Starting phenix.real_space_refine on Sun Mar 10 20:38:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ssx_10307/03_2024/6ssx_10307.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ssx_10307/03_2024/6ssx_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_10307/03_2024/6ssx_10307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ssx_10307/03_2024/6ssx_10307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ssx_10307/03_2024/6ssx_10307.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ssx_10307/03_2024/6ssx_10307.pdb" } resolution = 2.98 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= 0.000 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 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. 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-5265/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: 2.88, per 1000 atoms: 0.59 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: 1.94 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.61 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: 1.25 Time building geometry restraints manager: 2.08 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 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: 1.520 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: 4.700 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.670 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 % Allowed : 6.38 % Favored : 89.36 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.007 0.002 PHE D 94 TYR 0.021 0.005 TYR E 39 *********************** 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 : 0.518 Fit side-chains REVERT: B 80 LYS cc_start: 0.8097 (mttp) cc_final: 0.7744 (mtpt) REVERT: E 80 LYS cc_start: 0.8592 (mttp) cc_final: 0.8309 (mtpp) REVERT: F 65 ASN cc_start: 0.9013 (m-40) cc_final: 0.8790 (m-40) REVERT: J 80 LYS cc_start: 0.8250 (mttp) cc_final: 0.7879 (mtmt) outliers start: 20 outliers final: 4 residues processed: 67 average time/residue: 1.2514 time to fit residues: 87.3125 Evaluate side-chains 44 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR 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: 0.9990 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... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4910 Z= 0.213 Angle : 0.579 6.535 6630 Z= 0.332 Chirality : 0.052 0.135 870 Planarity : 0.002 0.014 830 Dihedral : 7.699 42.070 724 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.32 % Allowed : 9.15 % Favored : 85.53 % 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: -4.48 (0.27), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 50 PHE 0.002 0.000 PHE E 94 TYR 0.012 0.002 TYR B 39 *********************** 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 : 0.470 Fit side-chains REVERT: B 80 LYS cc_start: 0.8171 (mttp) cc_final: 0.7840 (mtpt) REVERT: D 80 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8319 (mtpm) REVERT: E 80 LYS cc_start: 0.8562 (mttp) cc_final: 0.8250 (mtpp) REVERT: J 58 LYS cc_start: 0.7647 (ttmt) cc_final: 0.6961 (tptm) REVERT: J 83 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7680 (mt-10) outliers start: 25 outliers final: 11 residues processed: 61 average time/residue: 1.1537 time to fit residues: 73.5253 Evaluate side-chains 49 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain H residue 44 THR 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: 4.9990 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 51 optimal weight: 0.0470 chunk 62 optimal weight: 4.9990 overall best weight: 1.8682 ------------------------------------------------------------------------------- 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: 0.7875 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4910 Z= 0.323 Angle : 0.594 6.203 6630 Z= 0.343 Chirality : 0.053 0.140 870 Planarity : 0.002 0.009 830 Dihedral : 7.463 41.488 723 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 4.68 % Allowed : 10.85 % Favored : 84.47 % 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: -4.49 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 50 PHE 0.004 0.001 PHE E 94 TYR 0.017 0.004 TYR I 39 *********************** 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 60 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 38 time to evaluate : 0.540 Fit side-chains REVERT: A 24 GLN cc_start: 0.8067 (mp10) cc_final: 0.7849 (mp10) REVERT: B 80 LYS cc_start: 0.8203 (mttp) cc_final: 0.7713 (mtpt) REVERT: E 80 LYS cc_start: 0.8584 (mttp) cc_final: 0.8249 (mtpp) REVERT: F 65 ASN cc_start: 0.8893 (m-40) cc_final: 0.8663 (m-40) REVERT: J 58 LYS cc_start: 0.7712 (ttmt) cc_final: 0.6949 (tptm) outliers start: 22 outliers final: 15 residues processed: 56 average time/residue: 1.2292 time to fit residues: 71.8186 Evaluate side-chains 53 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4910 Z= 0.358 Angle : 0.617 6.925 6630 Z= 0.356 Chirality : 0.053 0.141 870 Planarity : 0.002 0.010 830 Dihedral : 7.564 42.855 723 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 5.74 % Allowed : 11.06 % Favored : 83.19 % 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: -4.54 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.004 0.001 PHE E 94 TYR 0.018 0.004 TYR I 39 *********************** 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: 27 poor density : 47 time to evaluate : 0.542 Fit side-chains REVERT: B 80 LYS cc_start: 0.8130 (mttp) cc_final: 0.7715 (mtpp) REVERT: E 80 LYS cc_start: 0.8623 (mttp) cc_final: 0.8217 (mtpp) REVERT: H 60 LYS cc_start: 0.7678 (mttt) cc_final: 0.7340 (mtpp) REVERT: J 58 LYS cc_start: 0.7704 (ttmt) cc_final: 0.6987 (tptm) outliers start: 27 outliers final: 16 residues processed: 68 average time/residue: 1.2058 time to fit residues: 85.3885 Evaluate side-chains 62 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR 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: 1.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.7858 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4910 Z= 0.215 Angle : 0.562 7.053 6630 Z= 0.322 Chirality : 0.052 0.135 870 Planarity : 0.002 0.010 830 Dihedral : 6.875 41.837 722 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.47 % Allowed : 14.89 % Favored : 80.64 % 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: -4.52 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.002 0.000 PHE B 94 TYR 0.011 0.002 TYR B 39 *********************** 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 64 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 43 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8071 (mttp) cc_final: 0.7789 (mtpp) REVERT: D 80 LYS cc_start: 0.8598 (mtpm) cc_final: 0.8381 (mtpp) REVERT: E 80 LYS cc_start: 0.8516 (mttp) cc_final: 0.8212 (mtpp) REVERT: F 65 ASN cc_start: 0.8848 (m-40) cc_final: 0.8616 (m-40) REVERT: J 58 LYS cc_start: 0.7659 (ttmt) cc_final: 0.6955 (tptm) outliers start: 21 outliers final: 17 residues processed: 60 average time/residue: 1.1712 time to fit residues: 73.3833 Evaluate side-chains 60 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 44 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4910 Z= 0.248 Angle : 0.564 6.330 6630 Z= 0.325 Chirality : 0.052 0.137 870 Planarity : 0.002 0.010 830 Dihedral : 6.854 41.229 722 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.68 % Allowed : 15.11 % Favored : 80.21 % 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: -4.59 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.003 0.001 PHE D 94 TYR 0.013 0.003 TYR B 39 *********************** 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 66 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 44 time to evaluate : 0.567 Fit side-chains REVERT: B 80 LYS cc_start: 0.8036 (mttp) cc_final: 0.7721 (mtpp) REVERT: D 80 LYS cc_start: 0.8608 (mtpm) cc_final: 0.8396 (mtpp) REVERT: E 80 LYS cc_start: 0.8510 (mttp) cc_final: 0.8202 (mtpp) REVERT: H 60 LYS cc_start: 0.7614 (mttt) cc_final: 0.7302 (mtpp) REVERT: J 58 LYS cc_start: 0.7675 (ttmt) cc_final: 0.6963 (tptm) outliers start: 22 outliers final: 18 residues processed: 61 average time/residue: 1.2465 time to fit residues: 79.2572 Evaluate side-chains 60 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 42 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7938 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4910 Z= 0.407 Angle : 0.632 5.942 6630 Z= 0.366 Chirality : 0.054 0.141 870 Planarity : 0.002 0.011 830 Dihedral : 7.471 42.521 722 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 4.68 % Allowed : 15.32 % Favored : 80.00 % 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 (0.24), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.18), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.006 0.001 PHE D 94 TYR 0.020 0.004 TYR I 39 *********************** 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 75 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 53 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8156 (mttp) cc_final: 0.7784 (mtpt) REVERT: D 80 LYS cc_start: 0.8647 (mtpm) cc_final: 0.8436 (mtpp) REVERT: E 80 LYS cc_start: 0.8661 (mttp) cc_final: 0.8299 (mtpp) REVERT: F 65 ASN cc_start: 0.8923 (m-40) cc_final: 0.8717 (m-40) REVERT: H 60 LYS cc_start: 0.7696 (mttt) cc_final: 0.7361 (mtpp) REVERT: J 58 LYS cc_start: 0.7733 (ttmt) cc_final: 0.6997 (tptm) outliers start: 22 outliers final: 18 residues processed: 67 average time/residue: 1.2924 time to fit residues: 89.9991 Evaluate side-chains 70 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 52 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7872 moved from start: 0.2271 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= 0.207 Angle : 0.562 6.118 6630 Z= 0.324 Chirality : 0.052 0.136 870 Planarity : 0.002 0.010 830 Dihedral : 6.832 42.132 722 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 4.47 % Allowed : 16.17 % Favored : 79.36 % 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: -4.78 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.002 0.001 PHE B 94 TYR 0.011 0.002 TYR B 39 *********************** 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 70 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 49 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8073 (mttp) cc_final: 0.7479 (mtpp) REVERT: E 80 LYS cc_start: 0.8480 (mttp) cc_final: 0.8136 (mtpp) REVERT: H 60 LYS cc_start: 0.7608 (mttt) cc_final: 0.7295 (mtpp) REVERT: J 58 LYS cc_start: 0.7663 (ttmt) cc_final: 0.6928 (tptp) outliers start: 21 outliers final: 19 residues processed: 63 average time/residue: 1.2324 time to fit residues: 80.9630 Evaluate side-chains 66 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7924 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4910 Z= 0.356 Angle : 0.607 6.048 6630 Z= 0.352 Chirality : 0.053 0.138 870 Planarity : 0.002 0.010 830 Dihedral : 7.199 41.736 722 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.46 % Favored : 87.54 % Rotamer: Outliers : 5.11 % Allowed : 16.60 % Favored : 78.30 % 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: -4.95 (0.24), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.18), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.005 0.001 PHE D 94 TYR 0.017 0.004 TYR I 39 *********************** 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 75 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 51 time to evaluate : 0.543 Fit side-chains REVERT: B 80 LYS cc_start: 0.7998 (mttp) cc_final: 0.7567 (mtpp) REVERT: C 58 LYS cc_start: 0.7336 (ttmt) cc_final: 0.6772 (tmtm) REVERT: E 80 LYS cc_start: 0.8525 (mttp) cc_final: 0.8171 (mtpp) REVERT: F 65 ASN cc_start: 0.8916 (m-40) cc_final: 0.8693 (m-40) REVERT: G 65 ASN cc_start: 0.8784 (m-40) cc_final: 0.8547 (m110) REVERT: H 60 LYS cc_start: 0.7661 (mttt) cc_final: 0.7352 (mtpp) REVERT: J 58 LYS cc_start: 0.7716 (ttmt) cc_final: 0.6963 (tptp) outliers start: 24 outliers final: 20 residues processed: 68 average time/residue: 1.2945 time to fit residues: 91.5429 Evaluate side-chains 70 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 50 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7914 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4910 Z= 0.316 Angle : 0.598 6.012 6630 Z= 0.346 Chirality : 0.053 0.138 870 Planarity : 0.002 0.010 830 Dihedral : 7.140 42.719 722 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 4.04 % Allowed : 17.45 % Favored : 78.51 % 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: -4.97 (0.24), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.004 0.001 PHE D 94 TYR 0.015 0.003 TYR I 39 ********************** 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 69 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 0.529 Fit side-chains REVERT: B 80 LYS cc_start: 0.7971 (mttp) cc_final: 0.7587 (mtpt) REVERT: C 58 LYS cc_start: 0.7311 (ttmt) cc_final: 0.6771 (tmtm) REVERT: E 80 LYS cc_start: 0.8497 (mttp) cc_final: 0.8190 (mtpp) REVERT: H 60 LYS cc_start: 0.7645 (mttt) cc_final: 0.7329 (mtpp) REVERT: J 58 LYS cc_start: 0.7685 (ttmt) cc_final: 0.6936 (tptp) outliers start: 19 outliers final: 19 residues processed: 63 average time/residue: 1.3087 time to fit residues: 85.7039 Evaluate side-chains 69 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 0.0010 chunk 57 optimal weight: 6.9990 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: 0.0970 chunk 63 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.135604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.118497 restraints weight = 5738.971| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.07 r_work: 0.3791 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4910 Z= 0.307 Angle : 0.607 6.010 6630 Z= 0.348 Chirality : 0.053 0.137 870 Planarity : 0.002 0.020 830 Dihedral : 7.090 42.600 722 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 4.68 % Allowed : 17.23 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.00 (0.24), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.004 0.001 PHE D 94 TYR 0.014 0.003 TYR I 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2063.58 seconds wall clock time: 37 minutes 44.21 seconds (2264.21 seconds total)