Starting phenix.real_space_refine (version: dev) on Fri Feb 17 13:05:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ssx_10307/02_2023/6ssx_10307.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ssx_10307/02_2023/6ssx_10307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ssx_10307/02_2023/6ssx_10307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ssx_10307/02_2023/6ssx_10307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ssx_10307/02_2023/6ssx_10307.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ssx_10307/02_2023/6ssx_10307.pdb" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.002 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 Process input model Symmetric amino acids flipped Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 4900 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.98, per 1000 atoms: 0.61 Number of scatterers: 4900 At special positions: 0 Unit cell: (75.48, 117.623, 40.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 990 8.00 N 860 7.00 C 3050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.91 Conformation dependent library (CDL) restraints added in 862.1 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 63.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 23 removed outlier: 6.132A pdb=" N VAL A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA B 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N GLU B 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA A 19 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR B 22 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS A 21 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL B 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA C 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N GLU C 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA B 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N THR C 22 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS B 21 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL C 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ALA D 18 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA C 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLU D 20 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA C 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR D 22 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS C 21 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 57 removed outlier: 9.080A pdb=" N VAL A 37 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N VAL B 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N SER B 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N THR B 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N GLU B 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A 45 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N VAL B 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N HIS B 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL B 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLY A 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N THR B 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N ALA A 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N ALA B 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N VAL A 55 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N VAL B 37 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N VAL C 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N TYR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 9.916A pdb=" N SER C 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N GLY B 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N THR C 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N LYS B 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 10.583A pdb=" N GLU C 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N VAL C 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY B 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N HIS C 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL B 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL C 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLY B 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N THR C 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N ALA B 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ALA C 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N VAL B 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N VAL C 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N VAL D 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N TYR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 9.944A pdb=" N SER D 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N GLY C 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 9.923A pdb=" N THR D 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS C 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N GLU D 46 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS C 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N VAL D 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY C 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N HIS D 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL C 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL D 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLY C 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N THR D 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N ALA C 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N ALA D 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N VAL C 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N VAL D 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N VAL E 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N THR E 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LYS D 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N GLU E 46 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS D 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N VAL E 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY D 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N HIS E 50 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL D 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL E 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLY D 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N THR E 54 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ALA D 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N ALA E 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N VAL D 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 93 Processing sheet with id=AA7, first strand: chain 'F' and resid 15 through 23 removed outlier: 6.129A pdb=" N VAL F 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ALA G 18 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA F 17 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N GLU G 20 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA F 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N THR G 22 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS F 21 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL H 15 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA I 18 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA H 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLU I 20 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA H 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR I 22 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS H 21 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL I 15 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA J 18 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA I 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLU J 20 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA I 19 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR J 22 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS I 21 " --> pdb=" O THR J 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 37 through 57 removed outlier: 9.084A pdb=" N VAL F 37 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL G 40 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N TYR F 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N SER G 42 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLY F 41 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 9.824A pdb=" N THR G 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N LYS F 43 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N GLU G 46 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS F 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N VAL G 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY F 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS G 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL F 49 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL G 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLY F 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N THR G 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N ALA F 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ALA G 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N VAL F 55 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N VAL G 37 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N VAL H 40 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N SER H 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N GLY G 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N THR H 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N LYS G 43 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N GLU H 46 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS G 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N VAL H 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY G 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N HIS H 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL G 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL H 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY G 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N THR H 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N ALA G 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N ALA H 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N VAL G 55 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N VAL H 37 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N VAL I 40 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N TYR H 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N SER I 42 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N GLY H 41 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N THR I 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N LYS H 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 10.621A pdb=" N GLU I 46 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS H 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N VAL I 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY H 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS I 50 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL H 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL I 52 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY H 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N THR I 54 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N ALA H 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ALA I 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N VAL H 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N VAL I 37 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N VAL J 40 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N TYR I 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N SER J 42 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N GLY I 41 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N THR J 44 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS I 43 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU J 46 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS I 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N VAL J 48 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY I 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N HIS J 50 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL I 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL J 52 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY I 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N THR J 54 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N ALA I 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N ALA J 56 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N VAL I 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 61 through 66 Processing sheet with id=AB1, first strand: chain 'F' and resid 69 through 71 Processing sheet with id=AB2, first strand: chain 'F' and resid 75 through 79 Processing sheet with id=AB3, first strand: chain 'F' and resid 86 through 93 160 hydrogen bonds defined for protein. 480 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: 1.28 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 870 1.29 - 1.35: 770 1.35 - 1.41: 180 1.41 - 1.48: 831 1.48 - 1.54: 2259 Bond restraints: 4910 Sorted by residual: bond pdb=" CG LEU F 38 " pdb=" CD1 LEU F 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.58e+00 bond pdb=" CG LEU A 38 " pdb=" CD1 LEU A 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 bond pdb=" CG LEU C 38 " pdb=" CD1 LEU C 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CG LEU H 38 " pdb=" CD1 LEU H 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CG LEU I 38 " pdb=" CD1 LEU I 38 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.55e+00 ... (remaining 4905 not shown) Histogram of bond angle deviations from ideal: 105.19 - 110.41: 1346 110.41 - 115.62: 1998 115.62 - 120.84: 1648 120.84 - 126.06: 1618 126.06 - 131.27: 20 Bond angle restraints: 6630 Sorted by residual: angle pdb=" N THR I 44 " pdb=" CA THR I 44 " pdb=" C THR I 44 " ideal model delta sigma weight residual 109.23 113.56 -4.33 1.55e+00 4.16e-01 7.79e+00 angle pdb=" N THR E 44 " pdb=" CA THR E 44 " pdb=" C THR E 44 " ideal model delta sigma weight residual 109.23 113.51 -4.28 1.55e+00 4.16e-01 7.63e+00 angle pdb=" N THR J 44 " pdb=" CA THR J 44 " pdb=" C THR J 44 " ideal model delta sigma weight residual 109.23 113.51 -4.28 1.55e+00 4.16e-01 7.61e+00 angle pdb=" N THR C 44 " pdb=" CA THR C 44 " pdb=" C THR C 44 " ideal model delta sigma weight residual 109.23 113.50 -4.27 1.55e+00 4.16e-01 7.61e+00 angle pdb=" N THR G 44 " pdb=" CA THR G 44 " pdb=" C THR G 44 " ideal model delta sigma weight residual 109.23 113.50 -4.27 1.55e+00 4.16e-01 7.60e+00 ... (remaining 6625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 2500 16.71 - 33.41: 300 33.41 - 50.12: 20 50.12 - 66.82: 10 66.82 - 83.53: 10 Dihedral angle restraints: 2840 sinusoidal: 900 harmonic: 1940 Sorted by residual: dihedral pdb=" CA GLY G 73 " pdb=" C GLY G 73 " pdb=" N VAL G 74 " pdb=" CA VAL G 74 " ideal model delta harmonic sigma weight residual 180.00 148.94 31.06 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA GLY B 73 " pdb=" C GLY B 73 " pdb=" N VAL B 74 " pdb=" CA VAL B 74 " ideal model delta harmonic sigma weight residual 180.00 148.99 31.01 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA GLY F 73 " pdb=" C GLY F 73 " pdb=" N VAL F 74 " pdb=" CA VAL F 74 " ideal model delta harmonic sigma weight residual 180.00 149.00 31.00 0 5.00e+00 4.00e-02 3.84e+01 ... (remaining 2837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 428 0.040 - 0.079: 174 0.079 - 0.119: 200 0.119 - 0.159: 48 0.159 - 0.199: 20 Chirality restraints: 870 Sorted by residual: chirality pdb=" CB THR H 44 " pdb=" CA THR H 44 " pdb=" OG1 THR H 44 " pdb=" CG2 THR H 44 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CB THR E 44 " pdb=" CA THR E 44 " pdb=" OG1 THR E 44 " pdb=" CG2 THR E 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CB THR D 44 " pdb=" CA THR D 44 " pdb=" OG1 THR D 44 " pdb=" CG2 THR D 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.62e-01 ... (remaining 867 not shown) Planarity restraints: 830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 72 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C THR C 72 " -0.024 2.00e-02 2.50e+03 pdb=" O THR C 72 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY C 73 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 72 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C THR E 72 " -0.024 2.00e-02 2.50e+03 pdb=" O THR E 72 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY E 73 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 72 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C THR I 72 " -0.024 2.00e-02 2.50e+03 pdb=" O THR I 72 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY I 73 " 0.008 2.00e-02 2.50e+03 ... (remaining 827 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 2121 2.92 - 3.41: 4427 3.41 - 3.91: 8204 3.91 - 4.40: 9433 4.40 - 4.90: 17678 Nonbonded interactions: 41863 Sorted by model distance: nonbonded pdb=" OE1 GLN A 62 " pdb=" NE2 GLN B 62 " model vdw 2.424 2.520 nonbonded pdb=" OE1 GLN F 62 " pdb=" NE2 GLN G 62 " model vdw 2.454 2.520 nonbonded pdb=" N VAL F 74 " pdb=" O VAL G 74 " model vdw 2.479 2.520 nonbonded pdb=" N VAL A 74 " pdb=" O VAL B 74 " model vdw 2.480 2.520 nonbonded pdb=" N LYS A 58 " pdb=" O GLU B 57 " model vdw 2.483 2.520 ... (remaining 41858 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 3050 2.51 5 N 860 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.130 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: 0.000 Extract box with map and model: 4.740 Check model and map are aligned: 0.080 Process input model: 17.000 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.008 0.053 4910 Z= 0.540 Angle : 0.938 5.474 6630 Z= 0.553 Chirality : 0.069 0.199 870 Planarity : 0.004 0.014 830 Dihedral : 14.938 83.526 1620 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer Outliers : 4.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.41 % 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: -4.73 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.19), residues: 690 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 0.566 Fit side-chains outliers start: 20 outliers final: 4 residues processed: 67 average time/residue: 1.2612 time to fit residues: 87.9297 Evaluate side-chains 44 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.7450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4910 Z= 0.213 Angle : 0.580 6.683 6630 Z= 0.331 Chirality : 0.052 0.135 870 Planarity : 0.002 0.015 830 Dihedral : 7.065 25.367 720 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer Outliers : 5.32 % 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: -4.47 (0.27), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.21), residues: 690 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 41 time to evaluate : 0.498 Fit side-chains outliers start: 25 outliers final: 11 residues processed: 61 average time/residue: 1.1232 time to fit residues: 71.7503 Evaluate side-chains 48 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.466 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.0436 time to fit residues: 0.7117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 0.0170 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 overall best weight: 1.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 4910 Z= 0.281 Angle : 0.578 6.033 6630 Z= 0.333 Chirality : 0.053 0.140 870 Planarity : 0.002 0.009 830 Dihedral : 6.907 25.921 720 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer Outliers : 5.11 % 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: -4.47 (0.27), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.20), residues: 690 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 40 time to evaluate : 1.550 Fit side-chains outliers start: 24 outliers final: 15 residues processed: 61 average time/residue: 1.2581 time to fit residues: 80.4681 Evaluate side-chains 53 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 1.7486 time to fit residues: 2.5092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 0.0030 chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 67 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 4910 Z= 0.369 Angle : 0.623 6.993 6630 Z= 0.360 Chirality : 0.053 0.139 870 Planarity : 0.002 0.010 830 Dihedral : 7.144 26.443 720 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer Outliers : 5.53 % 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: -4.56 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.20), residues: 690 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 48 time to evaluate : 0.572 Fit side-chains outliers start: 26 outliers final: 17 residues processed: 69 average time/residue: 1.2962 time to fit residues: 93.0895 Evaluate side-chains 63 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 46 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.0493 time to fit residues: 0.7993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN F 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 4910 Z= 0.243 Angle : 0.574 6.777 6630 Z= 0.330 Chirality : 0.052 0.136 870 Planarity : 0.002 0.009 830 Dihedral : 6.684 26.285 720 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer Outliers : 4.89 % 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: -4.60 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.20), residues: 690 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 45 time to evaluate : 0.499 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 20 residues processed: 63 average time/residue: 1.1761 time to fit residues: 77.3506 Evaluate side-chains 64 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 44 time to evaluate : 0.563 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 5 average time/residue: 0.6020 time to fit residues: 3.8995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.039 4910 Z= 0.469 Angle : 0.664 6.953 6630 Z= 0.385 Chirality : 0.054 0.143 870 Planarity : 0.003 0.011 830 Dihedral : 7.380 27.550 720 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer Outliers : 5.11 % 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: -4.91 (0.24), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.18), residues: 690 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 56 time to evaluate : 0.544 Fit side-chains outliers start: 24 outliers final: 17 residues processed: 72 average time/residue: 1.2705 time to fit residues: 95.2044 Evaluate side-chains 71 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 0.514 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.3139 time to fit residues: 2.7912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.0470 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 41 optimal weight: 0.0870 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.0670 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 4910 Z= 0.151 Angle : 0.551 7.181 6630 Z= 0.315 Chirality : 0.052 0.129 870 Planarity : 0.002 0.010 830 Dihedral : 6.235 24.651 720 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer Outliers : 4.47 % 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: -4.66 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.20), residues: 690 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 45 time to evaluate : 0.538 Fit side-chains outliers start: 21 outliers final: 21 residues processed: 59 average time/residue: 1.1191 time to fit residues: 69.1680 Evaluate side-chains 62 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 41 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 7 average time/residue: 0.2880 time to fit residues: 3.0248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.035 4910 Z= 0.437 Angle : 0.641 6.043 6630 Z= 0.372 Chirality : 0.054 0.142 870 Planarity : 0.003 0.010 830 Dihedral : 7.086 27.252 720 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer Outliers : 5.11 % 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: -4.98 (0.24), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.18), residues: 690 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 50 time to evaluate : 0.594 Fit side-chains outliers start: 24 outliers final: 19 residues processed: 66 average time/residue: 1.2262 time to fit residues: 84.3312 Evaluate side-chains 68 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 49 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 6 average time/residue: 0.0472 time to fit residues: 1.2299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 4910 Z= 0.167 Angle : 0.559 6.382 6630 Z= 0.319 Chirality : 0.052 0.132 870 Planarity : 0.002 0.010 830 Dihedral : 6.201 24.731 720 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 4.04 % 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: -4.80 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.19), residues: 690 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 0.548 Fit side-chains outliers start: 19 outliers final: 18 residues processed: 59 average time/residue: 1.1466 time to fit residues: 71.0362 Evaluate side-chains 62 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 44 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 6 average time/residue: 0.0553 time to fit residues: 1.2782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 4910 Z= 0.255 Angle : 0.581 6.276 6630 Z= 0.332 Chirality : 0.052 0.135 870 Planarity : 0.002 0.018 830 Dihedral : 6.363 25.882 720 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer Outliers : 3.83 % 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: -4.88 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.19), residues: 690 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 0.547 Fit side-chains outliers start: 18 outliers final: 17 residues processed: 60 average time/residue: 1.1650 time to fit residues: 72.9287 Evaluate side-chains 61 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 44 time to evaluate : 0.515 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.0485 time to fit residues: 1.0294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.132452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.114012 restraints weight = 5677.334| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.17 r_work: 0.3731 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.045 4910 Z= 0.551 Angle : 0.722 7.121 6630 Z= 0.416 Chirality : 0.057 0.139 870 Planarity : 0.003 0.022 830 Dihedral : 7.417 28.474 720 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.19 % Favored : 86.81 % Rotamer Outliers : 4.26 % 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: -5.14 (0.23), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.18), residues: 690 =============================================================================== Job complete usr+sys time: 2020.98 seconds wall clock time: 37 minutes 14.79 seconds (2234.79 seconds total)