Starting phenix.real_space_refine on Sat Aug 23 13:50:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dz3_27787/08_2025/8dz3_27787.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dz3_27787/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dz3_27787/08_2025/8dz3_27787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dz3_27787/08_2025/8dz3_27787.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dz3_27787/08_2025/8dz3_27787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dz3_27787/08_2025/8dz3_27787.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.055 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.26, per 1000 atoms: 0.26 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: 0.95 Conformation dependent library (CDL) restraints added in 590.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.86 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: 2.31 Time building geometry restraints manager: 1.24 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.530 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.110 ------------------------------------------------------------------------------- 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 : 6.94 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (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 ARG 0.007 0.000 ARG P 54 TYR 0.014 0.001 TYR N 91 PHE 0.012 0.002 PHE O 29 TRP 0.010 0.001 TRP C 103 HIS 0.004 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00293 (13033) covalent geometry : angle 0.58511 (17672) SS BOND : bond 0.00185 ( 14) SS BOND : angle 0.64145 ( 28) hydrogen bonds : bond 0.22019 ( 451) hydrogen bonds : angle 9.07906 ( 1206) *********************** 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 : 0.457 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: 0.6774 time to fit residues: 156.2924 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 : 0.363 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN N 42 GLN N 79 GLN O 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.176117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120486 restraints weight = 12647.185| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.83 r_work: 0.3140 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13047 Z= 0.210 Angle : 0.636 8.491 17700 Z= 0.340 Chirality : 0.046 0.147 1883 Planarity : 0.005 0.066 2274 Dihedral : 6.928 58.555 1863 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.15 % Allowed : 14.88 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.30 (0.18), residues: 770 loop : -0.12 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 19 TYR 0.015 0.002 TYR N 91 PHE 0.021 0.002 PHE E 29 TRP 0.014 0.002 TRP O 52 HIS 0.009 0.003 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00497 (13033) covalent geometry : angle 0.63515 (17672) SS BOND : bond 0.00279 ( 14) SS BOND : angle 1.17703 ( 28) hydrogen bonds : bond 0.03649 ( 451) hydrogen bonds : angle 6.16411 ( 1206) *********************** 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 229 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 0.531 Fit side-chains REVERT: H 105 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: C 105 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8052 (pt0) REVERT: F 17 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7147 (tp30) REVERT: F 70 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7658 (mm-30) REVERT: M 105 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7681 (pm20) REVERT: O 3 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7318 (tp40) REVERT: Q 52 TRP cc_start: 0.8143 (OUTLIER) cc_final: 0.6090 (m-90) outliers start: 56 outliers final: 25 residues processed: 212 average time/residue: 0.6707 time to fit residues: 153.0358 Evaluate side-chains 198 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 L residue 79 GLN Chi-restraints excluded: chain L residue 105 GLU 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 55 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 109 VAL 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 70 GLU Chi-restraints excluded: chain M residue 52 TRP Chi-restraints excluded: chain M residue 105 GLN 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 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 48 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 O 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.178853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.125979 restraints weight = 12777.310| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.00 r_work: 0.3212 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13047 Z= 0.140 Angle : 0.548 8.455 17700 Z= 0.291 Chirality : 0.043 0.148 1883 Planarity : 0.004 0.061 2274 Dihedral : 6.117 58.402 1833 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.40 % Allowed : 17.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.26 (0.18), residues: 777 loop : -0.09 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 19 TYR 0.015 0.001 TYR Q 79 PHE 0.016 0.002 PHE E 29 TRP 0.011 0.001 TRP O 52 HIS 0.006 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00329 (13033) covalent geometry : angle 0.54720 (17672) SS BOND : bond 0.00241 ( 14) SS BOND : angle 0.83619 ( 28) hydrogen bonds : bond 0.02998 ( 451) hydrogen bonds : angle 5.60837 ( 1206) *********************** 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 216 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.498 Fit side-chains REVERT: H 46 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: H 105 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: C 74 SER cc_start: 0.8170 (OUTLIER) cc_final: 0.7885 (p) REVERT: C 105 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7999 (pt0) REVERT: F 17 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7172 (tp30) REVERT: F 105 GLU cc_start: 0.6732 (pt0) cc_final: 0.6264 (pt0) REVERT: M 74 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8421 (p) REVERT: M 108 MET cc_start: 0.8917 (tpt) cc_final: 0.7982 (tpt) REVERT: O 3 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7352 (tp40) REVERT: Q 52 TRP cc_start: 0.8209 (OUTLIER) cc_final: 0.6375 (m-90) outliers start: 46 outliers final: 17 residues processed: 197 average time/residue: 0.6956 time to fit residues: 147.0333 Evaluate side-chains 191 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 106 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain C residue 55 SER 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 30 SER Chi-restraints excluded: chain E residue 52 TRP Chi-restraints excluded: chain F residue 72 THR 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 82 MET Chi-restraints excluded: chain P residue 58 ILE 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 62 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN C 81 GLN N 42 GLN N 79 GLN R 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.175499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3301 r_free = 0.3301 target = 0.120374 restraints weight = 12830.217| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.89 r_work: 0.3129 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 13047 Z= 0.271 Angle : 0.683 9.042 17700 Z= 0.363 Chirality : 0.048 0.166 1883 Planarity : 0.006 0.073 2274 Dihedral : 6.462 58.557 1826 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.44 % Allowed : 17.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.07 (0.17), residues: 798 loop : -0.25 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 19 TYR 0.014 0.002 TYR N 91 PHE 0.020 0.003 PHE M 29 TRP 0.016 0.002 TRP O 52 HIS 0.010 0.003 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00649 (13033) covalent geometry : angle 0.68194 (17672) SS BOND : bond 0.00308 ( 14) SS BOND : angle 1.16427 ( 28) hydrogen bonds : bond 0.03491 ( 451) hydrogen bonds : angle 5.91659 ( 1206) *********************** 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 230 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 170 time to evaluate : 0.619 Fit side-chains REVERT: H 105 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: L 81 GLU cc_start: 0.7846 (pt0) cc_final: 0.7579 (pt0) REVERT: A 52 TRP cc_start: 0.7181 (m-90) cc_final: 0.6500 (m-10) REVERT: C 105 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: F 17 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7144 (tp30) REVERT: F 105 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6275 (pt0) REVERT: M 74 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8422 (p) REVERT: N 78 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6777 (tp) REVERT: O 3 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7182 (tp40) REVERT: P 42 GLN cc_start: 0.7674 (mt0) cc_final: 0.7425 (mm-40) REVERT: P 78 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.6190 (tt) REVERT: Q 52 TRP cc_start: 0.8173 (OUTLIER) cc_final: 0.5661 (m-90) REVERT: Q 85 GLU cc_start: 0.7675 (mp0) cc_final: 0.7340 (mm-30) outliers start: 60 outliers final: 29 residues processed: 206 average time/residue: 0.6748 time to fit residues: 149.3970 Evaluate side-chains 204 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 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 85 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 55 SER 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 52 TRP Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 45 ARG 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 13 VAL 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 122 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 97 optimal weight: 0.0050 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 11 ASN 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 = 0.3975 r_free = 0.3975 target = 0.178489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127584 restraints weight = 12728.940| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.65 r_work: 0.3191 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13047 Z= 0.129 Angle : 0.538 8.879 17700 Z= 0.285 Chirality : 0.043 0.140 1883 Planarity : 0.004 0.060 2274 Dihedral : 5.678 58.075 1824 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.92 % Allowed : 18.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.20 (0.18), residues: 777 loop : -0.17 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 19 TYR 0.014 0.001 TYR N 91 PHE 0.014 0.002 PHE E 29 TRP 0.010 0.001 TRP O 52 HIS 0.005 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00302 (13033) covalent geometry : angle 0.53727 (17672) SS BOND : bond 0.00263 ( 14) SS BOND : angle 0.67714 ( 28) hydrogen bonds : bond 0.02719 ( 451) hydrogen bonds : angle 5.41752 ( 1206) *********************** 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 225 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 172 time to evaluate : 0.478 Fit side-chains REVERT: H 46 GLU cc_start: 0.8499 (tt0) cc_final: 0.7989 (tt0) REVERT: H 105 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: L 81 GLU cc_start: 0.7991 (pt0) cc_final: 0.7737 (pt0) REVERT: A 52 TRP cc_start: 0.7027 (m-90) cc_final: 0.6274 (m-10) REVERT: C 16 ARG cc_start: 0.7118 (mmm-85) cc_final: 0.6629 (mmm-85) REVERT: F 17 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7141 (tp30) REVERT: M 74 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8473 (p) REVERT: M 108 MET cc_start: 0.8968 (tpt) cc_final: 0.8035 (tpt) REVERT: N 17 GLU cc_start: 0.7195 (mp0) cc_final: 0.6964 (mp0) REVERT: O 3 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7216 (tp40) REVERT: P 42 GLN cc_start: 0.7689 (mt0) cc_final: 0.7460 (mm-40) REVERT: Q 52 TRP cc_start: 0.8143 (OUTLIER) cc_final: 0.6060 (m-90) REVERT: Q 85 GLU cc_start: 0.7594 (mp0) cc_final: 0.7303 (mm-30) outliers start: 53 outliers final: 25 residues processed: 207 average time/residue: 0.6987 time to fit residues: 155.7675 Evaluate side-chains 198 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 26 SER 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 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 55 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 6 GLN 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 M residue 12 VAL 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 82 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 77 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 108 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 = 0.176825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.123397 restraints weight = 12737.600| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.87 r_work: 0.3178 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13047 Z= 0.150 Angle : 0.562 9.913 17700 Z= 0.295 Chirality : 0.043 0.139 1883 Planarity : 0.004 0.062 2274 Dihedral : 5.579 58.381 1824 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.92 % Allowed : 18.28 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.22 (0.18), residues: 777 loop : -0.15 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 19 TYR 0.014 0.002 TYR N 91 PHE 0.015 0.002 PHE E 29 TRP 0.011 0.001 TRP O 52 HIS 0.006 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00354 (13033) covalent geometry : angle 0.56131 (17672) SS BOND : bond 0.00232 ( 14) SS BOND : angle 1.04594 ( 28) hydrogen bonds : bond 0.02775 ( 451) hydrogen bonds : angle 5.37556 ( 1206) *********************** 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 223 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 0.349 Fit side-chains REVERT: H 46 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: H 82 SER cc_start: 0.8710 (OUTLIER) cc_final: 0.8494 (m) REVERT: H 105 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: A 52 TRP cc_start: 0.7013 (m-90) cc_final: 0.6261 (m-10) REVERT: C 13 GLN cc_start: 0.7612 (pt0) cc_final: 0.7237 (mt0) REVERT: C 105 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: F 17 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7138 (tp30) REVERT: F 70 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: M 74 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8451 (p) REVERT: N 78 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6526 (tp) REVERT: O 3 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7234 (tp40) REVERT: P 42 GLN cc_start: 0.7727 (mt0) cc_final: 0.7494 (mm-40) REVERT: Q 52 TRP cc_start: 0.8178 (OUTLIER) cc_final: 0.6065 (m-90) REVERT: Q 85 GLU cc_start: 0.7586 (mp0) cc_final: 0.7275 (mm-30) outliers start: 53 outliers final: 28 residues processed: 203 average time/residue: 0.6299 time to fit residues: 137.4744 Evaluate side-chains 203 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 82 SER 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 78 LEU 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 3 GLN 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 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 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 82 MET Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 58 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 141 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.175385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119308 restraints weight = 12605.489| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.81 r_work: 0.3209 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13047 Z= 0.187 Angle : 0.603 9.891 17700 Z= 0.316 Chirality : 0.045 0.144 1883 Planarity : 0.005 0.064 2274 Dihedral : 5.679 58.318 1823 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.44 % Allowed : 17.76 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.18 (0.18), residues: 791 loop : -0.26 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 19 TYR 0.015 0.002 TYR N 91 PHE 0.016 0.002 PHE E 29 TRP 0.011 0.002 TRP O 52 HIS 0.007 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00447 (13033) covalent geometry : angle 0.60233 (17672) SS BOND : bond 0.00280 ( 14) SS BOND : angle 1.10760 ( 28) hydrogen bonds : bond 0.02964 ( 451) hydrogen bonds : angle 5.49033 ( 1206) *********************** 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 227 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 0.491 Fit side-chains REVERT: H 82 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8477 (m) REVERT: H 105 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: L 81 GLU cc_start: 0.7960 (pt0) cc_final: 0.7689 (pt0) REVERT: C 105 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: F 17 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7127 (tp30) REVERT: F 70 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: F 105 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6042 (pt0) REVERT: M 74 SER cc_start: 0.8758 (OUTLIER) cc_final: 0.8480 (p) REVERT: N 78 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6676 (tp) REVERT: O 3 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7205 (tp40) REVERT: P 42 GLN cc_start: 0.7742 (mt0) cc_final: 0.7466 (mm-40) REVERT: Q 52 TRP cc_start: 0.8163 (OUTLIER) cc_final: 0.5858 (m-90) REVERT: Q 85 GLU cc_start: 0.7575 (mp0) cc_final: 0.7252 (mm-30) outliers start: 60 outliers final: 34 residues processed: 206 average time/residue: 0.6810 time to fit residues: 151.3328 Evaluate side-chains 208 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 82 SER Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 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 6 GLN Chi-restraints excluded: chain D residue 72 THR 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 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 F residue 105 GLU 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 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 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 30 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 45 optimal weight: 30.0000 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.176960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.121450 restraints weight = 12550.195| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.97 r_work: 0.3178 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13047 Z= 0.143 Angle : 0.560 9.589 17700 Z= 0.293 Chirality : 0.043 0.137 1883 Planarity : 0.004 0.061 2274 Dihedral : 5.454 58.784 1822 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.63 % Allowed : 18.28 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.22 (0.18), residues: 777 loop : -0.18 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 19 TYR 0.015 0.001 TYR Q 79 PHE 0.014 0.002 PHE E 29 TRP 0.010 0.001 TRP C 52 HIS 0.006 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00338 (13033) covalent geometry : angle 0.55954 (17672) SS BOND : bond 0.00252 ( 14) SS BOND : angle 0.95231 ( 28) hydrogen bonds : bond 0.02711 ( 451) hydrogen bonds : angle 5.34385 ( 1206) *********************** 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 220 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 0.554 Fit side-chains REVERT: H 46 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: H 50 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8641 (tp) REVERT: H 82 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8520 (m) REVERT: H 105 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: L 4 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7468 (mpt) REVERT: A 52 TRP cc_start: 0.6882 (m-90) cc_final: 0.6292 (m-10) REVERT: C 16 ARG cc_start: 0.7329 (mmm-85) cc_final: 0.7017 (mmm-85) REVERT: C 105 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: F 17 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7128 (tp30) REVERT: F 70 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: M 74 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8432 (p) REVERT: O 3 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7243 (tp40) REVERT: P 42 GLN cc_start: 0.7769 (mt0) cc_final: 0.7483 (mm-40) REVERT: Q 52 TRP cc_start: 0.8187 (OUTLIER) cc_final: 0.6099 (m-90) REVERT: Q 85 GLU cc_start: 0.7683 (mp0) cc_final: 0.7276 (mm-30) outliers start: 49 outliers final: 28 residues processed: 201 average time/residue: 0.6890 time to fit residues: 148.4369 Evaluate side-chains 208 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 82 SER 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 72 THR 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 105 GLN Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 11 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 O residue 3 GLN Chi-restraints excluded: chain O residue 82 MET 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 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 65 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 Q 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.176297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.120344 restraints weight = 12689.395| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.88 r_work: 0.3163 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13047 Z= 0.164 Angle : 0.585 9.785 17700 Z= 0.306 Chirality : 0.044 0.141 1883 Planarity : 0.005 0.062 2274 Dihedral : 5.495 58.616 1821 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.63 % Allowed : 18.80 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.18 (0.18), residues: 791 loop : -0.26 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 54 TYR 0.017 0.002 TYR Q 79 PHE 0.015 0.002 PHE E 29 TRP 0.010 0.001 TRP H 52 HIS 0.007 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00390 (13033) covalent geometry : angle 0.58363 (17672) SS BOND : bond 0.00269 ( 14) SS BOND : angle 1.07830 ( 28) hydrogen bonds : bond 0.02829 ( 451) hydrogen bonds : angle 5.40283 ( 1206) *********************** 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 219 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.487 Fit side-chains REVERT: H 50 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8645 (tp) REVERT: H 82 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8517 (m) REVERT: H 105 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: L 4 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7459 (mpt) REVERT: A 52 TRP cc_start: 0.6922 (m-90) cc_final: 0.6335 (m-10) REVERT: C 105 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7957 (pt0) REVERT: F 17 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7123 (tp30) REVERT: F 70 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: F 105 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6043 (pt0) REVERT: M 74 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8469 (p) REVERT: N 78 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6652 (tp) REVERT: O 3 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7238 (tp40) REVERT: P 42 GLN cc_start: 0.7784 (mt0) cc_final: 0.7487 (mm-40) REVERT: Q 19 ARG cc_start: 0.8045 (ttt-90) cc_final: 0.7732 (ttt-90) REVERT: Q 52 TRP cc_start: 0.8179 (OUTLIER) cc_final: 0.6124 (m-90) REVERT: Q 85 GLU cc_start: 0.7669 (mp0) cc_final: 0.7268 (mm-30) outliers start: 49 outliers final: 31 residues processed: 199 average time/residue: 0.6885 time to fit residues: 146.7266 Evaluate side-chains 210 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 82 SER 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 72 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 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 11 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 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 10 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain O residue 3 GLN 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 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 41 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 77 optimal weight: 0.0670 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 142 optimal weight: 0.0270 chunk 62 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.179866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.124534 restraints weight = 12754.733| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.86 r_work: 0.3225 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13047 Z= 0.098 Angle : 0.515 9.908 17700 Z= 0.267 Chirality : 0.042 0.134 1883 Planarity : 0.004 0.046 2274 Dihedral : 5.173 59.470 1821 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.52 % Allowed : 19.99 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.30 (0.18), residues: 777 loop : -0.10 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 54 TYR 0.013 0.001 TYR Q 79 PHE 0.013 0.001 PHE A 29 TRP 0.009 0.001 TRP C 52 HIS 0.005 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00226 (13033) covalent geometry : angle 0.51417 (17672) SS BOND : bond 0.00213 ( 14) SS BOND : angle 0.72754 ( 28) hydrogen bonds : bond 0.02405 ( 451) hydrogen bonds : angle 5.06307 ( 1206) ********************** 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 205 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.482 Fit side-chains REVERT: H 3 GLN cc_start: 0.8402 (mt0) cc_final: 0.7992 (tt0) REVERT: H 46 GLU cc_start: 0.8510 (tt0) cc_final: 0.7982 (tt0) REVERT: H 50 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8590 (tp) REVERT: H 75 MET cc_start: 0.7470 (ptm) cc_final: 0.7175 (pmm) REVERT: H 82 SER cc_start: 0.8682 (OUTLIER) cc_final: 0.8475 (m) REVERT: A 52 TRP cc_start: 0.6905 (m-90) cc_final: 0.6310 (m-10) REVERT: F 11 LEU cc_start: 0.8012 (pp) cc_final: 0.7553 (tp) REVERT: F 17 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7123 (tp30) REVERT: F 105 GLU cc_start: 0.6421 (pt0) cc_final: 0.5932 (pt0) REVERT: M 108 MET cc_start: 0.8985 (tpt) cc_final: 0.7990 (tpt) REVERT: P 42 GLN cc_start: 0.7754 (mt0) cc_final: 0.7518 (mm-40) REVERT: Q 19 ARG cc_start: 0.8045 (ttt-90) cc_final: 0.7536 (ttt-90) REVERT: Q 52 TRP cc_start: 0.8106 (OUTLIER) cc_final: 0.6253 (m-90) REVERT: Q 85 GLU cc_start: 0.7659 (mp0) cc_final: 0.7245 (mm-30) outliers start: 34 outliers final: 20 residues processed: 195 average time/residue: 0.7389 time to fit residues: 154.5747 Evaluate side-chains 194 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain L residue 72 THR 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 109 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain P residue 63 SER 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 63 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN C 81 GLN N 79 GLN Q 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.175834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122693 restraints weight = 12765.601| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.19 r_work: 0.3152 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13047 Z= 0.211 Angle : 0.626 10.052 17700 Z= 0.327 Chirality : 0.045 0.147 1883 Planarity : 0.005 0.066 2274 Dihedral : 5.311 58.588 1817 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.74 % Allowed : 19.54 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.19 (0.18), residues: 791 loop : -0.22 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 54 TYR 0.016 0.002 TYR M 79 PHE 0.015 0.002 PHE E 29 TRP 0.011 0.002 TRP N 96 HIS 0.008 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00502 (13033) covalent geometry : angle 0.62466 (17672) SS BOND : bond 0.00301 ( 14) SS BOND : angle 1.22102 ( 28) hydrogen bonds : bond 0.03047 ( 451) hydrogen bonds : angle 5.48183 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5670.99 seconds wall clock time: 97 minutes 9.23 seconds (5829.23 seconds total)