Starting phenix.real_space_refine on Thu Sep 18 06:10:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vyk_21462/09_2025/6vyk_21462_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vyk_21462/09_2025/6vyk_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 { model { file = "/net/cci-nas-00/data/ceres_data/6vyk_21462/09_2025/6vyk_21462_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vyk_21462/09_2025/6vyk_21462_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vyk_21462/09_2025/6vyk_21462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vyk_21462/09_2025/6vyk_21462.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.50, per 1000 atoms: 0.24 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: 1.29 Conformation dependent library (CDL) restraints added in 690.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.61 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: 2.57 Time building geometry restraints manager: 1.64 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'E' 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: 0.690 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.720 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- 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= 0.451 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 : 3.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 259 TYR 0.006 0.001 TYR G 75 PHE 0.015 0.002 PHE A 277 TRP 0.005 0.001 TRP D 251 Details of bonding type rmsd covalent geometry : bond 0.00996 (14805) covalent geometry : angle 1.73550 (20013) hydrogen bonds : bond 0.13308 ( 895) hydrogen bonds : angle 7.60404 ( 2646) *********************** 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 to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.521 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: 0.1675 time to fit residues: 75.7626 Evaluate side-chains 233 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.147123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.108954 restraints weight = 16792.536| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.71 r_work: 0.3084 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2193 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= 0.125 Angle : 1.280 33.981 20013 Z= 0.474 Chirality : 0.042 0.145 2408 Planarity : 0.004 0.048 2506 Dihedral : 15.093 179.002 2345 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.32 % Allowed : 7.01 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.19), residues: 1855 helix: -0.75 (0.15), residues: 1015 sheet: -0.93 (0.36), residues: 196 loop : -1.27 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 59 TYR 0.008 0.001 TYR A 27 PHE 0.010 0.001 PHE A 178 TRP 0.007 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00284 (14805) covalent geometry : angle 1.27963 (20013) hydrogen bonds : bond 0.03186 ( 895) hydrogen bonds : angle 4.55663 ( 2646) *********************** 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 260 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 0.555 Fit side-chains REVERT: A 56 MET cc_start: 0.7747 (ttm) cc_final: 0.7478 (ttm) REVERT: A 204 ILE cc_start: 0.8027 (tp) cc_final: 0.7801 (mt) REVERT: B 74 ARG cc_start: 0.7083 (ttt-90) cc_final: 0.6538 (ttp-110) REVERT: C 131 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7588 (mtm-85) REVERT: C 224 ARG cc_start: 0.8341 (mtp85) cc_final: 0.7985 (mtp180) REVERT: D 56 MET cc_start: 0.7740 (ttm) cc_final: 0.7460 (ttm) REVERT: D 252 ASP cc_start: 0.8927 (m-30) cc_final: 0.8505 (m-30) REVERT: E 279 ARG cc_start: 0.7261 (tpp-160) cc_final: 0.6794 (tpt-90) REVERT: F 74 ARG cc_start: 0.7242 (ttt-90) cc_final: 0.6759 (ttp-110) REVERT: F 131 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7334 (ptp90) REVERT: G 56 MET cc_start: 0.7583 (ttm) cc_final: 0.7380 (ttm) outliers start: 20 outliers final: 9 residues processed: 253 average time/residue: 0.1384 time to fit residues: 50.5345 Evaluate side-chains 228 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 219 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain G residue 47 MET 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 134 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 70 optimal weight: 0.0170 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 164 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.151339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.114570 restraints weight = 16665.962| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.53 r_work: 0.3072 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3022 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= 0.102 Angle : 1.262 33.188 20013 Z= 0.458 Chirality : 0.042 0.152 2408 Planarity : 0.003 0.046 2506 Dihedral : 13.704 174.355 2345 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.26 % Allowed : 10.19 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.20), residues: 1855 helix: 0.21 (0.16), residues: 1015 sheet: -1.09 (0.31), residues: 266 loop : -0.93 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 54 TYR 0.005 0.001 TYR A 27 PHE 0.007 0.001 PHE D 188 TRP 0.006 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00224 (14805) covalent geometry : angle 1.26234 (20013) hydrogen bonds : bond 0.02802 ( 895) hydrogen bonds : angle 4.05421 ( 2646) *********************** 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 275 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7643 (ttt-90) cc_final: 0.7182 (ttp80) REVERT: B 204 ILE cc_start: 0.8222 (tp) cc_final: 0.7991 (mt) REVERT: C 128 ARG cc_start: 0.8442 (mtt90) cc_final: 0.7967 (mtp-110) REVERT: C 224 ARG cc_start: 0.8502 (mtp85) cc_final: 0.8255 (mtp180) REVERT: D 56 MET cc_start: 0.7630 (ttm) cc_final: 0.7337 (ttm) REVERT: D 74 ARG cc_start: 0.7799 (ttt-90) cc_final: 0.7223 (ttp80) REVERT: D 204 ILE cc_start: 0.7937 (tp) cc_final: 0.7628 (mt) REVERT: D 252 ASP cc_start: 0.8998 (m-30) cc_final: 0.8628 (m-30) REVERT: E 279 ARG cc_start: 0.7183 (tpp-160) cc_final: 0.6873 (tpt-90) REVERT: F 35 LEU cc_start: 0.9046 (mm) cc_final: 0.8765 (mm) REVERT: F 126 MET cc_start: 0.7628 (mtt) cc_final: 0.7358 (mtp) REVERT: F 131 ARG cc_start: 0.7598 (mtm-85) cc_final: 0.7224 (ptp90) REVERT: G 56 MET cc_start: 0.7579 (ttm) cc_final: 0.7356 (ttm) REVERT: G 77 ILE cc_start: 0.8548 (mm) cc_final: 0.8306 (mt) REVERT: G 109 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7747 (mp) REVERT: G 204 ILE cc_start: 0.8456 (tt) cc_final: 0.8186 (mt) outliers start: 19 outliers final: 10 residues processed: 266 average time/residue: 0.1357 time to fit residues: 51.9180 Evaluate side-chains 229 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 218 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 233 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 165 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 78 optimal weight: 40.0000 chunk 81 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.138415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.098368 restraints weight = 16797.073| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.73 r_work: 0.2957 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14805 Z= 0.123 Angle : 1.264 33.081 20013 Z= 0.459 Chirality : 0.042 0.135 2408 Planarity : 0.003 0.033 2506 Dihedral : 13.243 171.329 2345 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.19 % Allowed : 12.50 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.20), residues: 1855 helix: 0.70 (0.17), residues: 1008 sheet: -0.79 (0.31), residues: 280 loop : -0.78 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 224 TYR 0.010 0.001 TYR G 250 PHE 0.010 0.001 PHE F 178 TRP 0.005 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00286 (14805) covalent geometry : angle 1.26431 (20013) hydrogen bonds : bond 0.02830 ( 895) hydrogen bonds : angle 4.01857 ( 2646) *********************** 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 254 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7773 (ttm) cc_final: 0.7509 (ttm) REVERT: C 62 ASP cc_start: 0.7977 (t0) cc_final: 0.7733 (t70) REVERT: D 56 MET cc_start: 0.7694 (ttm) cc_final: 0.7383 (ttm) REVERT: D 74 ARG cc_start: 0.7667 (ttt-90) cc_final: 0.7150 (ttp80) REVERT: D 204 ILE cc_start: 0.8053 (tp) cc_final: 0.7780 (mt) REVERT: E 42 LEU cc_start: 0.8495 (mt) cc_final: 0.8252 (mt) REVERT: E 279 ARG cc_start: 0.7253 (tpp-160) cc_final: 0.6842 (tpt-90) REVERT: F 35 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8807 (mm) REVERT: F 126 MET cc_start: 0.7790 (mtt) cc_final: 0.7521 (mtp) REVERT: F 131 ARG cc_start: 0.7454 (mtm-85) cc_final: 0.7199 (ptp90) REVERT: G 42 LEU cc_start: 0.8734 (mt) cc_final: 0.8511 (mt) REVERT: G 161 LYS cc_start: 0.8911 (mtmt) cc_final: 0.8644 (mtmm) outliers start: 18 outliers final: 12 residues processed: 246 average time/residue: 0.1566 time to fit residues: 54.0885 Evaluate side-chains 242 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 229 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 35 LEU 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 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 139 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 5 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 chunk 181 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.139025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.099295 restraints weight = 16808.846| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.74 r_work: 0.2969 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3878 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= 0.102 Angle : 1.255 33.114 20013 Z= 0.453 Chirality : 0.042 0.137 2408 Planarity : 0.003 0.034 2506 Dihedral : 12.700 170.686 2345 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.39 % Allowed : 13.36 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.20), residues: 1855 helix: 1.00 (0.17), residues: 1015 sheet: -0.96 (0.32), residues: 266 loop : -0.76 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 54 TYR 0.006 0.001 TYR B 135 PHE 0.010 0.001 PHE F 178 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00230 (14805) covalent geometry : angle 1.25517 (20013) hydrogen bonds : bond 0.02677 ( 895) hydrogen bonds : angle 3.87685 ( 2646) *********************** 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 260 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.7753 (ttm) cc_final: 0.7453 (ttm) REVERT: A 131 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7581 (mtm-85) REVERT: B 62 ASP cc_start: 0.8200 (t0) cc_final: 0.7868 (t0) REVERT: B 74 ARG cc_start: 0.7589 (ttp-110) cc_final: 0.7124 (ttp80) REVERT: C 62 ASP cc_start: 0.7953 (t0) cc_final: 0.7681 (t70) REVERT: C 128 ARG cc_start: 0.8336 (mtt-85) cc_final: 0.7777 (mtp-110) REVERT: D 56 MET cc_start: 0.7717 (ttm) cc_final: 0.7389 (ttm) REVERT: D 74 ARG cc_start: 0.7634 (ttt-90) cc_final: 0.7045 (ttp80) REVERT: D 204 ILE cc_start: 0.8088 (tp) cc_final: 0.7846 (mt) REVERT: E 279 ARG cc_start: 0.7346 (tpp-160) cc_final: 0.6870 (tpt-90) REVERT: F 35 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8673 (mm) REVERT: F 126 MET cc_start: 0.7924 (mtt) cc_final: 0.7722 (mtp) REVERT: F 131 ARG cc_start: 0.7500 (mtm-85) cc_final: 0.7069 (ptp90) REVERT: F 161 LYS cc_start: 0.8932 (mttt) cc_final: 0.8648 (mtmt) REVERT: G 77 ILE cc_start: 0.8428 (mm) cc_final: 0.8210 (mt) REVERT: G 161 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8641 (mtmm) REVERT: G 224 ARG cc_start: 0.8706 (mtp85) cc_final: 0.8447 (mtp180) outliers start: 21 outliers final: 12 residues processed: 251 average time/residue: 0.1524 time to fit residues: 53.7584 Evaluate side-chains 244 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 231 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain E residue 69 LEU 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 171 ILE Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain G residue 69 LEU 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 156 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 158 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN C 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.143166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.104863 restraints weight = 16600.530| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.61 r_work: 0.2917 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14805 Z= 0.121 Angle : 1.259 33.026 20013 Z= 0.456 Chirality : 0.042 0.139 2408 Planarity : 0.002 0.031 2506 Dihedral : 12.309 170.754 2345 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.46 % Allowed : 13.89 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.20), residues: 1855 helix: 1.14 (0.17), residues: 1015 sheet: -0.93 (0.33), residues: 266 loop : -0.70 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 54 TYR 0.007 0.001 TYR C 250 PHE 0.009 0.001 PHE F 178 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00280 (14805) covalent geometry : angle 1.25894 (20013) hydrogen bonds : bond 0.02788 ( 895) hydrogen bonds : angle 3.92802 ( 2646) *********************** 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 261 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.7729 (ttm) cc_final: 0.7527 (ttm) REVERT: A 134 GLU cc_start: 0.8203 (tt0) cc_final: 0.7978 (tt0) REVERT: A 224 ARG cc_start: 0.8631 (mtp85) cc_final: 0.8426 (mtp180) REVERT: B 62 ASP cc_start: 0.8190 (t0) cc_final: 0.7917 (t0) REVERT: B 74 ARG cc_start: 0.7721 (ttp-110) cc_final: 0.7195 (ttp80) REVERT: B 97 ILE cc_start: 0.8722 (mt) cc_final: 0.8481 (mt) REVERT: C 62 ASP cc_start: 0.8061 (t0) cc_final: 0.7794 (t70) REVERT: C 128 ARG cc_start: 0.8351 (mtt-85) cc_final: 0.7934 (mtp-110) REVERT: D 56 MET cc_start: 0.7759 (ttm) cc_final: 0.7362 (ttm) REVERT: D 74 ARG cc_start: 0.7696 (ttt-90) cc_final: 0.7200 (ttp80) REVERT: E 59 ARG cc_start: 0.7464 (mmt180) cc_final: 0.7232 (mpt-90) REVERT: E 279 ARG cc_start: 0.7465 (tpp-160) cc_final: 0.6988 (tpt-90) REVERT: F 35 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8733 (mm) REVERT: F 131 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.7123 (ptp90) REVERT: F 161 LYS cc_start: 0.8957 (mttt) cc_final: 0.8678 (mtmt) REVERT: G 77 ILE cc_start: 0.8539 (mm) cc_final: 0.8292 (mt) REVERT: G 161 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8705 (mtmm) REVERT: G 224 ARG cc_start: 0.8698 (mtp85) cc_final: 0.8452 (mtp180) outliers start: 22 outliers final: 14 residues processed: 250 average time/residue: 0.1538 time to fit residues: 54.0809 Evaluate side-chains 249 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 234 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain B residue 52 VAL 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 C residue 273 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 166 optimal weight: 4.9990 chunk 150 optimal weight: 0.0670 chunk 128 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 73 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 overall best weight: 1.0120 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.142349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.103532 restraints weight = 16631.731| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.66 r_work: 0.2916 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4324 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= 0.128 Angle : 1.261 33.072 20013 Z= 0.458 Chirality : 0.043 0.284 2408 Planarity : 0.003 0.051 2506 Dihedral : 12.095 170.085 2345 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.26 % Allowed : 14.35 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.20), residues: 1855 helix: 1.18 (0.17), residues: 1022 sheet: -0.98 (0.33), residues: 266 loop : -0.75 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 54 TYR 0.010 0.001 TYR C 250 PHE 0.009 0.001 PHE F 178 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00297 (14805) covalent geometry : angle 1.26133 (20013) hydrogen bonds : bond 0.02808 ( 895) hydrogen bonds : angle 3.95567 ( 2646) *********************** 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 253 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 234 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.7746 (ttm) cc_final: 0.7539 (ttm) REVERT: A 131 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7500 (ptp90) REVERT: A 224 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8407 (mtp180) REVERT: B 62 ASP cc_start: 0.8173 (t0) cc_final: 0.7909 (t0) REVERT: B 74 ARG cc_start: 0.7670 (ttp-110) cc_final: 0.7160 (ttp80) REVERT: B 97 ILE cc_start: 0.8724 (mt) cc_final: 0.8463 (mt) REVERT: B 151 PHE cc_start: 0.9009 (m-80) cc_final: 0.8755 (m-80) REVERT: C 62 ASP cc_start: 0.8029 (t0) cc_final: 0.7750 (t70) REVERT: C 128 ARG cc_start: 0.8394 (mtt-85) cc_final: 0.7868 (mtp-110) REVERT: D 56 MET cc_start: 0.7769 (ttm) cc_final: 0.7435 (ttm) REVERT: D 74 ARG cc_start: 0.7704 (ttt-90) cc_final: 0.7210 (ttp80) REVERT: E 42 LEU cc_start: 0.8450 (mt) cc_final: 0.8149 (mt) REVERT: E 279 ARG cc_start: 0.7507 (tpp-160) cc_final: 0.7003 (tpt-90) REVERT: F 131 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7101 (ptp90) REVERT: F 161 LYS cc_start: 0.8947 (mttt) cc_final: 0.8652 (mtmt) REVERT: G 77 ILE cc_start: 0.8489 (mm) cc_final: 0.8264 (mt) REVERT: G 161 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8673 (mtmm) REVERT: G 224 ARG cc_start: 0.8709 (mtp85) cc_final: 0.8467 (mtp180) outliers start: 19 outliers final: 13 residues processed: 243 average time/residue: 0.1541 time to fit residues: 52.6151 Evaluate side-chains 242 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 229 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 273 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 7 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.142376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.104072 restraints weight = 16626.761| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.60 r_work: 0.2903 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4460 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= 0.122 Angle : 1.260 33.008 20013 Z= 0.457 Chirality : 0.042 0.151 2408 Planarity : 0.003 0.059 2506 Dihedral : 11.834 169.759 2345 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.52 % Allowed : 14.62 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.20), residues: 1855 helix: 1.25 (0.17), residues: 1022 sheet: -0.98 (0.33), residues: 266 loop : -0.69 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 59 TYR 0.007 0.001 TYR C 250 PHE 0.009 0.001 PHE F 178 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00284 (14805) covalent geometry : angle 1.26040 (20013) hydrogen bonds : bond 0.02791 ( 895) hydrogen bonds : angle 3.95919 ( 2646) *********************** 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 264 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8960 (mt) cc_final: 0.8594 (mt) REVERT: A 224 ARG cc_start: 0.8626 (mtp85) cc_final: 0.8416 (mtp180) REVERT: B 62 ASP cc_start: 0.8154 (t0) cc_final: 0.7751 (t0) REVERT: B 74 ARG cc_start: 0.7840 (ttp-110) cc_final: 0.7565 (ttp80) REVERT: B 97 ILE cc_start: 0.8871 (mt) cc_final: 0.8620 (mt) REVERT: B 151 PHE cc_start: 0.8975 (m-80) cc_final: 0.8743 (m-80) REVERT: C 62 ASP cc_start: 0.8168 (t0) cc_final: 0.7922 (t70) REVERT: C 128 ARG cc_start: 0.8383 (mtt-85) cc_final: 0.7936 (mtp-110) REVERT: D 56 MET cc_start: 0.7759 (ttm) cc_final: 0.7429 (ttm) REVERT: D 74 ARG cc_start: 0.7837 (ttt-90) cc_final: 0.7357 (ttp80) REVERT: E 42 LEU cc_start: 0.8570 (mt) cc_final: 0.8266 (mt) REVERT: E 62 ASP cc_start: 0.7911 (t0) cc_final: 0.7632 (t0) REVERT: E 279 ARG cc_start: 0.7570 (tpp-160) cc_final: 0.7086 (tpt-90) REVERT: F 131 ARG cc_start: 0.7550 (mtm-85) cc_final: 0.7153 (ptp90) REVERT: F 161 LYS cc_start: 0.9006 (mttt) cc_final: 0.8733 (mtmt) REVERT: G 77 ILE cc_start: 0.8624 (mm) cc_final: 0.8400 (mt) REVERT: G 161 LYS cc_start: 0.8994 (mtmt) cc_final: 0.8771 (mtmm) REVERT: G 224 ARG cc_start: 0.8718 (mtp85) cc_final: 0.8494 (mtp180) outliers start: 23 outliers final: 16 residues processed: 255 average time/residue: 0.1482 time to fit residues: 53.4280 Evaluate side-chains 261 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 245 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 B residue 155 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain E residue 155 MET 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 95 SER 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 73 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.134021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.093784 restraints weight = 16903.728| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.71 r_work: 0.2829 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4556 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= 0.156 Angle : 1.275 33.014 20013 Z= 0.467 Chirality : 0.045 0.346 2408 Planarity : 0.003 0.065 2506 Dihedral : 11.726 169.875 2345 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.32 % Allowed : 15.34 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.20), residues: 1855 helix: 1.17 (0.16), residues: 1022 sheet: -0.95 (0.31), residues: 280 loop : -0.79 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 54 TYR 0.010 0.001 TYR C 250 PHE 0.010 0.001 PHE F 178 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00369 (14805) covalent geometry : angle 1.27474 (20013) hydrogen bonds : bond 0.02972 ( 895) hydrogen bonds : angle 4.11466 ( 2646) *********************** 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 266 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8903 (mt) cc_final: 0.8535 (mt) REVERT: A 131 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7619 (ptp90) REVERT: A 224 ARG cc_start: 0.8720 (mtp85) cc_final: 0.8507 (mtp180) REVERT: B 55 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6553 (tt) REVERT: B 62 ASP cc_start: 0.8204 (t0) cc_final: 0.7766 (t0) REVERT: B 74 ARG cc_start: 0.7689 (ttp-110) cc_final: 0.7421 (ttp80) REVERT: B 97 ILE cc_start: 0.8797 (mt) cc_final: 0.8564 (mt) REVERT: B 151 PHE cc_start: 0.9002 (m-80) cc_final: 0.8745 (m-80) REVERT: C 62 ASP cc_start: 0.8058 (t0) cc_final: 0.7773 (t70) REVERT: C 128 ARG cc_start: 0.8442 (mtt-85) cc_final: 0.7873 (mtp-110) REVERT: D 56 MET cc_start: 0.7708 (ttm) cc_final: 0.7358 (ttm) REVERT: D 74 ARG cc_start: 0.7692 (ttt-90) cc_final: 0.7189 (ttp80) REVERT: E 42 LEU cc_start: 0.8523 (mt) cc_final: 0.8192 (mt) REVERT: E 62 ASP cc_start: 0.7991 (t0) cc_final: 0.7683 (t70) REVERT: E 279 ARG cc_start: 0.7550 (tpp-160) cc_final: 0.7147 (tpt-90) REVERT: F 131 ARG cc_start: 0.7511 (mtm-85) cc_final: 0.7084 (ptp90) REVERT: F 161 LYS cc_start: 0.8983 (mttt) cc_final: 0.8727 (mtmt) REVERT: G 77 ILE cc_start: 0.8434 (mm) cc_final: 0.8198 (mt) REVERT: G 161 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8668 (mtmm) REVERT: G 224 ARG cc_start: 0.8720 (mtp85) cc_final: 0.8499 (mtp180) outliers start: 20 outliers final: 15 residues processed: 258 average time/residue: 0.1475 time to fit residues: 54.1003 Evaluate side-chains 246 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 230 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 B residue 155 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain E residue 155 MET 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 95 SER 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 4 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 78 optimal weight: 40.0000 chunk 148 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 98 optimal weight: 0.2980 chunk 128 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.147154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.105571 restraints weight = 16507.294| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.73 r_work: 0.2935 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14805 Z= 0.109 Angle : 1.273 33.001 20013 Z= 0.462 Chirality : 0.044 0.335 2408 Planarity : 0.003 0.060 2506 Dihedral : 11.357 168.839 2345 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.26 % Allowed : 15.87 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.20), residues: 1855 helix: 1.35 (0.16), residues: 1022 sheet: -0.92 (0.34), residues: 245 loop : -0.99 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 59 TYR 0.006 0.001 TYR C 250 PHE 0.008 0.001 PHE F 178 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00248 (14805) covalent geometry : angle 1.27269 (20013) hydrogen bonds : bond 0.02792 ( 895) hydrogen bonds : angle 4.01154 ( 2646) ********************** 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 271 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 252 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8951 (mt) cc_final: 0.8591 (mt) REVERT: A 224 ARG cc_start: 0.8604 (mtp85) cc_final: 0.8389 (mtp180) REVERT: B 55 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6606 (tt) REVERT: B 62 ASP cc_start: 0.8272 (t0) cc_final: 0.7859 (t0) REVERT: B 97 ILE cc_start: 0.8893 (mt) cc_final: 0.8683 (mt) REVERT: C 62 ASP cc_start: 0.8168 (t0) cc_final: 0.7887 (t70) REVERT: D 42 LEU cc_start: 0.8959 (mt) cc_final: 0.8683 (mt) REVERT: D 56 MET cc_start: 0.7713 (ttm) cc_final: 0.7353 (ttm) REVERT: D 74 ARG cc_start: 0.7798 (ttt-90) cc_final: 0.7314 (ttp80) REVERT: D 131 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.7262 (ptp90) REVERT: E 42 LEU cc_start: 0.8564 (mt) cc_final: 0.8235 (mt) REVERT: E 62 ASP cc_start: 0.8035 (t0) cc_final: 0.7699 (t0) REVERT: E 74 ARG cc_start: 0.7705 (ttt-90) cc_final: 0.7236 (ttp-110) REVERT: E 279 ARG cc_start: 0.7621 (tpp-160) cc_final: 0.7249 (tpt-90) REVERT: F 131 ARG cc_start: 0.7648 (mtm-85) cc_final: 0.7259 (ptp90) REVERT: F 161 LYS cc_start: 0.9048 (mttt) cc_final: 0.8792 (mtmt) REVERT: G 77 ILE cc_start: 0.8522 (mm) cc_final: 0.8282 (mt) REVERT: G 161 LYS cc_start: 0.9026 (mtmt) cc_final: 0.8776 (mtmm) REVERT: G 224 ARG cc_start: 0.8721 (mtp85) cc_final: 0.8487 (mtp180) outliers start: 19 outliers final: 13 residues processed: 264 average time/residue: 0.1437 time to fit residues: 53.9611 Evaluate side-chains 272 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 258 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain E residue 155 MET 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 95 SER Chi-restraints excluded: chain G residue 127 PHE 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 65 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 170 optimal weight: 0.3980 chunk 106 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.146492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.104863 restraints weight = 16408.891| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.73 r_work: 0.2929 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4730 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= 0.118 Angle : 1.274 33.053 20013 Z= 0.464 Chirality : 0.044 0.335 2408 Planarity : 0.003 0.054 2506 Dihedral : 11.119 168.578 2345 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.12 % Allowed : 15.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.20), residues: 1855 helix: 1.37 (0.16), residues: 1022 sheet: -1.16 (0.29), residues: 315 loop : -0.87 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 54 TYR 0.008 0.001 TYR C 250 PHE 0.008 0.001 PHE F 178 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00271 (14805) covalent geometry : angle 1.27410 (20013) hydrogen bonds : bond 0.02826 ( 895) hydrogen bonds : angle 4.04782 ( 2646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4099.88 seconds wall clock time: 70 minutes 54.17 seconds (4254.17 seconds total)