERT: M 79 TYR cc_start: 0.8710 (m-80) cc_final: 0.8283 (m-80) REVERT: O 28 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7928 (t) REVERT: R 18 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7772 (ttp80) REVERT: Q 72 ASP cc_start: 0.7268 (p0) cc_final: 0.7045 (p0) REVERT: Q 79 TYR cc_start: 0.8008 (m-80) cc_final: 0.7755 (m-80) REVERT: Q 100 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8832 (m-80) REVERT: T 33 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7534 (mp) REVERT: T 89 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: S 29 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8186 (t80) REVERT: S 71 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7371 (ttm170) REVERT: S 95 ASP cc_start: 0.7401 (t70) cc_final: 0.7125 (t0) REVERT: V 2 ILE cc_start: 0.8217 (mp) cc_final: 0.7883 (mp) REVERT: V 4 MET cc_start: 0.8112 (tpp) cc_final: 0.7777 (tpp) REVERT: V 50 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8683 (tp-100) REVERT: U 13 GLN cc_start: 0.8915 (mp10) cc_final: 0.8522 (mm-40) REVERT: U 108 LEU cc_start: 0.8932 (tt) cc_final: 0.8646 (mp) REVERT: X 86 TYR cc_start: 0.6407 (m-80) cc_final: 0.6205 (m-80) REVERT: X 87 TYR cc_start: 0.6377 (m-80) cc_final: 0.6038 (m-80) REVERT: X 94 TYR cc_start: 0.7739 (m-80) cc_final: 0.7359 (m-80) REVERT: X 98 PHE cc_start: 0.5515 (OUTLIER) cc_final: 0.4960 (m-10) REVERT: W 6 GLU cc_start: 0.3597 (mp0) cc_final: 0.1937 (tp30) outliers start: 69 outliers final: 45 residues processed: 269 average time/residue: 0.1596 time to fit residues: 61.7284 Evaluate side-chains 267 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 208 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain B residue 11 LEU 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 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 71 ARG Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 3 GLN 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 28 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 72 THR 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 83 ARG 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 89 GLN Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 29 PHE Chi-restraints excluded: chain S residue 71 ARG Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain V residue 27 GLN 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 X residue 104 LEU Chi-restraints excluded: chain W residue 35 HIS Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain W residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 203 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 107 optimal weight: 0.0970 chunk 182 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 N 6 GLN T 89 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 HIS ** 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 = 0.3755 r_free = 0.3755 target = 0.090845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.066138 restraints weight = 52701.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.065753 restraints weight = 47908.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066447 restraints weight = 48238.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.067305 restraints weight = 27972.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067914 restraints weight = 23677.920| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18943 Z= 0.120 Angle : 0.603 11.239 25713 Z= 0.311 Chirality : 0.044 0.243 2752 Planarity : 0.004 0.049 3329 Dihedral : 4.357 24.542 2629 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.52 % Favored : 96.05 % Rotamer: Outliers : 3.15 % Allowed : 17.93 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.57 (0.17), residues: 940 loop : -0.43 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 56 TYR 0.012 0.001 TYR X 87 PHE 0.021 0.001 PHE S 67 TRP 0.018 0.001 TRP X 35 HIS 0.006 0.001 HIS W 35 Details of bonding type rmsd covalent geometry : bond 0.00283 (18923) covalent geometry : angle 0.60165 (25673) SS BOND : bond 0.00443 ( 20) SS BOND : angle 1.28257 ( 40) hydrogen bonds : bond 0.02911 ( 609) hydrogen bonds : angle 5.93443 ( 1524) *********************** 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 295 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 232 time to evaluate : 0.560 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: 0.8826 (t0) cc_final: 0.8592 (t0) REVERT: H 59 TYR cc_start: 0.9069 (m-80) cc_final: 0.8732 (m-80) REVERT: H 91 TYR cc_start: 0.8183 (m-80) cc_final: 0.7793 (m-80) REVERT: D 6 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.5769 (pp30) REVERT: D 27 GLN cc_start: 0.9147 (pm20) cc_final: 0.8724 (pm20) REVERT: C 71 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8724 (ptm160) REVERT: C 89 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9104 (tp) REVERT: F 105 GLU cc_start: 0.6618 (tp30) cc_final: 0.6319 (tp30) REVERT: E 28 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7811 (p) REVERT: M 71 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7458 (ttm-80) REVERT: M 79 TYR cc_start: 0.8669 (m-80) cc_final: 0.8316 (m-80) REVERT: O 28 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7843 (t) REVERT: R 18 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7820 (ttp80) REVERT: Q 37 VAL cc_start: 0.9152 (t) cc_final: 0.8894 (m) REVERT: Q 79 TYR cc_start: 0.8021 (m-80) cc_final: 0.7761 (m-80) REVERT: Q 100 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8596 (m-80) REVERT: T 33 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7548 (mp) REVERT: T 89 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: S 71 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8210 (ttm170) REVERT: S 95 ASP cc_start: 0.7413 (t70) cc_final: 0.7160 (t0) REVERT: V 2 ILE cc_start: 0.8331 (mp) cc_final: 0.8029 (mp) REVERT: V 4 MET cc_start: 0.8109 (tpp) cc_final: 0.7827 (tpp) REVERT: V 27 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: V 50 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8480 (tp-100) REVERT: X 21 ILE cc_start: 0.6420 (OUTLIER) cc_final: 0.6154 (tp) REVERT: X 87 TYR cc_start: 0.5707 (m-80) cc_final: 0.5408 (m-80) REVERT: X 98 PHE cc_start: 0.5134 (OUTLIER) cc_final: 0.4821 (m-80) REVERT: W 6 GLU cc_start: 0.3006 (mp0) cc_final: 0.1622 (tp30) REVERT: W 105 ARG cc_start: 0.6885 (mmp80) cc_final: 0.6546 (mmp80) outliers start: 63 outliers final: 41 residues processed: 281 average time/residue: 0.1592 time to fit residues: 64.3985 Evaluate side-chains 265 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 211 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 84 ASP 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 B residue 107 LYS Chi-restraints excluded: chain A residue 100 ASP 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 71 ARG Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain F residue 3 GLN 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 E residue 101 ASP Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 39 LYS 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 83 ARG 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 89 GLN Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 71 ARG Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain V residue 27 GLN 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 X residue 104 LEU Chi-restraints excluded: chain W residue 35 HIS Chi-restraints excluded: chain W residue 82 LEU 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 74 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 144 optimal weight: 0.0470 chunk 142 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 204 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 207 optimal weight: 50.0000 overall best weight: 2.5084 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 82AASN ** X 90 HIS ** 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 = 0.3745 r_free = 0.3745 target = 0.090294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063228 restraints weight = 52295.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.062235 restraints weight = 34184.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.062816 restraints weight = 26666.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.063169 restraints weight = 23682.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.063306 restraints weight = 21100.389| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18943 Z= 0.155 Angle : 0.641 14.361 25713 Z= 0.329 Chirality : 0.044 0.267 2752 Planarity : 0.004 0.050 3329 Dihedral : 4.364 24.450 2629 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.74 % Favored : 95.83 % Rotamer: Outliers : 2.90 % Allowed : 18.13 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.47 (0.17), residues: 950 loop : -0.41 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 56 TYR 0.020 0.001 TYR C 79 PHE 0.021 0.002 PHE S 67 TRP 0.018 0.001 TRP X 35 HIS 0.006 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00369 (18923) covalent geometry : angle 0.63853 (25673) SS BOND : bond 0.00449 ( 20) SS BOND : angle 1.44336 ( 40) hydrogen bonds : bond 0.02901 ( 609) hydrogen bonds : angle 5.89963 ( 1524) ********************** 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 274 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 0.685 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: 0.8898 (t0) cc_final: 0.8627 (t0) REVERT: H 91 TYR cc_start: 0.8168 (m-80) cc_final: 0.7782 (m-80) REVERT: B 18 ARG cc_start: 0.8812 (ttp80) cc_final: 0.8567 (ttp80) REVERT: D 6 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.5724 (pp30) REVERT: D 27 GLN cc_start: 0.9133 (pm20) cc_final: 0.8711 (pm20) REVERT: C 89 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.9056 (tp) REVERT: F 105 GLU cc_start: 0.6616 (tp30) cc_final: 0.6295 (tp30) REVERT: E 6 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: E 28 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7812 (p) REVERT: E 82 MET cc_start: 0.8408 (mmt) cc_final: 0.7955 (mmt) REVERT: M 71 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7496 (ttm-80) REVERT: M 79 TYR cc_start: 0.8655 (m-80) cc_final: 0.8310 (m-80) REVERT: O 28 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7917 (t) REVERT: R 18 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7752 (ttp80) REVERT: Q 79 TYR cc_start: 0.8112 (m-80) cc_final: 0.7782 (m-80) REVERT: Q 100 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8862 (m-80) REVERT: T 33 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7394 (mp) REVERT: S 95 ASP cc_start: 0.7436 (t70) cc_final: 0.7160 (t0) REVERT: V 2 ILE cc_start: 0.8185 (mp) cc_final: 0.7858 (mp) REVERT: V 4 MET cc_start: 0.8090 (tpp) cc_final: 0.7691 (tpp) REVERT: V 27 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: V 50 GLN cc_start: 0.9336 (mm-40) cc_final: 0.8844 (tp-100) REVERT: X 21 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6309 (tp) REVERT: X 87 TYR cc_start: 0.6398 (m-80) cc_final: 0.6080 (m-80) REVERT: X 98 PHE cc_start: 0.5575 (OUTLIER) cc_final: 0.5246 (m-80) outliers start: 58 outliers final: 41 residues processed: 260 average time/residue: 0.1642 time to fit residues: 61.4593 Evaluate side-chains 262 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 B residue 107 LYS Chi-restraints excluded: chain A residue 100 ASP 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 E residue 6 GLU 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 E residue 101 ASP Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 39 LYS 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 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 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 83 ARG 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 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 V residue 27 GLN 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 X residue 104 LEU Chi-restraints excluded: chain W residue 35 HIS Chi-restraints excluded: chain W residue 82 LEU 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 0 optimal weight: 20.0000 chunk 225 optimal weight: 40.0000 chunk 89 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 79 optimal weight: 0.0570 chunk 82 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 overall best weight: 2.5304 ------------------------------------------------------------------------------- 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 ** 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 ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 HIS ** 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 = 0.3746 r_free = 0.3746 target = 0.090428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.066596 restraints weight = 52819.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.067118 restraints weight = 49765.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.067363 restraints weight = 48877.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.068352 restraints weight = 27290.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.068863 restraints weight = 22361.689| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18943 Z= 0.154 Angle : 0.630 13.770 25713 Z= 0.324 Chirality : 0.044 0.259 2752 Planarity : 0.004 0.060 3329 Dihedral : 4.375 24.377 2629 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.91 % Favored : 95.66 % Rotamer: Outliers : 2.95 % Allowed : 18.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.46 (0.17), residues: 950 loop : -0.41 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 56 TYR 0.017 0.001 TYR C 79 PHE 0.020 0.002 PHE S 67 TRP 0.018 0.001 TRP X 35 HIS 0.006 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00367 (18923) covalent geometry : angle 0.62741 (25673) SS BOND : bond 0.00451 ( 20) SS BOND : angle 1.46191 ( 40) hydrogen bonds : bond 0.02911 ( 609) hydrogen bonds : angle 5.85600 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2629.85 seconds wall clock time: 46 minutes 35.95 seconds (2795.95 seconds total)