Starting phenix.real_space_refine on Wed Jun 11 05:41:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dz3_27787/06_2025/8dz3_27787.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dz3_27787/06_2025/8dz3_27787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dz3_27787/06_2025/8dz3_27787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dz3_27787/06_2025/8dz3_27787.map" model { file = "/net/cci-nas-00/data/ceres_data/8dz3_27787/06_2025/8dz3_27787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dz3_27787/06_2025/8dz3_27787.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.055 sd= 0.218 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 63 5.16 5 C 7994 2.51 5 N 2205 2.21 5 O 2464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12726 Number of models: 1 Model: "" Number of chains: 15 Chain: "I" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 392 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 14, 'TRANS': 41} Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "A" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "B" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "D" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "E" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "M" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "O" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "Q" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "R" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 7.74, per 1000 atoms: 0.61 Number of scatterers: 12726 At special positions: 0 Unit cell: (105.678, 119.016, 132.354, 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 63 16.00 O 2464 8.00 N 2205 7.00 C 7994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 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: 2.76 Conformation dependent library (CDL) restraints added in 1.6 seconds 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2982 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 42 sheets defined 5.7% alpha, 51.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.558A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.920A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.143A pdb=" N PHE B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.527A pdb=" N THR E 31 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.927A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.538A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.517A pdb=" N TYR O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 removed outlier: 4.049A pdb=" N PHE P 83 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.570A pdb=" N THR Q 31 " --> pdb=" O SER Q 28 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR Q 32 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 28 through 32' Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.893A pdb=" N PHE R 83 " --> pdb=" O SER R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.834A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.612A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA H 100F" --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 6 removed outlier: 5.460A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N VAL L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.207A pdb=" N SER L 65 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.598A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.523A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.935A pdb=" N MET A 34 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.367A pdb=" N ILE A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 5 through 6 removed outlier: 5.963A pdb=" N THR B 69 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N GLN B 27 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N SER B 67 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 11.265A pdb=" N VAL B 29 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N SER B 65 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.621A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.647A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.468A pdb=" N GLY C 10 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET C 34 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.468A pdb=" N GLY C 10 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 100F" --> pdb=" O GLY C 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 5 through 6 removed outlier: 11.913A pdb=" N CYS D 23 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 10.911A pdb=" N THR D 74 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N ALA D 25 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 11.513A pdb=" N THR D 72 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N GLN D 27 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU D 70 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY D 68 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.553A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.774A pdb=" N MET E 34 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.575A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA E 100F" --> pdb=" O GLY E 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 5 through 6 removed outlier: 6.031A pdb=" N THR F 69 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N GLN F 27 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 9.819A pdb=" N SER F 67 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N VAL F 29 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N SER F 65 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.673A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.572A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.200A pdb=" N GLY M 10 " --> pdb=" O ILE M 110 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET M 34 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.200A pdb=" N GLY M 10 " --> pdb=" O ILE M 110 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 5 through 6 removed outlier: 5.308A pdb=" N THR N 69 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N GLN N 27 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N SER N 67 " --> pdb=" O GLN N 27 " (cutoff:3.500A) removed outlier: 11.455A pdb=" N VAL N 29 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N SER N 65 " --> pdb=" O VAL N 29 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.570A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.509A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.511A pdb=" N THR O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.792A pdb=" N MET O 34 " --> pdb=" O LEU O 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.634A pdb=" N CYS O 92 " --> pdb=" O TRP O 103 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TRP O 103 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA O 100F" --> pdb=" O GLY O 96 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 5 through 6 removed outlier: 5.839A pdb=" N THR P 69 " --> pdb=" O ALA P 25 " (cutoff:3.500A) removed outlier: 10.589A pdb=" N GLN P 27 " --> pdb=" O SER P 67 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N SER P 67 " --> pdb=" O GLN P 27 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N VAL P 29 " --> pdb=" O SER P 65 " (cutoff:3.500A) removed outlier: 11.126A pdb=" N SER P 65 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.670A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.351A pdb=" N GLY Q 10 " --> pdb=" O ILE Q 110 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET Q 34 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.351A pdb=" N GLY Q 10 " --> pdb=" O ILE Q 110 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS Q 92 " --> pdb=" O TRP Q 103 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP Q 103 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG Q 94 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA Q 100F" --> pdb=" O GLY Q 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 5 through 6 removed outlier: 11.947A pdb=" N CYS R 23 " --> pdb=" O THR R 74 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N THR R 74 " --> pdb=" O CYS R 23 " (cutoff:3.500A) removed outlier: 11.675A pdb=" N ALA R 25 " --> pdb=" O THR R 72 " (cutoff:3.500A) removed outlier: 11.424A pdb=" N THR R 72 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 10.783A pdb=" N GLN R 27 " --> pdb=" O GLU R 70 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU R 70 " --> pdb=" O GLN R 27 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.792A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.535A pdb=" N THR R 97 " --> pdb=" O GLN R 90 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.15 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4129 1.34 - 1.46: 3277 1.46 - 1.58: 5529 1.58 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 13033 Sorted by residual: bond pdb=" CB GLU N 105 " pdb=" CG GLU N 105 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" C ARG E 64 " pdb=" N GLY E 65 " ideal model delta sigma weight residual 1.333 1.319 0.014 1.36e-02 5.41e+03 9.96e-01 bond pdb=" C SER N 7 " pdb=" N PRO N 8 " ideal model delta sigma weight residual 1.332 1.345 -0.013 1.34e-02 5.57e+03 9.88e-01 bond pdb=" C ARG O 64 " pdb=" N GLY O 65 " ideal model delta sigma weight residual 1.333 1.319 0.013 1.36e-02 5.41e+03 9.59e-01 bond pdb=" CG GLU N 105 " pdb=" CD GLU N 105 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.60e-01 ... (remaining 13028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 17459 2.08 - 4.16: 191 4.16 - 6.24: 20 6.24 - 8.32: 1 8.32 - 10.40: 1 Bond angle restraints: 17672 Sorted by residual: angle pdb=" CA LEU N 11 " pdb=" CB LEU N 11 " pdb=" CG LEU N 11 " ideal model delta sigma weight residual 116.30 126.70 -10.40 3.50e+00 8.16e-02 8.83e+00 angle pdb=" C PHE M 100G" pdb=" N ASP M 101 " pdb=" CA ASP M 101 " ideal model delta sigma weight residual 120.44 124.10 -3.66 1.30e+00 5.92e-01 7.94e+00 angle pdb=" C GLY N 50 " pdb=" N ALA N 51 " pdb=" CA ALA N 51 " ideal model delta sigma weight residual 121.54 126.84 -5.30 1.91e+00 2.74e-01 7.71e+00 angle pdb=" C THR M 100C" pdb=" N GLY M 100D" pdb=" CA GLY M 100D" ideal model delta sigma weight residual 121.41 116.14 5.27 1.96e+00 2.60e-01 7.24e+00 angle pdb=" C THR E 100C" pdb=" N GLY E 100D" pdb=" CA GLY E 100D" ideal model delta sigma weight residual 121.41 116.36 5.05 1.96e+00 2.60e-01 6.65e+00 ... (remaining 17667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 6817 17.65 - 35.29: 534 35.29 - 52.94: 205 52.94 - 70.59: 38 70.59 - 88.24: 14 Dihedral angle restraints: 7608 sinusoidal: 2905 harmonic: 4703 Sorted by residual: dihedral pdb=" CA HIS M 35 " pdb=" C HIS M 35 " pdb=" N TRP M 36 " pdb=" CA TRP M 36 " ideal model delta harmonic sigma weight residual 180.00 163.81 16.19 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CG ARG A 64 " pdb=" CD ARG A 64 " pdb=" NE ARG A 64 " pdb=" CZ ARG A 64 " ideal model delta sinusoidal sigma weight residual -90.00 -134.37 44.37 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CB GLU O 61 " pdb=" CG GLU O 61 " pdb=" CD GLU O 61 " pdb=" OE1 GLU O 61 " ideal model delta sinusoidal sigma weight residual 0.00 -88.24 88.24 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 7605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1090 0.027 - 0.055: 518 0.055 - 0.082: 131 0.082 - 0.109: 97 0.109 - 0.136: 47 Chirality restraints: 1883 Sorted by residual: chirality pdb=" CA ILE D 48 " pdb=" N ILE D 48 " pdb=" C ILE D 48 " pdb=" CB ILE D 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL M 89 " pdb=" N VAL M 89 " pdb=" C VAL M 89 " pdb=" CB VAL M 89 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE P 48 " pdb=" N ILE P 48 " pdb=" C ILE P 48 " pdb=" CB ILE P 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 1880 not shown) Planarity restraints: 2274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 13 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO I 14 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO I 14 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 14 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 43 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO R 44 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 44 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 44 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA N 43 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO N 44 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO N 44 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO N 44 " 0.018 5.00e-02 4.00e+02 ... (remaining 2271 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 92 2.58 - 3.16: 9356 3.16 - 3.74: 19316 3.74 - 4.32: 29464 4.32 - 4.90: 49952 Nonbonded interactions: 108180 Sorted by model distance: nonbonded pdb=" OG SER N 26 " pdb=" OE1 GLN N 27 " model vdw 1.994 3.040 nonbonded pdb=" OH TYR B 36 " pdb=" OE1 GLN B 89 " model vdw 2.217 3.040 nonbonded pdb=" O ARG A 66 " pdb=" OG SER A 82A" model vdw 2.217 3.040 nonbonded pdb=" OH TYR N 36 " pdb=" OE1 GLN N 89 " model vdw 2.232 3.040 nonbonded pdb=" O SER Q 82B" pdb=" OG SER Q 82B" model vdw 2.240 3.040 ... (remaining 108175 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' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.630 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 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:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13047 Z= 0.142 Angle : 0.585 10.398 17700 Z= 0.330 Chirality : 0.041 0.136 1883 Planarity : 0.004 0.048 2274 Dihedral : 15.529 88.236 4584 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.48 % Allowed : 16.95 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.26 (0.18), residues: 791 loop : -0.05 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 103 HIS 0.004 0.001 HIS M 35 PHE 0.012 0.002 PHE O 29 TYR 0.014 0.001 TYR N 91 ARG 0.007 0.000 ARG P 54 Details of bonding type rmsd hydrogen bonds : bond 0.22019 ( 451) hydrogen bonds : angle 9.07906 ( 1206) SS BOND : bond 0.00185 ( 14) SS BOND : angle 0.64145 ( 28) covalent geometry : bond 0.00293 (13033) covalent geometry : angle 0.58511 (17672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 1.486 Fit side-chains REVERT: C 13 GLN cc_start: 0.7539 (pt0) cc_final: 0.7291 (mt0) REVERT: Q 52 TRP cc_start: 0.7984 (OUTLIER) cc_final: 0.5409 (m-90) outliers start: 47 outliers final: 39 residues processed: 214 average time/residue: 1.3596 time to fit residues: 314.4554 Evaluate side-chains 210 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 52 TRP Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 52 TRP Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain Q residue 52 TRP Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN N 79 GLN O 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.177579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125413 restraints weight = 12660.578| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.80 r_work: 0.3121 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13047 Z= 0.161 Angle : 0.586 8.266 17700 Z= 0.312 Chirality : 0.045 0.141 1883 Planarity : 0.005 0.059 2274 Dihedral : 6.530 58.659 1863 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.26 % Allowed : 15.54 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.35 (0.18), residues: 770 loop : -0.06 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 52 HIS 0.007 0.002 HIS M 35 PHE 0.020 0.002 PHE E 29 TYR 0.015 0.002 TYR N 91 ARG 0.006 0.000 ARG Q 19 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 451) hydrogen bonds : angle 5.99634 ( 1206) SS BOND : bond 0.00241 ( 14) SS BOND : angle 1.00947 ( 28) covalent geometry : bond 0.00377 (13033) covalent geometry : angle 0.58486 (17672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 1.465 Fit side-chains REVERT: H 46 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: H 105 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7549 (pm20) REVERT: C 105 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8033 (pt0) REVERT: F 17 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7117 (tp30) REVERT: F 70 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: F 105 GLU cc_start: 0.6716 (pt0) cc_final: 0.6294 (pt0) REVERT: M 108 MET cc_start: 0.8943 (tpt) cc_final: 0.8155 (tpt) REVERT: O 3 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7364 (tp40) REVERT: Q 19 ARG cc_start: 0.7948 (ttt-90) cc_final: 0.7709 (ttt-90) outliers start: 44 outliers final: 15 residues processed: 205 average time/residue: 1.4489 time to fit residues: 319.8145 Evaluate side-chains 189 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 TRP Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain M residue 52 TRP Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 131 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 44 optimal weight: 30.0000 chunk 27 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 11 ASN B 37 GLN C 81 GLN N 79 GLN O 39 GLN R 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.174099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.118014 restraints weight = 12696.654| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.87 r_work: 0.3106 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 13047 Z= 0.294 Angle : 0.710 8.623 17700 Z= 0.379 Chirality : 0.050 0.173 1883 Planarity : 0.006 0.075 2274 Dihedral : 6.287 58.566 1825 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.44 % Allowed : 16.06 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.08 (0.17), residues: 798 loop : -0.26 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP O 52 HIS 0.010 0.003 HIS H 35 PHE 0.022 0.003 PHE M 29 TYR 0.016 0.003 TYR P 49 ARG 0.006 0.001 ARG O 83 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 451) hydrogen bonds : angle 6.09733 ( 1206) SS BOND : bond 0.00324 ( 14) SS BOND : angle 1.29067 ( 28) covalent geometry : bond 0.00703 (13033) covalent geometry : angle 0.70918 (17672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 1.463 Fit side-chains REVERT: H 105 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: L 81 GLU cc_start: 0.7963 (pt0) cc_final: 0.7704 (pt0) REVERT: C 105 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8131 (pt0) REVERT: F 17 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7197 (tp30) REVERT: F 70 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: F 105 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6286 (pt0) REVERT: M 74 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8413 (p) REVERT: O 3 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7199 (tp40) REVERT: O 19 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8309 (ttp80) REVERT: P 42 GLN cc_start: 0.7690 (mt0) cc_final: 0.7441 (mm-40) REVERT: Q 52 TRP cc_start: 0.8180 (OUTLIER) cc_final: 0.5809 (m-90) REVERT: Q 85 GLU cc_start: 0.7684 (mp0) cc_final: 0.7375 (mm-30) outliers start: 60 outliers final: 28 residues processed: 203 average time/residue: 1.4328 time to fit residues: 313.4553 Evaluate side-chains 199 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 TRP Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 52 TRP Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 52 TRP Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 65 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 155 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 152 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN N 42 GLN N 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.179195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.124902 restraints weight = 12623.803| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.81 r_work: 0.3157 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13047 Z= 0.091 Angle : 0.500 9.141 17700 Z= 0.265 Chirality : 0.042 0.140 1883 Planarity : 0.004 0.047 2274 Dihedral : 5.172 56.947 1822 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.81 % Allowed : 18.21 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.26 (0.18), residues: 777 loop : -0.14 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 52 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE M 29 TYR 0.013 0.001 TYR Q 79 ARG 0.005 0.000 ARG Q 19 Details of bonding type rmsd hydrogen bonds : bond 0.02522 ( 451) hydrogen bonds : angle 5.32813 ( 1206) SS BOND : bond 0.00259 ( 14) SS BOND : angle 0.59923 ( 28) covalent geometry : bond 0.00206 (13033) covalent geometry : angle 0.49996 (17672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 1.507 Fit side-chains REVERT: H 46 GLU cc_start: 0.8546 (tt0) cc_final: 0.8091 (tt0) REVERT: H 105 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: L 81 GLU cc_start: 0.8001 (pt0) cc_final: 0.7747 (pt0) REVERT: A 52 TRP cc_start: 0.6885 (m-90) cc_final: 0.6116 (m-10) REVERT: C 16 ARG cc_start: 0.7115 (mmm-85) cc_final: 0.6765 (mmm-85) REVERT: F 4 MET cc_start: 0.7981 (tmt) cc_final: 0.7781 (tmt) REVERT: F 17 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7099 (tp30) REVERT: M 108 MET cc_start: 0.9023 (tpt) cc_final: 0.8089 (tpt) REVERT: O 3 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7184 (tp40) REVERT: O 16 ARG cc_start: 0.7822 (tpp80) cc_final: 0.7238 (mmm-85) REVERT: P 42 GLN cc_start: 0.7696 (mt0) cc_final: 0.7417 (mm-40) REVERT: P 78 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6175 (tt) REVERT: Q 52 TRP cc_start: 0.8309 (OUTLIER) cc_final: 0.6001 (m-90) REVERT: Q 85 GLU cc_start: 0.7605 (mp0) cc_final: 0.7272 (mm-30) outliers start: 38 outliers final: 11 residues processed: 199 average time/residue: 1.5085 time to fit residues: 322.6033 Evaluate side-chains 187 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 52 TRP Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 52 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 44 optimal weight: 30.0000 chunk 114 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 86 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN C 81 GLN N 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.175708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.119256 restraints weight = 12669.822| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.88 r_work: 0.3131 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13047 Z= 0.191 Angle : 0.594 9.463 17700 Z= 0.313 Chirality : 0.045 0.143 1883 Planarity : 0.005 0.065 2274 Dihedral : 4.995 52.001 1817 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.07 % Allowed : 17.32 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.15 (0.18), residues: 798 loop : -0.17 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 52 HIS 0.008 0.002 HIS M 35 PHE 0.017 0.002 PHE E 29 TYR 0.016 0.002 TYR N 91 ARG 0.007 0.000 ARG Q 19 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 451) hydrogen bonds : angle 5.52256 ( 1206) SS BOND : bond 0.00268 ( 14) SS BOND : angle 1.21265 ( 28) covalent geometry : bond 0.00455 (13033) covalent geometry : angle 0.59283 (17672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 171 time to evaluate : 1.408 Fit side-chains REVERT: H 46 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: H 105 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7520 (pm20) REVERT: L 81 GLU cc_start: 0.7982 (pt0) cc_final: 0.7714 (pt0) REVERT: A 52 TRP cc_start: 0.6983 (m-90) cc_final: 0.6283 (m-10) REVERT: C 105 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7986 (pt0) REVERT: F 17 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7123 (tp30) REVERT: N 17 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: N 78 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6625 (tp) REVERT: O 3 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7212 (tp40) REVERT: P 42 GLN cc_start: 0.7707 (mt0) cc_final: 0.7464 (mm-40) REVERT: P 78 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6211 (tt) REVERT: Q 52 TRP cc_start: 0.8175 (OUTLIER) cc_final: 0.5802 (m-90) REVERT: Q 85 GLU cc_start: 0.7609 (mp0) cc_final: 0.7298 (mm-30) REVERT: Q 112 SER cc_start: 0.6149 (p) cc_final: 0.5947 (t) outliers start: 55 outliers final: 22 residues processed: 202 average time/residue: 1.5767 time to fit residues: 344.5018 Evaluate side-chains 198 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 52 TRP Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 52 TRP Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 156 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN N 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.176715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123250 restraints weight = 12948.735| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.83 r_work: 0.3180 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13047 Z= 0.172 Angle : 0.582 9.594 17700 Z= 0.306 Chirality : 0.044 0.143 1883 Planarity : 0.005 0.065 2274 Dihedral : 4.894 52.738 1816 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.22 % Allowed : 17.54 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.13 (0.18), residues: 798 loop : -0.19 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 52 HIS 0.007 0.002 HIS M 35 PHE 0.016 0.002 PHE E 29 TYR 0.015 0.002 TYR N 91 ARG 0.005 0.000 ARG Q 19 Details of bonding type rmsd hydrogen bonds : bond 0.02883 ( 451) hydrogen bonds : angle 5.46513 ( 1206) SS BOND : bond 0.00271 ( 14) SS BOND : angle 0.97852 ( 28) covalent geometry : bond 0.00408 (13033) covalent geometry : angle 0.58096 (17672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 1.490 Fit side-chains REVERT: H 46 GLU cc_start: 0.8512 (tt0) cc_final: 0.8076 (tt0) REVERT: H 105 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: L 81 GLU cc_start: 0.7923 (pt0) cc_final: 0.7661 (pt0) REVERT: A 52 TRP cc_start: 0.7022 (m-90) cc_final: 0.6329 (m-10) REVERT: C 74 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7919 (p) REVERT: F 17 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7158 (tp30) REVERT: F 70 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: M 74 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8471 (p) REVERT: N 78 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6697 (tp) REVERT: O 3 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7238 (tp40) REVERT: P 42 GLN cc_start: 0.7718 (mt0) cc_final: 0.7473 (mm-40) REVERT: P 78 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6192 (tt) REVERT: Q 52 TRP cc_start: 0.8174 (OUTLIER) cc_final: 0.5849 (m-90) REVERT: Q 85 GLU cc_start: 0.7599 (mp0) cc_final: 0.7274 (mm-30) outliers start: 57 outliers final: 31 residues processed: 205 average time/residue: 1.4043 time to fit residues: 310.3771 Evaluate side-chains 203 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 TRP Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 52 TRP Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN N 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.176897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.120461 restraints weight = 12593.194| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.92 r_work: 0.3173 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13047 Z= 0.141 Angle : 0.552 9.327 17700 Z= 0.290 Chirality : 0.043 0.138 1883 Planarity : 0.004 0.060 2274 Dihedral : 4.757 52.078 1815 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.07 % Allowed : 17.91 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.22 (0.18), residues: 777 loop : -0.16 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 52 HIS 0.006 0.002 HIS M 35 PHE 0.014 0.002 PHE E 29 TYR 0.014 0.001 TYR N 91 ARG 0.008 0.000 ARG Q 19 Details of bonding type rmsd hydrogen bonds : bond 0.02706 ( 451) hydrogen bonds : angle 5.34457 ( 1206) SS BOND : bond 0.00258 ( 14) SS BOND : angle 0.88946 ( 28) covalent geometry : bond 0.00333 (13033) covalent geometry : angle 0.55165 (17672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 1.159 Fit side-chains REVERT: H 46 GLU cc_start: 0.8525 (tt0) cc_final: 0.8053 (tt0) REVERT: H 50 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8634 (tp) REVERT: H 105 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: L 4 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7398 (mpt) REVERT: A 52 TRP cc_start: 0.6999 (m-90) cc_final: 0.6282 (m-10) REVERT: C 105 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7944 (pt0) REVERT: F 17 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7117 (tp30) REVERT: F 70 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7586 (mm-30) REVERT: M 108 MET cc_start: 0.8989 (tpt) cc_final: 0.8061 (tpt) REVERT: N 78 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6662 (tp) REVERT: O 3 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7242 (tp40) REVERT: P 42 GLN cc_start: 0.7728 (mt0) cc_final: 0.7481 (mm-40) REVERT: P 78 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.6132 (tt) REVERT: Q 19 ARG cc_start: 0.8131 (ttt-90) cc_final: 0.7794 (ttt-90) REVERT: Q 52 TRP cc_start: 0.8166 (OUTLIER) cc_final: 0.5804 (m-90) REVERT: Q 85 GLU cc_start: 0.7642 (mp0) cc_final: 0.7256 (mm-30) outliers start: 55 outliers final: 31 residues processed: 205 average time/residue: 1.3994 time to fit residues: 309.1965 Evaluate side-chains 205 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 TRP Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 52 TRP Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 52 TRP Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 66 optimal weight: 0.0030 chunk 67 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 9 optimal weight: 0.0070 chunk 25 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 overall best weight: 1.1412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN N 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.179523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.125408 restraints weight = 12762.332| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.83 r_work: 0.3195 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13047 Z= 0.107 Angle : 0.515 9.622 17700 Z= 0.269 Chirality : 0.042 0.135 1883 Planarity : 0.004 0.050 2274 Dihedral : 4.536 51.783 1815 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.33 % Allowed : 18.73 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.26 (0.18), residues: 777 loop : -0.11 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 52 HIS 0.005 0.001 HIS M 35 PHE 0.013 0.001 PHE A 29 TYR 0.012 0.001 TYR Q 79 ARG 0.006 0.000 ARG Q 19 Details of bonding type rmsd hydrogen bonds : bond 0.02470 ( 451) hydrogen bonds : angle 5.12510 ( 1206) SS BOND : bond 0.00215 ( 14) SS BOND : angle 0.80204 ( 28) covalent geometry : bond 0.00250 (13033) covalent geometry : angle 0.51463 (17672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 1.542 Fit side-chains REVERT: H 46 GLU cc_start: 0.8543 (tt0) cc_final: 0.8027 (tt0) REVERT: H 50 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8595 (tp) REVERT: H 75 MET cc_start: 0.7514 (ptm) cc_final: 0.7201 (pmm) REVERT: H 105 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: A 52 TRP cc_start: 0.6964 (m-90) cc_final: 0.6275 (m-10) REVERT: C 74 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7896 (p) REVERT: C 109 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7570 (p) REVERT: D 45 ARG cc_start: 0.8342 (ttp-170) cc_final: 0.8012 (ptt180) REVERT: F 17 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7110 (tp30) REVERT: F 70 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: M 74 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8410 (p) REVERT: M 108 MET cc_start: 0.8980 (tpt) cc_final: 0.8033 (tpt) REVERT: O 3 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7192 (tp40) REVERT: P 42 GLN cc_start: 0.7751 (mt0) cc_final: 0.7517 (mm-40) REVERT: P 78 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.6113 (tt) REVERT: Q 52 TRP cc_start: 0.8148 (OUTLIER) cc_final: 0.5861 (m-90) REVERT: Q 85 GLU cc_start: 0.7640 (mp0) cc_final: 0.7239 (mm-30) outliers start: 45 outliers final: 23 residues processed: 208 average time/residue: 1.3926 time to fit residues: 312.5814 Evaluate side-chains 206 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 TRP Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 52 TRP Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 52 TRP Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN F 100 GLN N 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.178466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127481 restraints weight = 12753.918| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.75 r_work: 0.3167 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13047 Z= 0.143 Angle : 0.556 9.897 17700 Z= 0.291 Chirality : 0.043 0.136 1883 Planarity : 0.004 0.061 2274 Dihedral : 4.682 51.585 1815 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.89 % Allowed : 19.69 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.17 (0.18), residues: 798 loop : -0.09 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 52 HIS 0.006 0.002 HIS M 35 PHE 0.014 0.002 PHE E 29 TYR 0.014 0.002 TYR Q 79 ARG 0.009 0.000 ARG Q 19 Details of bonding type rmsd hydrogen bonds : bond 0.02686 ( 451) hydrogen bonds : angle 5.25156 ( 1206) SS BOND : bond 0.00236 ( 14) SS BOND : angle 0.93313 ( 28) covalent geometry : bond 0.00337 (13033) covalent geometry : angle 0.55486 (17672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 1.473 Fit side-chains REVERT: H 46 GLU cc_start: 0.8570 (tt0) cc_final: 0.8076 (tt0) REVERT: H 50 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8630 (tp) REVERT: H 105 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: L 4 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7302 (mpt) REVERT: L 81 GLU cc_start: 0.7972 (pt0) cc_final: 0.7740 (pt0) REVERT: A 52 TRP cc_start: 0.7010 (m-90) cc_final: 0.6293 (m-10) REVERT: C 74 SER cc_start: 0.8165 (OUTLIER) cc_final: 0.7929 (p) REVERT: D 45 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8044 (ptt180) REVERT: F 17 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7130 (tp30) REVERT: F 70 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7534 (mm-30) REVERT: F 105 GLU cc_start: 0.6451 (pt0) cc_final: 0.5982 (pt0) REVERT: M 74 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8428 (p) REVERT: M 108 MET cc_start: 0.8999 (tpt) cc_final: 0.8123 (tpt) REVERT: O 3 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7228 (tp40) REVERT: P 42 GLN cc_start: 0.7771 (mt0) cc_final: 0.7504 (mm-40) REVERT: P 78 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.6103 (tt) REVERT: Q 52 TRP cc_start: 0.8140 (OUTLIER) cc_final: 0.5780 (m-90) REVERT: Q 85 GLU cc_start: 0.7654 (mp0) cc_final: 0.7255 (mm-30) outliers start: 39 outliers final: 23 residues processed: 195 average time/residue: 1.4903 time to fit residues: 312.4241 Evaluate side-chains 202 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 TRP Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 52 TRP Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 52 TRP Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 157 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 143 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN N 79 GLN Q 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.176699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.121870 restraints weight = 12751.627| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.83 r_work: 0.3168 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13047 Z= 0.211 Angle : 0.631 10.029 17700 Z= 0.331 Chirality : 0.046 0.150 1883 Planarity : 0.005 0.068 2274 Dihedral : 5.023 52.576 1815 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.55 % Allowed : 19.32 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.17 (0.18), residues: 791 loop : -0.21 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 96 HIS 0.008 0.002 HIS M 35 PHE 0.017 0.002 PHE N 98 TYR 0.017 0.002 TYR Q 79 ARG 0.006 0.000 ARG P 54 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 451) hydrogen bonds : angle 5.56117 ( 1206) SS BOND : bond 0.00315 ( 14) SS BOND : angle 1.17984 ( 28) covalent geometry : bond 0.00504 (13033) covalent geometry : angle 0.62933 (17672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 1.423 Fit side-chains REVERT: H 46 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: H 105 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7495 (pm20) REVERT: L 4 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7372 (mpt) REVERT: L 81 GLU cc_start: 0.7998 (pt0) cc_final: 0.7740 (pt0) REVERT: C 74 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7971 (p) REVERT: C 105 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: F 17 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7127 (tp30) REVERT: F 70 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7576 (mm-30) REVERT: F 105 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6039 (pt0) REVERT: M 74 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8440 (p) REVERT: N 78 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6743 (tp) REVERT: O 3 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7210 (tp40) REVERT: P 42 GLN cc_start: 0.7760 (mt0) cc_final: 0.7464 (mm-40) REVERT: P 78 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6135 (tt) REVERT: Q 52 TRP cc_start: 0.8165 (OUTLIER) cc_final: 0.5859 (m-90) REVERT: Q 85 GLU cc_start: 0.7671 (mp0) cc_final: 0.7281 (mm-30) outliers start: 48 outliers final: 24 residues processed: 198 average time/residue: 1.4476 time to fit residues: 308.7414 Evaluate side-chains 203 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 52 TRP Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 52 TRP Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 52 TRP Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 137 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 30.0000 chunk 25 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN N 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.176059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122714 restraints weight = 12695.594| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.24 r_work: 0.3162 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 13047 Z= 0.234 Angle : 0.654 10.305 17700 Z= 0.344 Chirality : 0.046 0.154 1883 Planarity : 0.005 0.071 2274 Dihedral : 5.217 55.522 1815 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.18 % Allowed : 19.76 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.11 (0.18), residues: 791 loop : -0.31 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 96 HIS 0.009 0.003 HIS M 35 PHE 0.017 0.002 PHE N 98 TYR 0.019 0.002 TYR Q 79 ARG 0.006 0.001 ARG P 54 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 451) hydrogen bonds : angle 5.67977 ( 1206) SS BOND : bond 0.00354 ( 14) SS BOND : angle 1.24298 ( 28) covalent geometry : bond 0.00558 (13033) covalent geometry : angle 0.65295 (17672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12351.45 seconds wall clock time: 212 minutes 10.89 seconds (12730.89 seconds total)