Starting phenix.real_space_refine on Fri Sep 27 01:07:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyk_21462/09_2024/6vyk_21462_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyk_21462/09_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_21462/09_2024/6vyk_21462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyk_21462/09_2024/6vyk_21462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyk_21462/09_2024/6vyk_21462_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyk_21462/09_2024/6vyk_21462_neut.cif" } 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. Time to flip 7 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.41, per 1000 atoms: 0.58 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 2.0 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... Secondary structure from input PDB file: 56 helices and 9 sheets defined 56.2% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.849A pdb=" N ASN A 20 " --> pdb=" O TRP A 16 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 16 through 21' Processing helix chain 'A' and resid 23 through 58 removed outlier: 3.586A pdb=" N TYR A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 31 " --> pdb=" O TYR A 27 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 90 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 93 through 111 Processing helix chain 'A' and resid 111 through 127 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 172 Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.823A pdb=" N ILE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 265 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 21 removed outlier: 3.850A pdb=" N ASN B 20 " --> pdb=" O TRP B 16 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 16 through 21' Processing helix chain 'B' and resid 23 through 58 removed outlier: 3.585A pdb=" N TYR B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 31 " --> pdb=" O TYR B 27 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE B 43 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 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 93 through 111 Processing helix chain 'B' and resid 111 through 127 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 172 Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.822A pdb=" N ILE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 265 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 21 removed outlier: 3.850A pdb=" N ASN C 20 " --> pdb=" O TRP C 16 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 21' Processing helix chain 'C' and resid 23 through 58 removed outlier: 3.587A pdb=" N TYR C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 31 " --> pdb=" O TYR C 27 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE C 43 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 90 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 93 through 111 Processing helix chain 'C' and resid 111 through 127 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 172 Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.822A pdb=" N ILE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 265 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 21 removed outlier: 3.849A pdb=" N ASN D 20 " --> pdb=" O TRP D 16 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 16 through 21' Processing helix chain 'D' and resid 23 through 58 removed outlier: 3.586A pdb=" N TYR D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 31 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 90 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 93 through 111 Processing helix chain 'D' and resid 111 through 127 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 172 Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.822A pdb=" N ILE D 208 " --> pdb=" O ILE D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 265 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 21 removed outlier: 3.850A pdb=" N ASN E 20 " --> pdb=" O TRP E 16 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 16 through 21' Processing helix chain 'E' and resid 23 through 58 removed outlier: 3.586A pdb=" N TYR E 27 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN E 30 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE E 43 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 90 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 93 through 111 Processing helix chain 'E' and resid 111 through 127 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 172 Processing helix chain 'E' and resid 197 through 212 removed outlier: 3.822A pdb=" N ILE E 208 " --> pdb=" O ILE E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 265 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 21 removed outlier: 3.849A pdb=" N ASN F 20 " --> pdb=" O TRP F 16 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN F 21 " --> pdb=" O LEU F 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 16 through 21' Processing helix chain 'F' and resid 23 through 58 removed outlier: 3.586A pdb=" N TYR F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN F 30 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE F 31 " --> pdb=" O TYR F 27 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE F 43 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 90 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 93 through 111 Processing helix chain 'F' and resid 111 through 127 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 172 Processing helix chain 'F' and resid 197 through 212 removed outlier: 3.821A pdb=" N ILE F 208 " --> pdb=" O ILE F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 265 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 21 removed outlier: 3.850A pdb=" N ASN G 20 " --> pdb=" O TRP G 16 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN G 21 " --> pdb=" O LEU G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 16 through 21' Processing helix chain 'G' and resid 23 through 58 removed outlier: 3.587A pdb=" N TYR G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE G 31 " --> pdb=" O TYR G 27 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE G 43 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 90 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 93 through 111 Processing helix chain 'G' and resid 111 through 127 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 172 Processing helix chain 'G' and resid 197 through 212 removed outlier: 3.822A pdb=" N ILE G 208 " --> pdb=" O ILE G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 265 removed outlier: 3.704A pdb=" N ASP G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing sheet with id=AA1, 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) removed outlier: 3.612A pdb=" N ILE A 162 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 164 " --> pdb=" O ILE G 175 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE G 175 " --> pdb=" O VAL A 164 " (cutoff:3.500A) 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) removed outlier: 3.575A pdb=" N ILE F 175 " --> pdb=" O VAL G 164 " (cutoff:3.500A) 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) removed outlier: 3.532A pdb=" N ILE F 162 " --> pdb=" O ASN E 177 " (cutoff:3.500A) 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) removed outlier: 3.656A pdb=" N ILE E 162 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 175 " --> pdb=" O VAL E 164 " (cutoff:3.500A) 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) removed outlier: 3.576A pdb=" N ILE D 162 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 175 " --> pdb=" O VAL D 164 " (cutoff:3.500A) 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) removed outlier: 3.539A pdb=" N ILE C 162 " --> pdb=" O ASN B 177 " (cutoff:3.500A) 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=AA2, 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=AA3, first strand: chain 'A' and resid 273 through 279 removed outlier: 6.651A pdb=" N ASP A 274 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL B 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N PHE B 277 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LYS A 278 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ARG B 279 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP B 274 " --> pdb=" O MET C 273 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL C 275 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN B 276 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE C 277 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LYS B 278 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ARG C 279 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL D 275 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN C 276 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N PHE D 277 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LYS C 278 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N ARG D 279 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASN D 276 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N PHE E 277 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS D 278 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ARG E 279 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASP E 274 " --> pdb=" O MET F 273 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL F 275 " --> pdb=" O ASP E 274 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASN E 276 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N PHE F 277 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LYS E 278 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N ARG F 279 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASP F 274 " --> pdb=" O MET G 273 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL G 275 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ASN F 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE G 277 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS F 278 " --> pdb=" O PHE G 277 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ARG G 279 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN G 276 " --> pdb=" O MET A 273 " (cutoff:3.500A) Processing sheet with id=AA4, 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=AA5, 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=AA6, 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=AA7, 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=AA8, 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=AA9, 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) 895 hydrogen bonds defined for protein. 2646 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: 4.56 Time building geometry restraints manager: 4.23 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: 0.00 - 10.70: 19958 10.70 - 21.39: 13 21.39 - 32.09: 35 32.09 - 42.78: 1 42.78 - 53.48: 6 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: 248 2.68 - 3.23: 14711 3.23 - 3.79: 21612 3.79 - 4.34: 31978 4.34 - 4.90: 51312 Nonbonded interactions: 119861 Sorted by model distance: nonbonded pdb=" O ILE E 37 " pdb=" OG1 THR E 81 " model vdw 2.122 3.040 nonbonded pdb=" O ILE A 37 " pdb=" OG1 THR A 81 " model vdw 2.122 3.040 nonbonded pdb=" O ILE F 37 " pdb=" OG1 THR F 81 " model vdw 2.122 3.040 nonbonded pdb=" O ILE C 37 " pdb=" OG1 THR C 81 " model vdw 2.122 3.040 nonbonded pdb=" O ILE G 37 " pdb=" OG1 THR G 81 " model vdw 2.123 3.040 ... (remaining 119856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' 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: 1.200 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.920 Find NCS groups from input model: 0.750 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: 0.010 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: 39.560 ------------------------------------------------------------------------------- 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= 0.652 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 : 1.690 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: 0.3189 time to fit residues: 144.3459 Evaluate side-chains 233 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.598 ------------------------------------------------------------------------------- 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: 0.5980 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 174 ASN C 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14805 Z= 0.174 Angle : 1.281 33.798 20013 Z= 0.474 Chirality : 0.043 0.152 2408 Planarity : 0.004 0.047 2506 Dihedral : 14.970 178.609 2345 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.26 % Allowed : 7.34 % Favored : 91.40 % 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: -1.51 (0.19), residues: 1855 helix: -0.71 (0.15), residues: 1015 sheet: -0.92 (0.36), residues: 196 loop : -1.26 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 240 PHE 0.011 0.001 PHE A 178 TYR 0.010 0.001 TYR A 27 ARG 0.006 0.000 ARG E 59 *********************** 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 269 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 250 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.8547 (mm) cc_final: 0.8238 (mm) REVERT: B 74 ARG cc_start: 0.7146 (ttt-90) cc_final: 0.6916 (ttp-110) REVERT: C 224 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7744 (mtp180) REVERT: F 74 ARG cc_start: 0.7145 (ttt-90) cc_final: 0.6925 (ttp-110) REVERT: G 77 ILE cc_start: 0.8762 (mm) cc_final: 0.8516 (mm) REVERT: G 204 ILE cc_start: 0.8089 (tp) cc_final: 0.7760 (mt) REVERT: G 274 ASP cc_start: 0.7828 (m-30) cc_final: 0.7600 (m-30) outliers start: 19 outliers final: 7 residues processed: 262 average time/residue: 0.2700 time to fit residues: 102.6517 Evaluate side-chains 219 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 212 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 44 ILE 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 179 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7965 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14805 Z= 0.191 Angle : 1.273 33.068 20013 Z= 0.465 Chirality : 0.042 0.144 2408 Planarity : 0.003 0.036 2506 Dihedral : 13.795 174.835 2345 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.12 % Allowed : 10.05 % Favored : 88.82 % 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: -0.69 (0.20), residues: 1855 helix: 0.22 (0.16), residues: 1008 sheet: -1.37 (0.29), residues: 315 loop : -0.87 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 240 PHE 0.009 0.001 PHE G 277 TYR 0.006 0.001 TYR C 27 ARG 0.006 0.000 ARG A 54 *********************** 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 278 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 261 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 74 ARG cc_start: 0.7680 (ttt-90) cc_final: 0.7391 (ttp80) REVERT: E 88 ARG cc_start: 0.8537 (tpm170) cc_final: 0.8167 (mmm160) REVERT: G 77 ILE cc_start: 0.8767 (mm) cc_final: 0.8548 (mm) REVERT: G 109 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7715 (mp) outliers start: 17 outliers final: 9 residues processed: 269 average time/residue: 0.2779 time to fit residues: 108.2861 Evaluate side-chains 225 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 215 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 181 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14805 Z= 0.208 Angle : 1.273 33.087 20013 Z= 0.463 Chirality : 0.043 0.196 2408 Planarity : 0.003 0.039 2506 Dihedral : 13.357 172.187 2345 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.12 % Allowed : 13.03 % Favored : 85.85 % 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: 0.63 (0.17), residues: 1008 sheet: -1.31 (0.29), residues: 315 loop : -0.83 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 240 PHE 0.011 0.001 PHE C 130 TYR 0.006 0.001 TYR G 250 ARG 0.011 0.000 ARG C 128 *********************** 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 250 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 233 time to evaluate : 1.568 Fit side-chains REVERT: A 109 LEU cc_start: 0.8369 (mp) cc_final: 0.8162 (mp) REVERT: B 74 ARG cc_start: 0.7797 (ttp-110) cc_final: 0.7445 (ttp80) REVERT: D 74 ARG cc_start: 0.7693 (ttt-90) cc_final: 0.7453 (ttp80) REVERT: E 42 LEU cc_start: 0.8461 (mt) cc_final: 0.8258 (mt) REVERT: E 88 ARG cc_start: 0.8624 (tpm170) cc_final: 0.8019 (mmm160) REVERT: G 77 ILE cc_start: 0.8795 (mm) cc_final: 0.8565 (mm) outliers start: 17 outliers final: 9 residues processed: 245 average time/residue: 0.2991 time to fit residues: 103.0139 Evaluate side-chains 235 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 226 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 100 LEU 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: 0.0070 chunk 99 optimal weight: 0.2980 chunk 2 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 72 optimal weight: 0.0370 chunk 150 optimal weight: 0.0570 chunk 121 optimal weight: 0.6980 chunk 0 optimal weight: 40.0000 chunk 89 optimal weight: 0.2980 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 0.0370 overall best weight: 0.0872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14805 Z= 0.109 Angle : 1.257 33.207 20013 Z= 0.453 Chirality : 0.041 0.180 2408 Planarity : 0.003 0.044 2506 Dihedral : 12.631 169.459 2345 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.32 % Allowed : 13.16 % Favored : 85.52 % 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: 1.05 (0.17), residues: 1008 sheet: -0.67 (0.32), residues: 280 loop : -0.90 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 240 PHE 0.010 0.001 PHE A 130 TYR 0.006 0.001 TYR C 135 ARG 0.009 0.000 ARG A 131 *********************** 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 296 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 276 time to evaluate : 1.668 Fit side-chains REVERT: A 42 LEU cc_start: 0.8724 (mt) cc_final: 0.8419 (mt) REVERT: B 74 ARG cc_start: 0.7752 (ttp-110) cc_final: 0.7434 (ttp80) REVERT: D 74 ARG cc_start: 0.7694 (ttt-90) cc_final: 0.7446 (ttp80) REVERT: E 88 ARG cc_start: 0.8497 (tpm170) cc_final: 0.7959 (mmm160) REVERT: E 149 GLN cc_start: 0.7939 (mt0) cc_final: 0.7711 (mt0) REVERT: G 77 ILE cc_start: 0.8777 (mm) cc_final: 0.8542 (mm) outliers start: 20 outliers final: 12 residues processed: 283 average time/residue: 0.3007 time to fit residues: 123.5983 Evaluate side-chains 255 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 243 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain G residue 69 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 176 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4218 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= 0.166 Angle : 1.265 33.045 20013 Z= 0.459 Chirality : 0.042 0.245 2408 Planarity : 0.003 0.055 2506 Dihedral : 12.379 170.207 2345 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.39 % Allowed : 14.48 % Favored : 84.13 % 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: 0.45 (0.20), residues: 1855 helix: 1.22 (0.17), residues: 1008 sheet: -0.60 (0.32), residues: 280 loop : -0.77 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 251 PHE 0.010 0.001 PHE A 130 TYR 0.010 0.001 TYR C 250 ARG 0.006 0.000 ARG F 131 *********************** 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 272 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 251 time to evaluate : 1.747 Fit side-chains REVERT: A 42 LEU cc_start: 0.8728 (mt) cc_final: 0.8415 (mt) REVERT: A 97 ILE cc_start: 0.8653 (mt) cc_final: 0.8416 (mp) REVERT: B 74 ARG cc_start: 0.7838 (ttp-110) cc_final: 0.7481 (ttp80) REVERT: D 74 ARG cc_start: 0.7729 (ttt-90) cc_final: 0.7441 (ttp80) REVERT: E 59 ARG cc_start: 0.7066 (mpt-90) cc_final: 0.6865 (mpt-90) REVERT: E 88 ARG cc_start: 0.8552 (tpm170) cc_final: 0.7981 (mmm160) REVERT: G 77 ILE cc_start: 0.8793 (mm) cc_final: 0.8556 (mm) outliers start: 21 outliers final: 15 residues processed: 262 average time/residue: 0.2974 time to fit residues: 111.0395 Evaluate side-chains 256 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 241 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 233 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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: 0.8016 moved from start: 0.4380 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= 0.215 Angle : 1.271 33.061 20013 Z= 0.464 Chirality : 0.043 0.228 2408 Planarity : 0.003 0.058 2506 Dihedral : 12.288 170.409 2345 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.32 % Allowed : 14.88 % Favored : 83.80 % 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: 0.44 (0.20), residues: 1855 helix: 1.21 (0.17), residues: 1015 sheet: -0.62 (0.33), residues: 280 loop : -0.80 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 251 PHE 0.013 0.001 PHE A 130 TYR 0.009 0.001 TYR C 250 ARG 0.006 0.000 ARG F 131 *********************** 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 256 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 236 time to evaluate : 1.597 Fit side-chains revert: symmetry clash REVERT: A 97 ILE cc_start: 0.8722 (mt) cc_final: 0.8454 (mt) REVERT: B 74 ARG cc_start: 0.7860 (ttp-110) cc_final: 0.7496 (ttp80) REVERT: B 97 ILE cc_start: 0.8777 (mt) cc_final: 0.8528 (mt) REVERT: D 46 ARG cc_start: 0.7875 (tpp80) cc_final: 0.7459 (tpp80) REVERT: D 74 ARG cc_start: 0.7775 (ttt-90) cc_final: 0.7457 (ttp80) REVERT: G 77 ILE cc_start: 0.8820 (mm) cc_final: 0.8614 (mm) outliers start: 20 outliers final: 16 residues processed: 247 average time/residue: 0.3224 time to fit residues: 113.6558 Evaluate side-chains 247 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 231 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 155 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 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 233 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 104 optimal weight: 30.0000 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 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: 0.7999 moved from start: 0.4548 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= 0.169 Angle : 1.270 33.018 20013 Z= 0.461 Chirality : 0.043 0.358 2408 Planarity : 0.003 0.053 2506 Dihedral : 12.014 169.549 2345 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.32 % Allowed : 15.01 % Favored : 83.66 % 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: 0.51 (0.20), residues: 1855 helix: 1.32 (0.17), residues: 1015 sheet: -0.53 (0.31), residues: 294 loop : -0.91 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 251 PHE 0.010 0.001 PHE F 178 TYR 0.005 0.001 TYR B 135 ARG 0.008 0.000 ARG E 59 *********************** 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 253 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 233 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8761 (mt) cc_final: 0.8444 (mt) REVERT: A 97 ILE cc_start: 0.8685 (mt) cc_final: 0.8436 (mt) REVERT: B 97 ILE cc_start: 0.8743 (mt) cc_final: 0.8493 (mt) REVERT: D 74 ARG cc_start: 0.7799 (ttt-90) cc_final: 0.7532 (ttp80) REVERT: E 74 ARG cc_start: 0.7669 (ttt-90) cc_final: 0.7389 (ttp-110) REVERT: G 77 ILE cc_start: 0.8819 (mm) cc_final: 0.8616 (mm) outliers start: 20 outliers final: 14 residues processed: 244 average time/residue: 0.2968 time to fit residues: 101.9976 Evaluate side-chains 241 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 227 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 159 ASP 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 233 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 9.9990 chunk 168 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8006 moved from start: 0.4649 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 : 1.274 32.998 20013 Z= 0.464 Chirality : 0.044 0.314 2408 Planarity : 0.003 0.050 2506 Dihedral : 11.751 169.665 2345 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.46 % Allowed : 15.54 % Favored : 83.00 % 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: 0.54 (0.20), residues: 1855 helix: 1.35 (0.17), residues: 1015 sheet: -0.53 (0.31), residues: 294 loop : -0.91 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 251 PHE 0.010 0.001 PHE F 178 TYR 0.006 0.001 TYR E 250 ARG 0.008 0.000 ARG E 59 *********************** 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 255 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 233 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8770 (mt) cc_final: 0.8447 (mt) REVERT: A 97 ILE cc_start: 0.8679 (mt) cc_final: 0.8423 (mt) REVERT: B 97 ILE cc_start: 0.8768 (mt) cc_final: 0.8510 (mt) REVERT: D 74 ARG cc_start: 0.7796 (ttt-90) cc_final: 0.7558 (ttp80) REVERT: E 74 ARG cc_start: 0.7664 (ttt-90) cc_final: 0.7386 (ttp-110) outliers start: 22 outliers final: 18 residues processed: 246 average time/residue: 0.2907 time to fit residues: 101.5985 Evaluate side-chains 244 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 226 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 155 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 F residue 35 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 233 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 120 optimal weight: 0.0870 chunk 181 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 111 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 ASN F 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14805 Z= 0.255 Angle : 1.287 33.035 20013 Z= 0.474 Chirality : 0.046 0.384 2408 Planarity : 0.003 0.043 2506 Dihedral : 11.711 169.702 2345 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.59 % Allowed : 16.07 % Favored : 82.34 % 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: 0.45 (0.20), residues: 1855 helix: 1.21 (0.16), residues: 1022 sheet: -0.59 (0.31), residues: 294 loop : -0.80 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 251 PHE 0.012 0.001 PHE F 178 TYR 0.010 0.001 TYR E 250 ARG 0.008 0.000 ARG E 59 ********************** 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 251 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 227 time to evaluate : 1.488 Fit side-chains REVERT: A 42 LEU cc_start: 0.8781 (mt) cc_final: 0.8444 (mt) REVERT: A 97 ILE cc_start: 0.8640 (mt) cc_final: 0.8333 (mt) REVERT: B 97 ILE cc_start: 0.8835 (mt) cc_final: 0.8559 (mt) REVERT: D 74 ARG cc_start: 0.7781 (ttt-90) cc_final: 0.7529 (ttp80) REVERT: E 74 ARG cc_start: 0.7657 (ttt-90) cc_final: 0.7360 (ttp-110) outliers start: 24 outliers final: 19 residues processed: 242 average time/residue: 0.3135 time to fit residues: 106.7829 Evaluate side-chains 232 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 213 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 233 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.144559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.102574 restraints weight = 16543.114| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.73 r_work: 0.2899 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14805 Z= 0.241 Angle : 1.289 33.001 20013 Z= 0.474 Chirality : 0.046 0.361 2408 Planarity : 0.003 0.059 2506 Dihedral : 11.549 169.121 2345 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.65 % Allowed : 16.53 % Favored : 81.81 % 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: 0.40 (0.20), residues: 1855 helix: 1.20 (0.16), residues: 1022 sheet: -0.70 (0.31), residues: 294 loop : -0.83 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 251 PHE 0.011 0.001 PHE F 178 TYR 0.009 0.001 TYR E 250 ARG 0.014 0.001 ARG C 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3313.45 seconds wall clock time: 59 minutes 25.23 seconds (3565.23 seconds total)