Starting phenix.real_space_refine on Sat Mar 16 12:12:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyk_21462/03_2024/6vyk_21462_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyk_21462/03_2024/6vyk_21462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyk_21462/03_2024/6vyk_21462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyk_21462/03_2024/6vyk_21462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyk_21462/03_2024/6vyk_21462_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyk_21462/03_2024/6vyk_21462_neut_updated.pdb" } resolution = 3.2 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= 0.013 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 42 5.16 5 C 9464 2.51 5 N 2492 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 46": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "F ARG 46": "NH1" <-> "NH2" Residue "G ARG 46": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14623 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2035 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "B" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2035 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "C" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2035 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "D" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2035 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "E" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2035 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "F" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2035 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "G" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2035 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PCW': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PCW': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PCW': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.79, per 1000 atoms: 0.53 Number of scatterers: 14623 At special positions: 0 Unit cell: (97, 96, 149, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 7 15.00 O 2618 8.00 N 2492 7.00 C 9464 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: 6.17 Conformation dependent library (CDL) restraints added in 2.6 seconds 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3444 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 14 sheets defined 51.3% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 removed outlier: 4.164A pdb=" N ASN A 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 57 removed outlier: 4.029A pdb=" N VAL A 29 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN A 30 " --> pdb=" O TYR A 27 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE A 39 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL A 40 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU A 42 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 43 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 46 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 48 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 52 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 57 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 89 removed outlier: 3.649A pdb=" N PHE A 68 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.989A pdb=" N ASN A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 198 through 211 removed outlier: 3.823A pdb=" N ILE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 264 removed outlier: 3.704A pdb=" N ASP A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 20 removed outlier: 4.164A pdb=" N ASN B 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 57 removed outlier: 4.028A pdb=" N VAL B 29 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN B 30 " --> pdb=" O TYR B 27 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE B 39 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B 40 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU B 42 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 43 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 46 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE B 48 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL B 52 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 57 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 89 removed outlier: 3.650A pdb=" N PHE B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.990A pdb=" N ASN B 117 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 198 through 211 removed outlier: 3.822A pdb=" N ILE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 264 removed outlier: 3.704A pdb=" N ASP B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 20 removed outlier: 4.164A pdb=" N ASN C 20 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 57 removed outlier: 4.028A pdb=" N VAL C 29 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN C 30 " --> pdb=" O TYR C 27 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE C 39 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL C 40 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU C 42 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE C 43 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 46 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL C 52 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 57 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 89 removed outlier: 3.649A pdb=" N PHE C 68 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 79 " --> pdb=" O TYR C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 110 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.990A pdb=" N ASN C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 198 through 211 removed outlier: 3.822A pdb=" N ILE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 264 removed outlier: 3.705A pdb=" N ASP C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 removed outlier: 4.164A pdb=" N ASN D 20 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 57 removed outlier: 4.029A pdb=" N VAL D 29 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN D 30 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE D 39 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL D 40 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU D 42 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE D 43 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE D 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG D 46 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL D 52 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 55 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 57 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 89 removed outlier: 3.649A pdb=" N PHE D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 79 " --> pdb=" O TYR D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 110 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.990A pdb=" N ASN D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 198 through 211 removed outlier: 3.822A pdb=" N ILE D 208 " --> pdb=" O ILE D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 264 removed outlier: 3.705A pdb=" N ASP D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 20 removed outlier: 4.164A pdb=" N ASN E 20 " --> pdb=" O LEU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 57 removed outlier: 4.029A pdb=" N VAL E 29 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN E 30 " --> pdb=" O TYR E 27 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE E 39 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL E 40 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU E 42 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE E 43 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 44 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG E 46 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL E 52 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU E 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE E 57 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 89 removed outlier: 3.650A pdb=" N PHE E 68 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 79 " --> pdb=" O TYR E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 110 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.990A pdb=" N ASN E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 198 through 211 removed outlier: 3.822A pdb=" N ILE E 208 " --> pdb=" O ILE E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 264 removed outlier: 3.704A pdb=" N ASP E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 20 removed outlier: 4.164A pdb=" N ASN F 20 " --> pdb=" O LEU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 57 removed outlier: 4.029A pdb=" N VAL F 29 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN F 30 " --> pdb=" O TYR F 27 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE F 39 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL F 40 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU F 42 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE F 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG F 46 " --> pdb=" O ILE F 43 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE F 48 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL F 52 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU F 55 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE F 57 " --> pdb=" O ARG F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 89 removed outlier: 3.650A pdb=" N PHE F 68 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 79 " --> pdb=" O TYR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 110 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.989A pdb=" N ASN F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL F 125 " --> pdb=" O GLY F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 198 through 211 removed outlier: 3.821A pdb=" N ILE F 208 " --> pdb=" O ILE F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 264 removed outlier: 3.705A pdb=" N ASP F 262 " --> pdb=" O LYS F 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 20 removed outlier: 4.164A pdb=" N ASN G 20 " --> pdb=" O LEU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 57 removed outlier: 4.030A pdb=" N VAL G 29 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN G 30 " --> pdb=" O TYR G 27 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE G 39 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL G 40 " --> pdb=" O ILE G 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU G 42 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE G 43 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE G 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG G 46 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL G 52 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU G 55 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE G 57 " --> pdb=" O ARG G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 89 removed outlier: 3.650A pdb=" N PHE G 68 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA G 79 " --> pdb=" O TYR G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 110 Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.990A pdb=" N ASN G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL G 125 " --> pdb=" O GLY G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 171 Processing helix chain 'G' and resid 198 through 211 removed outlier: 3.822A pdb=" N ILE G 208 " --> pdb=" O ILE G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 264 removed outlier: 3.704A pdb=" N ASP G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 135 through 137 removed outlier: 7.091A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.167A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 135 through 137 removed outlier: 7.090A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.167A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 135 through 137 removed outlier: 7.090A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.166A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 135 through 137 removed outlier: 7.090A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.167A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 135 through 137 removed outlier: 7.091A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.166A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 135 through 137 removed outlier: 7.091A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.167A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 135 through 137 removed outlier: 7.091A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.166A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 6.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2345 1.31 - 1.43: 3554 1.43 - 1.56: 8644 1.56 - 1.68: 172 1.68 - 1.81: 90 Bond restraints: 14805 Sorted by residual: bond pdb=" C11 PCW D 301 " pdb=" O3 PCW D 301 " ideal model delta sigma weight residual 1.326 1.434 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C11 PCW A 301 " pdb=" O3 PCW A 301 " ideal model delta sigma weight residual 1.326 1.434 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" C11 PCW B 301 " pdb=" O3 PCW B 301 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C11 PCW F 402 " pdb=" O3 PCW F 402 " ideal model delta sigma weight residual 1.326 1.432 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C11 PCW C 301 " pdb=" O3 PCW C 301 " ideal model delta sigma weight residual 1.326 1.432 -0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 14800 not shown) Histogram of bond angle deviations from ideal: 83.79 - 99.55: 35 99.55 - 115.31: 9379 115.31 - 131.07: 10564 131.07 - 146.83: 28 146.83 - 162.59: 7 Bond angle restraints: 20013 Sorted by residual: angle pdb=" C6 PCW D 301 " pdb=" N PCW D 301 " pdb=" C8 PCW D 301 " ideal model delta sigma weight residual 109.11 162.59 -53.48 3.00e+00 1.11e-01 3.18e+02 angle pdb=" C6 PCW F 401 " pdb=" N PCW F 401 " pdb=" C8 PCW F 401 " ideal model delta sigma weight residual 109.11 161.18 -52.07 3.00e+00 1.11e-01 3.01e+02 angle pdb=" C6 PCW B 301 " pdb=" N PCW B 301 " pdb=" C8 PCW B 301 " ideal model delta sigma weight residual 109.11 160.94 -51.83 3.00e+00 1.11e-01 2.98e+02 angle pdb=" C6 PCW C 301 " pdb=" N PCW C 301 " pdb=" C8 PCW C 301 " ideal model delta sigma weight residual 109.11 159.74 -50.63 3.00e+00 1.11e-01 2.85e+02 angle pdb=" C6 PCW A 301 " pdb=" N PCW A 301 " pdb=" C8 PCW A 301 " ideal model delta sigma weight residual 109.11 158.58 -49.47 3.00e+00 1.11e-01 2.72e+02 ... (remaining 20008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.70: 8772 34.70 - 69.41: 169 69.41 - 104.11: 5 104.11 - 138.81: 0 138.81 - 173.51: 14 Dihedral angle restraints: 8960 sinusoidal: 3612 harmonic: 5348 Sorted by residual: dihedral pdb=" N PCW D 301 " pdb=" C4 PCW D 301 " pdb=" C5 PCW D 301 " pdb=" O4P PCW D 301 " ideal model delta sinusoidal sigma weight residual 293.34 119.83 173.51 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N PCW B 301 " pdb=" C4 PCW B 301 " pdb=" C5 PCW B 301 " pdb=" O4P PCW B 301 " ideal model delta sinusoidal sigma weight residual 293.34 120.29 173.05 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N PCW F 402 " pdb=" C4 PCW F 402 " pdb=" C5 PCW F 402 " pdb=" O4P PCW F 402 " ideal model delta sinusoidal sigma weight residual 293.34 126.88 166.46 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 8957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2327 0.117 - 0.234: 43 0.234 - 0.351: 17 0.351 - 0.468: 14 0.468 - 0.585: 7 Chirality restraints: 2408 Sorted by residual: chirality pdb=" CB VAL D 29 " pdb=" CA VAL D 29 " pdb=" CG1 VAL D 29 " pdb=" CG2 VAL D 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.58 2.00e-01 2.50e+01 8.55e+00 chirality pdb=" CB VAL F 29 " pdb=" CA VAL F 29 " pdb=" CG1 VAL F 29 " pdb=" CG2 VAL F 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.41e+00 chirality pdb=" CB VAL G 29 " pdb=" CA VAL G 29 " pdb=" CG1 VAL G 29 " pdb=" CG2 VAL G 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.39e+00 ... (remaining 2405 not shown) Planarity restraints: 2506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 270 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 271 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 270 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO C 271 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 271 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 271 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 270 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO F 271 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 271 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 271 " 0.025 5.00e-02 4.00e+02 ... (remaining 2503 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 270 2.68 - 3.23: 14817 3.23 - 3.79: 21663 3.79 - 4.34: 32346 4.34 - 4.90: 51321 Nonbonded interactions: 120417 Sorted by model distance: nonbonded pdb=" O ILE E 37 " pdb=" OG1 THR E 81 " model vdw 2.122 2.440 nonbonded pdb=" O ILE A 37 " pdb=" OG1 THR A 81 " model vdw 2.122 2.440 nonbonded pdb=" O ILE F 37 " pdb=" OG1 THR F 81 " model vdw 2.122 2.440 nonbonded pdb=" O ILE C 37 " pdb=" OG1 THR C 81 " model vdw 2.122 2.440 nonbonded pdb=" O ILE G 37 " pdb=" OG1 THR G 81 " model vdw 2.123 2.440 ... (remaining 120412 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' and resid 14 through 280) selection = (chain 'B' and resid 14 through 280) selection = (chain 'C' and resid 14 through 280) selection = (chain 'D' and resid 14 through 280) selection = chain 'E' selection = (chain 'F' and resid 14 through 280) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 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: 2.870 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 41.590 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 0.010 0.108 14805 Z= 0.657 Angle : 1.735 53.479 20013 Z= 0.679 Chirality : 0.072 0.585 2408 Planarity : 0.004 0.045 2506 Dihedral : 15.956 173.513 5516 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -3.22 (0.17), residues: 1855 helix: -2.22 (0.14), residues: 1001 sheet: -1.72 (0.30), residues: 252 loop : -1.71 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 251 PHE 0.015 0.002 PHE A 277 TYR 0.006 0.001 TYR G 75 ARG 0.002 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8414 (mm) cc_final: 0.8202 (mm) REVERT: A 186 ASN cc_start: 0.8347 (m-40) cc_final: 0.8144 (m-40) REVERT: A 190 ILE cc_start: 0.8882 (mm) cc_final: 0.8651 (mp) REVERT: A 252 ASP cc_start: 0.8272 (m-30) cc_final: 0.7905 (m-30) REVERT: C 199 ASP cc_start: 0.7300 (m-30) cc_final: 0.6998 (m-30) REVERT: F 213 ASP cc_start: 0.7383 (p0) cc_final: 0.7146 (p0) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.3208 time to fit residues: 144.4703 Evaluate side-chains 233 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 142 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN C 174 ASN C 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14805 Z= 0.164 Angle : 1.267 35.623 20013 Z= 0.463 Chirality : 0.042 0.138 2408 Planarity : 0.004 0.032 2506 Dihedral : 14.772 176.121 2345 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.06 % Allowed : 6.88 % Favored : 92.06 % 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: -1.99 (0.19), residues: 1855 helix: -0.99 (0.15), residues: 994 sheet: -1.82 (0.28), residues: 315 loop : -1.17 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 240 PHE 0.008 0.001 PHE D 188 TYR 0.008 0.001 TYR C 75 ARG 0.006 0.000 ARG D 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 236 time to evaluate : 1.595 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8331 (mm) cc_final: 0.8056 (mm) REVERT: D 37 ILE cc_start: 0.8311 (mm) cc_final: 0.8092 (mm) REVERT: F 131 ARG cc_start: 0.7027 (mtm-85) cc_final: 0.6765 (ptp90) REVERT: G 82 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8473 (mp) REVERT: G 204 ILE cc_start: 0.7998 (tp) cc_final: 0.7674 (mt) outliers start: 16 outliers final: 6 residues processed: 247 average time/residue: 0.2795 time to fit residues: 98.7013 Evaluate side-chains 216 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 209 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 179 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 112 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 56 optimal weight: 0.1980 chunk 132 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.7922 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14805 Z= 0.167 Angle : 1.163 32.824 20013 Z= 0.426 Chirality : 0.041 0.140 2408 Planarity : 0.003 0.035 2506 Dihedral : 13.797 174.437 2345 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.06 % Allowed : 9.99 % Favored : 88.96 % 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: -1.42 (0.20), residues: 1855 helix: -0.48 (0.16), residues: 994 sheet: -1.59 (0.29), residues: 315 loop : -0.99 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 251 PHE 0.007 0.001 PHE D 188 TYR 0.004 0.001 TYR B 250 ARG 0.006 0.000 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 218 time to evaluate : 1.530 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8342 (mm) cc_final: 0.8056 (mm) REVERT: B 204 ILE cc_start: 0.8256 (tp) cc_final: 0.8040 (mt) REVERT: D 37 ILE cc_start: 0.8327 (mm) cc_final: 0.8086 (mm) REVERT: D 74 ARG cc_start: 0.7718 (ttt-90) cc_final: 0.7336 (ttp80) REVERT: F 37 ILE cc_start: 0.8428 (mm) cc_final: 0.8089 (mm) REVERT: F 131 ARG cc_start: 0.7024 (mtm-85) cc_final: 0.6744 (ptp90) REVERT: G 77 ILE cc_start: 0.8717 (mm) cc_final: 0.8468 (mm) outliers start: 16 outliers final: 11 residues processed: 232 average time/residue: 0.2887 time to fit residues: 94.8150 Evaluate side-chains 220 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 209 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 179 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 chunk 86 optimal weight: 0.2980 chunk 157 optimal weight: 0.0370 chunk 47 optimal weight: 5.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14805 Z= 0.175 Angle : 1.161 32.655 20013 Z= 0.424 Chirality : 0.041 0.144 2408 Planarity : 0.003 0.028 2506 Dihedral : 12.717 173.484 2345 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.26 % Allowed : 11.84 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1855 helix: -0.05 (0.16), residues: 1001 sheet: -1.29 (0.30), residues: 301 loop : -0.85 (0.29), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 240 PHE 0.010 0.001 PHE F 277 TYR 0.005 0.001 TYR B 250 ARG 0.008 0.000 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 233 time to evaluate : 1.632 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8347 (mm) cc_final: 0.8048 (mm) REVERT: D 74 ARG cc_start: 0.7739 (ttt-90) cc_final: 0.7402 (ttp80) REVERT: E 218 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7743 (p0) REVERT: F 37 ILE cc_start: 0.8474 (mm) cc_final: 0.8109 (mm) REVERT: G 77 ILE cc_start: 0.8741 (mm) cc_final: 0.8505 (mm) REVERT: G 224 ARG cc_start: 0.8317 (mtp85) cc_final: 0.8116 (mtp180) outliers start: 19 outliers final: 15 residues processed: 247 average time/residue: 0.2984 time to fit residues: 104.0123 Evaluate side-chains 226 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 210 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 181 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 72 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 0 optimal weight: 40.0000 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN B 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14805 Z= 0.249 Angle : 1.169 32.876 20013 Z= 0.431 Chirality : 0.042 0.183 2408 Planarity : 0.003 0.026 2506 Dihedral : 12.454 173.016 2345 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.59 % Allowed : 13.36 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.20), residues: 1855 helix: 0.07 (0.16), residues: 1001 sheet: -1.00 (0.30), residues: 315 loop : -0.94 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 240 PHE 0.009 0.001 PHE E 277 TYR 0.007 0.001 TYR G 250 ARG 0.007 0.000 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 226 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8380 (mm) cc_final: 0.8127 (mm) REVERT: A 97 ILE cc_start: 0.8884 (mt) cc_final: 0.8565 (mp) REVERT: B 97 ILE cc_start: 0.8773 (mt) cc_final: 0.8512 (mt) REVERT: D 74 ARG cc_start: 0.7755 (ttt-90) cc_final: 0.7414 (ttp80) REVERT: G 77 ILE cc_start: 0.8798 (mm) cc_final: 0.8529 (mm) outliers start: 24 outliers final: 16 residues processed: 240 average time/residue: 0.2983 time to fit residues: 100.1524 Evaluate side-chains 230 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 214 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 181 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 176 optimal weight: 0.0370 chunk 146 optimal weight: 0.0270 chunk 81 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN F 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14805 Z= 0.138 Angle : 1.154 32.782 20013 Z= 0.420 Chirality : 0.041 0.133 2408 Planarity : 0.003 0.025 2506 Dihedral : 11.889 175.290 2345 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.32 % Allowed : 14.68 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1855 helix: 0.44 (0.17), residues: 980 sheet: -0.80 (0.31), residues: 315 loop : -0.73 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 240 PHE 0.008 0.001 PHE E 188 TYR 0.004 0.001 TYR F 250 ARG 0.006 0.000 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 233 time to evaluate : 1.547 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8285 (mm) cc_final: 0.8083 (mm) REVERT: A 97 ILE cc_start: 0.8780 (mt) cc_final: 0.8511 (mp) REVERT: B 97 ILE cc_start: 0.8701 (mt) cc_final: 0.8450 (mt) REVERT: D 74 ARG cc_start: 0.7736 (ttt-90) cc_final: 0.7410 (ttp80) REVERT: E 149 GLN cc_start: 0.7969 (mt0) cc_final: 0.7738 (mt0) REVERT: G 77 ILE cc_start: 0.8739 (mm) cc_final: 0.8492 (mm) outliers start: 20 outliers final: 14 residues processed: 246 average time/residue: 0.2995 time to fit residues: 103.9174 Evaluate side-chains 233 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 219 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 181 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.0570 chunk 19 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN F 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14805 Z= 0.191 Angle : 1.159 32.743 20013 Z= 0.424 Chirality : 0.041 0.130 2408 Planarity : 0.003 0.051 2506 Dihedral : 11.584 175.313 2345 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.59 % Allowed : 14.68 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1855 helix: 0.47 (0.16), residues: 987 sheet: -0.59 (0.30), residues: 329 loop : -0.76 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 240 PHE 0.007 0.001 PHE A 130 TYR 0.013 0.001 TYR G 250 ARG 0.011 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 210 time to evaluate : 1.528 Fit side-chains REVERT: A 97 ILE cc_start: 0.8795 (mt) cc_final: 0.8501 (mp) REVERT: B 97 ILE cc_start: 0.8779 (mt) cc_final: 0.8520 (mt) REVERT: D 74 ARG cc_start: 0.7810 (ttt-90) cc_final: 0.7487 (ttp80) REVERT: E 149 GLN cc_start: 0.7993 (mt0) cc_final: 0.7755 (mt0) REVERT: G 77 ILE cc_start: 0.8764 (mm) cc_final: 0.8509 (mm) outliers start: 24 outliers final: 21 residues processed: 222 average time/residue: 0.2875 time to fit residues: 91.4473 Evaluate side-chains 228 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 187 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 30.0000 chunk 52 optimal weight: 40.0000 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14805 Z= 0.162 Angle : 1.156 32.789 20013 Z= 0.421 Chirality : 0.041 0.133 2408 Planarity : 0.003 0.052 2506 Dihedral : 11.113 175.998 2345 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.52 % Allowed : 15.28 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1855 helix: 0.64 (0.17), residues: 980 sheet: -0.50 (0.31), residues: 329 loop : -0.77 (0.30), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 240 PHE 0.007 0.001 PHE A 130 TYR 0.008 0.001 TYR G 250 ARG 0.014 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 228 time to evaluate : 1.653 Fit side-chains REVERT: A 97 ILE cc_start: 0.8779 (mt) cc_final: 0.8517 (mp) REVERT: B 97 ILE cc_start: 0.8798 (mt) cc_final: 0.8536 (mt) REVERT: D 74 ARG cc_start: 0.7808 (ttt-90) cc_final: 0.7494 (ttp80) REVERT: D 128 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7730 (mtt90) REVERT: E 149 GLN cc_start: 0.7995 (mt0) cc_final: 0.7756 (mt0) REVERT: G 77 ILE cc_start: 0.8747 (mm) cc_final: 0.8503 (mm) outliers start: 23 outliers final: 21 residues processed: 241 average time/residue: 0.2958 time to fit residues: 100.4427 Evaluate side-chains 237 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 216 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 181 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN F 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14805 Z= 0.179 Angle : 1.159 33.080 20013 Z= 0.423 Chirality : 0.041 0.132 2408 Planarity : 0.003 0.057 2506 Dihedral : 10.750 176.307 2345 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.46 % Allowed : 15.61 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1855 helix: 0.64 (0.17), residues: 980 sheet: -0.47 (0.31), residues: 329 loop : -0.71 (0.30), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 251 PHE 0.007 0.001 PHE D 188 TYR 0.007 0.001 TYR C 250 ARG 0.013 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 210 time to evaluate : 1.477 Fit side-chains REVERT: A 97 ILE cc_start: 0.8816 (mt) cc_final: 0.8526 (mp) REVERT: B 97 ILE cc_start: 0.8830 (mt) cc_final: 0.8561 (mt) REVERT: C 128 ARG cc_start: 0.7515 (mtp-110) cc_final: 0.7278 (mtp-110) REVERT: C 159 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7502 (t70) REVERT: D 74 ARG cc_start: 0.7760 (ttt-90) cc_final: 0.7514 (ttp80) REVERT: D 128 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7786 (mtt90) REVERT: E 149 GLN cc_start: 0.8007 (mt0) cc_final: 0.7769 (mt0) REVERT: G 77 ILE cc_start: 0.8757 (mm) cc_final: 0.8510 (mm) outliers start: 22 outliers final: 21 residues processed: 223 average time/residue: 0.2983 time to fit residues: 93.9251 Evaluate side-chains 229 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 207 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 181 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 82 optimal weight: 0.0010 chunk 120 optimal weight: 0.0980 chunk 181 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14805 Z= 0.180 Angle : 1.158 33.587 20013 Z= 0.423 Chirality : 0.041 0.130 2408 Planarity : 0.003 0.058 2506 Dihedral : 10.335 176.979 2345 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.26 % Allowed : 16.07 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1855 helix: 0.63 (0.17), residues: 987 sheet: -0.74 (0.31), residues: 315 loop : -0.70 (0.29), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 240 PHE 0.008 0.001 PHE D 188 TYR 0.007 0.001 TYR C 250 ARG 0.014 0.000 ARG B 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 206 time to evaluate : 1.543 Fit side-chains REVERT: A 97 ILE cc_start: 0.8810 (mt) cc_final: 0.8526 (mp) REVERT: B 97 ILE cc_start: 0.8832 (mt) cc_final: 0.8570 (mt) REVERT: C 128 ARG cc_start: 0.7551 (mtp-110) cc_final: 0.7337 (mtp-110) REVERT: C 159 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7508 (t70) REVERT: D 74 ARG cc_start: 0.7754 (ttt-90) cc_final: 0.7524 (ttp80) REVERT: D 128 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7803 (mtt90) REVERT: E 149 GLN cc_start: 0.8023 (mt0) cc_final: 0.7779 (mt0) REVERT: G 77 ILE cc_start: 0.8755 (mm) cc_final: 0.8508 (mm) outliers start: 19 outliers final: 18 residues processed: 218 average time/residue: 0.2973 time to fit residues: 91.7582 Evaluate side-chains 223 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 181 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 1.9990 chunk 153 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 50.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.146183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.104813 restraints weight = 16571.066| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.71 r_work: 0.2924 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14805 Z= 0.189 Angle : 1.161 33.519 20013 Z= 0.425 Chirality : 0.041 0.133 2408 Planarity : 0.003 0.060 2506 Dihedral : 10.191 177.622 2345 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.46 % Allowed : 16.01 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1855 helix: 0.59 (0.17), residues: 994 sheet: -0.75 (0.31), residues: 315 loop : -0.66 (0.30), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 251 PHE 0.008 0.001 PHE D 188 TYR 0.010 0.001 TYR C 250 ARG 0.014 0.000 ARG B 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3261.60 seconds wall clock time: 59 minutes 4.87 seconds (3544.87 seconds total)