Starting phenix.real_space_refine on Fri Jan 19 22:13:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz3_27787/01_2024/8dz3_27787.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz3_27787/01_2024/8dz3_27787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz3_27787/01_2024/8dz3_27787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz3_27787/01_2024/8dz3_27787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz3_27787/01_2024/8dz3_27787.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz3_27787/01_2024/8dz3_27787.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.055 sd= 0.218 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7994 2.51 5 N 2205 2.21 5 O 2464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 6": "OE1" <-> "OE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C ASP 76": "OD1" <-> "OD2" Residue "D PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E ASP 86": "OD1" <-> "OD2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 76": "OD1" <-> "OD2" Residue "M ASP 98": "OD1" <-> "OD2" Residue "N GLU 70": "OE1" <-> "OE2" Residue "N PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 105": "OE1" <-> "OE2" Residue "O ASP 76": "OD1" <-> "OD2" Residue "O ASP 101": "OD1" <-> "OD2" Residue "P PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 46": "OE1" <-> "OE2" Residue "Q ASP 53": "OD1" <-> "OD2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 101": "OD1" <-> "OD2" Residue "R ASP 82": "OD1" <-> "OD2" Residue "R PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12726 Number of models: 1 Model: "" Number of chains: 15 Chain: "I" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 392 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 14, 'TRANS': 41} Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "A" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "B" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "D" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "E" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "M" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "O" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "Q" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "R" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 6.95, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.56 Conformation dependent library (CDL) restraints added in 2.4 seconds 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2982 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 42 sheets defined 5.7% alpha, 51.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.558A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.920A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.143A pdb=" N PHE B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.527A pdb=" N THR E 31 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.927A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.538A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.517A pdb=" N TYR O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 removed outlier: 4.049A pdb=" N PHE P 83 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.570A pdb=" N THR Q 31 " --> pdb=" O SER Q 28 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR Q 32 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 28 through 32' Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.893A pdb=" N PHE R 83 " --> pdb=" O SER R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.834A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.612A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA H 100F" --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 6 removed outlier: 5.460A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N VAL L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.207A pdb=" N SER L 65 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.598A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.523A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.935A pdb=" N MET A 34 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.367A pdb=" N ILE A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 5 through 6 removed outlier: 5.963A pdb=" N THR B 69 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N GLN B 27 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N SER B 67 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 11.265A pdb=" N VAL B 29 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N SER B 65 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.621A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.647A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.468A pdb=" N GLY C 10 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET C 34 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.468A pdb=" N GLY C 10 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 100F" --> pdb=" O GLY C 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 5 through 6 removed outlier: 11.913A pdb=" N CYS D 23 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 10.911A pdb=" N THR D 74 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N ALA D 25 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 11.513A pdb=" N THR D 72 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N GLN D 27 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU D 70 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY D 68 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.553A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.774A pdb=" N MET E 34 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.575A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA E 100F" --> pdb=" O GLY E 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 5 through 6 removed outlier: 6.031A pdb=" N THR F 69 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N GLN F 27 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 9.819A pdb=" N SER F 67 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N VAL F 29 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N SER F 65 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.673A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.572A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.200A pdb=" N GLY M 10 " --> pdb=" O ILE M 110 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET M 34 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.200A pdb=" N GLY M 10 " --> pdb=" O ILE M 110 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 5 through 6 removed outlier: 5.308A pdb=" N THR N 69 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N GLN N 27 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N SER N 67 " --> pdb=" O GLN N 27 " (cutoff:3.500A) removed outlier: 11.455A pdb=" N VAL N 29 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N SER N 65 " --> pdb=" O VAL N 29 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.570A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.509A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.511A pdb=" N THR O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.792A pdb=" N MET O 34 " --> pdb=" O LEU O 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.634A pdb=" N CYS O 92 " --> pdb=" O TRP O 103 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TRP O 103 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA O 100F" --> pdb=" O GLY O 96 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 5 through 6 removed outlier: 5.839A pdb=" N THR P 69 " --> pdb=" O ALA P 25 " (cutoff:3.500A) removed outlier: 10.589A pdb=" N GLN P 27 " --> pdb=" O SER P 67 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N SER P 67 " --> pdb=" O GLN P 27 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N VAL P 29 " --> pdb=" O SER P 65 " (cutoff:3.500A) removed outlier: 11.126A pdb=" N SER P 65 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.670A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.575A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.351A pdb=" N GLY Q 10 " --> pdb=" O ILE Q 110 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET Q 34 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.351A pdb=" N GLY Q 10 " --> pdb=" O ILE Q 110 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS Q 92 " --> pdb=" O TRP Q 103 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP Q 103 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG Q 94 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA Q 100F" --> pdb=" O GLY Q 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 5 through 6 removed outlier: 11.947A pdb=" N CYS R 23 " --> pdb=" O THR R 74 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N THR R 74 " --> pdb=" O CYS R 23 " (cutoff:3.500A) removed outlier: 11.675A pdb=" N ALA R 25 " --> pdb=" O THR R 72 " (cutoff:3.500A) removed outlier: 11.424A pdb=" N THR R 72 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 10.783A pdb=" N GLN R 27 " --> pdb=" O GLU R 70 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU R 70 " --> pdb=" O GLN R 27 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.792A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.535A pdb=" N THR R 97 " --> pdb=" O GLN R 90 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.17 Time building geometry restraints manager: 4.97 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: 99.54 - 106.46: 350 106.46 - 113.39: 6793 113.39 - 120.31: 4399 120.31 - 127.23: 5955 127.23 - 134.16: 175 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 2.440 nonbonded pdb=" OH TYR B 36 " pdb=" OE1 GLN B 89 " model vdw 2.217 2.440 nonbonded pdb=" O ARG A 66 " pdb=" OG SER A 82A" model vdw 2.217 2.440 nonbonded pdb=" OH TYR N 36 " pdb=" OE1 GLN N 89 " model vdw 2.232 2.440 nonbonded pdb=" O SER Q 82B" pdb=" OG SER Q 82B" model vdw 2.240 2.440 ... (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 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.160 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 36.480 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 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:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.220 ------------------------------------------------------------------------------- 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 13033 Z= 0.190 Angle : 0.585 10.398 17672 Z= 0.330 Chirality : 0.041 0.136 1883 Planarity : 0.004 0.048 2274 Dihedral : 15.529 88.236 4584 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.48 % Allowed : 16.95 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.26 (0.18), residues: 791 loop : -0.05 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 103 HIS 0.004 0.001 HIS M 35 PHE 0.012 0.002 PHE O 29 TYR 0.014 0.001 TYR N 91 ARG 0.007 0.000 ARG P 54 *********************** 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 fitting. rotamer outliers: 47 poor density : 174 time to evaluate : 1.332 Fit side-chains REVERT: C 13 GLN cc_start: 0.7539 (pt0) cc_final: 0.7291 (mt0) REVERT: Q 52 TRP cc_start: 0.7984 (OUTLIER) cc_final: 0.5409 (m-90) outliers start: 47 outliers final: 39 residues processed: 214 average time/residue: 1.3284 time to fit residues: 308.3115 Evaluate side-chains 210 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 170 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 52 TRP Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 52 TRP Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain Q residue 52 TRP Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 0.0570 chunk 124 optimal weight: 10.0000 chunk 48 optimal weight: 0.0270 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 11 ASN A 81 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN N 79 GLN O 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13033 Z= 0.119 Angle : 0.485 8.154 17672 Z= 0.255 Chirality : 0.042 0.139 1883 Planarity : 0.004 0.041 2274 Dihedral : 5.689 59.422 1863 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.22 % Allowed : 16.06 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.49 (0.18), residues: 770 loop : 0.06 (0.23), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 103 HIS 0.002 0.001 HIS M 35 PHE 0.010 0.001 PHE E 29 TYR 0.011 0.001 TYR Q 79 ARG 0.006 0.000 ARG Q 19 *********************** 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 213 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 1.446 Fit side-chains REVERT: H 3 GLN cc_start: 0.8211 (mt0) cc_final: 0.7798 (tt0) REVERT: H 46 GLU cc_start: 0.8449 (tt0) cc_final: 0.8048 (tt0) REVERT: H 105 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7581 (pm20) REVERT: L 4 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7221 (mpt) REVERT: C 13 GLN cc_start: 0.7594 (pt0) cc_final: 0.7340 (mt0) REVERT: C 105 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7819 (pt0) REVERT: F 105 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6133 (pt0) REVERT: O 3 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7228 (tp40) REVERT: O 16 ARG cc_start: 0.7631 (tpp80) cc_final: 0.7088 (mmm-85) outliers start: 30 outliers final: 6 residues processed: 198 average time/residue: 1.4361 time to fit residues: 306.5606 Evaluate side-chains 181 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 170 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 3 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 128 optimal weight: 0.0570 chunk 143 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN B 37 GLN C 81 GLN N 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13033 Z= 0.270 Angle : 0.574 8.573 17672 Z= 0.303 Chirality : 0.045 0.148 1883 Planarity : 0.005 0.059 2274 Dihedral : 4.669 49.592 1816 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.70 % Allowed : 16.73 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.39 (0.18), residues: 770 loop : 0.02 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 52 HIS 0.008 0.002 HIS H 35 PHE 0.018 0.002 PHE E 29 TYR 0.015 0.002 TYR N 91 ARG 0.007 0.000 ARG Q 19 *********************** 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 218 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 168 time to evaluate : 1.468 Fit side-chains REVERT: H 46 GLU cc_start: 0.8579 (tt0) cc_final: 0.8112 (tt0) REVERT: H 105 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: L 81 GLU cc_start: 0.7843 (pt0) cc_final: 0.7551 (pt0) REVERT: C 13 GLN cc_start: 0.7551 (pt0) cc_final: 0.7308 (mt0) REVERT: C 105 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7900 (pt0) REVERT: F 17 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7199 (tp30) REVERT: F 70 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: F 105 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6225 (pt0) REVERT: M 105 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: O 3 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7212 (tp40) REVERT: Q 19 ARG cc_start: 0.7836 (ttt-90) cc_final: 0.7337 (ttt-90) REVERT: Q 52 TRP cc_start: 0.8032 (OUTLIER) cc_final: 0.6137 (m-90) outliers start: 50 outliers final: 22 residues processed: 201 average time/residue: 1.4585 time to fit residues: 317.4422 Evaluate side-chains 197 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain 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 77 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 TRP Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 105 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 52 TRP 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 R residue 31 SER 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 142 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 13033 Z= 0.439 Angle : 0.695 9.060 17672 Z= 0.368 Chirality : 0.049 0.167 1883 Planarity : 0.006 0.072 2274 Dihedral : 5.167 53.010 1814 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.37 % Allowed : 17.10 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.19 (0.17), residues: 791 loop : -0.22 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP O 52 HIS 0.009 0.003 HIS H 35 PHE 0.023 0.003 PHE M 29 TYR 0.016 0.003 TYR P 86 ARG 0.006 0.001 ARG O 83 *********************** 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 229 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 170 time to evaluate : 1.436 Fit side-chains REVERT: H 105 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: L 4 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7383 (mpt) REVERT: L 81 GLU cc_start: 0.7749 (pt0) cc_final: 0.7455 (pt0) REVERT: C 105 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7980 (pt0) REVERT: F 17 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7127 (tp30) REVERT: F 70 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: F 105 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6238 (pt0) REVERT: M 74 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8515 (p) REVERT: M 105 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: O 3 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7178 (tp40) REVERT: P 78 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5935 (tt) REVERT: Q 52 TRP cc_start: 0.8022 (OUTLIER) cc_final: 0.5771 (m-90) outliers start: 59 outliers final: 32 residues processed: 202 average time/residue: 1.4509 time to fit residues: 316.4724 Evaluate side-chains 210 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 4 MET 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 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 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 D residue 77 SER 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 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 105 GLU Chi-restraints excluded: chain M residue 52 TRP Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 52 TRP Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 6 GLU Chi-restraints excluded: chain Q residue 52 TRP Chi-restraints excluded: chain R residue 31 SER 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 87 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN A 39 GLN B 38 GLN C 13 GLN C 73 ASN C 81 GLN N 42 GLN N 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13033 Z= 0.221 Angle : 0.551 9.318 17672 Z= 0.291 Chirality : 0.043 0.141 1883 Planarity : 0.004 0.062 2274 Dihedral : 4.743 51.700 1814 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.15 % Allowed : 16.95 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.20 (0.18), residues: 777 loop : -0.08 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 103 HIS 0.006 0.002 HIS H 35 PHE 0.016 0.002 PHE E 29 TYR 0.016 0.002 TYR N 91 ARG 0.005 0.000 ARG Q 19 *********************** 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 fitting. rotamer outliers: 56 poor density : 169 time to evaluate : 1.471 Fit side-chains REVERT: H 46 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: H 105 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: L 81 GLU cc_start: 0.7757 (pt0) cc_final: 0.7473 (pt0) REVERT: C 105 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7919 (pt0) REVERT: F 17 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7151 (tp30) REVERT: F 70 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: O 3 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7123 (tp40) REVERT: Q 52 TRP cc_start: 0.8012 (OUTLIER) cc_final: 0.5759 (m-90) outliers start: 56 outliers final: 27 residues processed: 202 average time/residue: 1.5302 time to fit residues: 332.6490 Evaluate side-chains 199 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 72 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain B residue 85 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 C residue 110 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 TRP Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 52 TRP Chi-restraints excluded: chain 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 33 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain Q residue 52 TRP Chi-restraints excluded: chain R residue 31 SER 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 138 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 O 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 13033 Z= 0.375 Angle : 0.651 10.072 17672 Z= 0.344 Chirality : 0.047 0.155 1883 Planarity : 0.005 0.073 2274 Dihedral : 5.101 53.022 1814 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.89 % Allowed : 16.95 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.07 (0.18), residues: 798 loop : -0.18 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 52 HIS 0.009 0.003 HIS M 35 PHE 0.019 0.002 PHE M 29 TYR 0.014 0.002 TYR N 91 ARG 0.007 0.001 ARG Q 19 *********************** 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 235 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 169 time to evaluate : 1.498 Fit side-chains REVERT: H 6 GLU cc_start: 0.8929 (mp0) cc_final: 0.8708 (mp0) REVERT: H 105 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: L 81 GLU cc_start: 0.7761 (pt0) cc_final: 0.7477 (pt0) REVERT: A 52 TRP cc_start: 0.7131 (m-90) cc_final: 0.6475 (m-10) REVERT: C 74 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.8095 (p) REVERT: C 105 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7949 (pt0) REVERT: D 82 ASP cc_start: 0.6410 (m-30) cc_final: 0.5964 (t0) REVERT: F 17 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7151 (tp30) REVERT: F 70 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: F 105 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.5851 (mt-10) REVERT: M 74 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8525 (p) REVERT: M 105 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: N 78 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6691 (tp) REVERT: O 3 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.7122 (tp40) REVERT: Q 52 TRP cc_start: 0.8010 (OUTLIER) cc_final: 0.5853 (m-90) outliers start: 66 outliers final: 32 residues processed: 207 average time/residue: 1.4285 time to fit residues: 319.2207 Evaluate side-chains 210 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 1.477 ------------------------------------------------------------------------------- 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 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 C residue 3 GLN 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 D residue 77 SER 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 63 SER Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 52 TRP Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 105 GLN 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 105 GLN 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 R residue 31 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 17 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 112 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 61 optimal weight: 0.0980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 81 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN N 79 GLN O 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13033 Z= 0.145 Angle : 0.506 10.143 17672 Z= 0.265 Chirality : 0.042 0.135 1883 Planarity : 0.004 0.046 2274 Dihedral : 4.544 53.112 1814 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.59 % Allowed : 19.25 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.24 (0.18), residues: 777 loop : -0.03 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 103 HIS 0.004 0.001 HIS M 35 PHE 0.012 0.001 PHE E 29 TYR 0.013 0.001 TYR Q 79 ARG 0.008 0.000 ARG Q 19 *********************** 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 203 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 1.430 Fit side-chains REVERT: H 46 GLU cc_start: 0.8569 (tt0) cc_final: 0.8082 (tt0) REVERT: H 50 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8700 (tp) REVERT: H 105 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: L 81 GLU cc_start: 0.7770 (pt0) cc_final: 0.7487 (pt0) REVERT: A 52 TRP cc_start: 0.7119 (m-90) cc_final: 0.6474 (m-10) REVERT: C 105 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7884 (pt0) REVERT: D 82 ASP cc_start: 0.6276 (m-30) cc_final: 0.5848 (t0) REVERT: D 86 TYR cc_start: 0.8004 (m-80) cc_final: 0.7716 (m-80) REVERT: F 70 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: F 105 GLU cc_start: 0.6543 (pt0) cc_final: 0.5868 (mt-10) REVERT: O 3 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7087 (tp40) REVERT: Q 52 TRP cc_start: 0.7991 (OUTLIER) cc_final: 0.5821 (m-90) outliers start: 35 outliers final: 16 residues processed: 190 average time/residue: 1.5042 time to fit residues: 307.6214 Evaluate side-chains 189 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 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 N residue 33 LEU Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain Q residue 52 TRP Chi-restraints excluded: chain R residue 32 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 O 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 13033 Z= 0.427 Angle : 0.684 10.486 17672 Z= 0.360 Chirality : 0.048 0.163 1883 Planarity : 0.006 0.076 2274 Dihedral : 5.178 53.288 1814 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.52 % Allowed : 17.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.05 (0.18), residues: 798 loop : -0.20 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 94 HIS 0.010 0.003 HIS M 35 PHE 0.018 0.003 PHE E 29 TYR 0.015 0.003 TYR P 86 ARG 0.008 0.001 ARG Q 19 *********************** 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 227 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 166 time to evaluate : 1.438 Fit side-chains REVERT: H 6 GLU cc_start: 0.8893 (mp0) cc_final: 0.8691 (mp0) REVERT: H 46 GLU cc_start: 0.8629 (tt0) cc_final: 0.8222 (tt0) REVERT: H 105 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: L 81 GLU cc_start: 0.7789 (pt0) cc_final: 0.7499 (pt0) REVERT: A 52 TRP cc_start: 0.7184 (m-90) cc_final: 0.6445 (m-10) REVERT: C 74 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.8102 (p) REVERT: C 105 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: D 82 ASP cc_start: 0.6450 (OUTLIER) cc_final: 0.5949 (t0) REVERT: E 19 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8750 (ttt180) REVERT: F 17 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7087 (tp30) REVERT: F 70 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7395 (mm-30) REVERT: M 74 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8522 (p) REVERT: M 105 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: N 78 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6635 (tp) REVERT: O 3 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7133 (tp40) REVERT: Q 52 TRP cc_start: 0.8013 (OUTLIER) cc_final: 0.5567 (m-90) outliers start: 61 outliers final: 30 residues processed: 206 average time/residue: 1.4231 time to fit residues: 315.8646 Evaluate side-chains 206 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 165 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 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 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 C residue 74 SER Chi-restraints excluded: chain C residue 82 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 D residue 77 SER Chi-restraints excluded: chain D residue 82 ASP 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 19 ARG 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 63 SER Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 52 TRP Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 105 GLN 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 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 31 SER Chi-restraints excluded: chain R residue 32 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 62 optimal weight: 0.0060 chunk 112 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 81 GLN N 42 GLN N 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13033 Z= 0.233 Angle : 0.568 10.576 17672 Z= 0.297 Chirality : 0.044 0.142 1883 Planarity : 0.004 0.062 2274 Dihedral : 4.813 53.337 1814 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.11 % Allowed : 19.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.17 (0.18), residues: 777 loop : -0.10 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 52 HIS 0.007 0.002 HIS M 35 PHE 0.016 0.002 PHE E 29 TYR 0.016 0.002 TYR M 79 ARG 0.008 0.000 ARG Q 19 *********************** 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 207 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 165 time to evaluate : 1.473 Fit side-chains REVERT: H 46 GLU cc_start: 0.8611 (tt0) cc_final: 0.8161 (tt0) REVERT: H 105 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: L 81 GLU cc_start: 0.7791 (pt0) cc_final: 0.7495 (pt0) REVERT: A 52 TRP cc_start: 0.7188 (m-90) cc_final: 0.6431 (m-10) REVERT: C 74 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8127 (p) REVERT: C 105 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7905 (pt0) REVERT: D 82 ASP cc_start: 0.6290 (OUTLIER) cc_final: 0.5853 (t0) REVERT: D 86 TYR cc_start: 0.7896 (m-80) cc_final: 0.7623 (m-80) REVERT: F 17 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7128 (tp30) REVERT: F 70 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7373 (mm-30) REVERT: F 105 GLU cc_start: 0.6565 (pt0) cc_final: 0.6134 (pt0) REVERT: M 105 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: O 3 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7130 (tp40) REVERT: O 108 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8558 (mmm) REVERT: Q 19 ARG cc_start: 0.8162 (ttt-90) cc_final: 0.7629 (ttt-90) REVERT: Q 52 TRP cc_start: 0.8009 (OUTLIER) cc_final: 0.5800 (m-90) REVERT: R 102 THR cc_start: 0.7013 (m) cc_final: 0.6803 (m) outliers start: 42 outliers final: 25 residues processed: 192 average time/residue: 1.5968 time to fit residues: 330.0213 Evaluate side-chains 201 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 3 GLN 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 77 SER Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 52 TRP 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 105 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 52 TRP Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 108 MET 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 31 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 92 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 O 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13033 Z= 0.284 Angle : 0.603 10.466 17672 Z= 0.316 Chirality : 0.045 0.146 1883 Planarity : 0.005 0.066 2274 Dihedral : 4.901 52.331 1814 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.63 % Allowed : 18.95 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: 0.07 (0.18), residues: 798 loop : -0.11 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 52 HIS 0.007 0.002 HIS M 35 PHE 0.016 0.002 PHE E 29 TYR 0.018 0.002 TYR R 49 ARG 0.009 0.001 ARG Q 19 ********************** 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 213 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 164 time to evaluate : 1.400 Fit side-chains REVERT: H 46 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: H 50 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8772 (tp) REVERT: H 105 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7623 (pm20) REVERT: L 81 GLU cc_start: 0.7781 (pt0) cc_final: 0.7484 (pt0) REVERT: A 52 TRP cc_start: 0.7207 (m-90) cc_final: 0.6431 (m-10) REVERT: C 74 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.8144 (p) REVERT: C 105 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7944 (pt0) REVERT: D 82 ASP cc_start: 0.6417 (OUTLIER) cc_final: 0.5933 (t0) REVERT: F 17 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7136 (tp30) REVERT: F 70 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: F 105 GLU cc_start: 0.6537 (pt0) cc_final: 0.6182 (pt0) REVERT: M 74 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8530 (p) REVERT: M 105 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: N 78 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6679 (tp) REVERT: O 3 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7127 (tp40) REVERT: Q 19 ARG cc_start: 0.8180 (ttt-90) cc_final: 0.7598 (ttt-90) REVERT: Q 31 THR cc_start: 0.8321 (p) cc_final: 0.7904 (t) REVERT: Q 52 TRP cc_start: 0.8007 (OUTLIER) cc_final: 0.5856 (m-90) outliers start: 49 outliers final: 31 residues processed: 196 average time/residue: 1.4856 time to fit residues: 315.3860 Evaluate side-chains 207 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 164 time to evaluate : 1.444 ------------------------------------------------------------------------------- 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 50 LEU 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 79 GLN 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 C residue 3 GLN 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 77 SER Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 106 ILE 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 63 SER 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 M residue 105 GLN 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 82 MET 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 31 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 38 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 O 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.174160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.123498 restraints weight = 12760.595| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.59 r_work: 0.3186 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 13033 Z= 0.482 Angle : 0.732 10.810 17672 Z= 0.386 Chirality : 0.050 0.170 1883 Planarity : 0.006 0.077 2274 Dihedral : 5.399 53.470 1814 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.29 % Allowed : 18.28 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1629 helix: None (None), residues: 0 sheet: -0.05 (0.18), residues: 798 loop : -0.32 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP N 96 HIS 0.009 0.003 HIS H 35 PHE 0.021 0.003 PHE M 29 TYR 0.022 0.003 TYR M 79 ARG 0.009 0.001 ARG Q 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5306.53 seconds wall clock time: 94 minutes 48.61 seconds (5688.61 seconds total)