Starting phenix.real_space_refine on Wed Mar 4 15:34:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vyk_21462/03_2026/6vyk_21462_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vyk_21462/03_2026/6vyk_21462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vyk_21462/03_2026/6vyk_21462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vyk_21462/03_2026/6vyk_21462.map" model { file = "/net/cci-nas-00/data/ceres_data/6vyk_21462/03_2026/6vyk_21462_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vyk_21462/03_2026/6vyk_21462_neut.cif" } 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-dev-5986/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: 3.37, per 1000 atoms: 0.23 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: 1.33 Conformation dependent library (CDL) restraints added in 469.8 milliseconds 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: 0.46 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: 2.24 Time building geometry restraints manager: 1.71 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: 0.710 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.940 Find NCS groups from input model: 0.110 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- 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 are 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 : 0.443 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8421 (mm) cc_final: 0.8208 (mm) REVERT: A 190 ILE cc_start: 0.8874 (mm) cc_final: 0.8637 (mp) REVERT: A 252 ASP cc_start: 0.8262 (m-30) cc_final: 0.7907 (m-30) REVERT: C 199 ASP cc_start: 0.7287 (m-30) cc_final: 0.6999 (m-30) REVERT: F 213 ASP cc_start: 0.7390 (p0) cc_final: 0.7156 (p0) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.1551 time to fit residues: 70.0682 Evaluate side-chains 232 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.147255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.109026 restraints weight = 16782.401| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.70 r_work: 0.3031 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14805 Z= 0.128 Angle : 1.281 33.890 20013 Z= 0.474 Chirality : 0.043 0.146 2408 Planarity : 0.004 0.047 2506 Dihedral : 14.996 178.825 2345 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.26 % Allowed : 7.28 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.19), residues: 1855 helix: -0.71 (0.15), residues: 1015 sheet: -0.92 (0.36), residues: 196 loop : -1.26 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 59 TYR 0.010 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 0.00288 (14805) covalent geometry : angle 1.28065 (20013) hydrogen bonds : bond 0.03114 ( 895) hydrogen bonds : angle 4.54423 ( 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: 19 poor density : 241 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.7740 (ttm) cc_final: 0.7426 (ttm) REVERT: B 37 ILE cc_start: 0.8452 (mm) cc_final: 0.8159 (mm) REVERT: B 74 ARG cc_start: 0.7131 (ttt-90) cc_final: 0.6605 (ttp-110) REVERT: C 131 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7587 (mtm-85) REVERT: C 224 ARG cc_start: 0.8353 (mtp85) cc_final: 0.8006 (mtp180) REVERT: D 56 MET cc_start: 0.7759 (ttm) cc_final: 0.7457 (ttm) REVERT: D 252 ASP cc_start: 0.8928 (m-30) cc_final: 0.8505 (m-30) REVERT: E 279 ARG cc_start: 0.7251 (tpp-160) cc_final: 0.6792 (tpt-90) REVERT: F 74 ARG cc_start: 0.7260 (ttt-90) cc_final: 0.6799 (ttp-110) REVERT: F 131 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.7264 (ptp90) REVERT: G 46 ARG cc_start: 0.7157 (mtm110) cc_final: 0.6926 (mmm160) REVERT: G 56 MET cc_start: 0.7568 (ttm) cc_final: 0.7367 (ttm) REVERT: G 204 ILE cc_start: 0.8070 (tp) cc_final: 0.7633 (mt) REVERT: G 274 ASP cc_start: 0.8703 (m-30) cc_final: 0.8402 (m-30) outliers start: 19 outliers final: 8 residues processed: 254 average time/residue: 0.1333 time to fit residues: 48.5116 Evaluate side-chains 222 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 214 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 179 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 134 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.134208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.093793 restraints weight = 17004.294| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.75 r_work: 0.2892 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14805 Z= 0.180 Angle : 1.288 33.101 20013 Z= 0.475 Chirality : 0.044 0.165 2408 Planarity : 0.003 0.040 2506 Dihedral : 14.105 178.607 2345 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.12 % Allowed : 10.52 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1855 helix: 0.09 (0.16), residues: 1008 sheet: -1.49 (0.29), residues: 315 loop : -0.87 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 54 TYR 0.008 0.001 TYR B 250 PHE 0.012 0.001 PHE F 178 TRP 0.007 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00424 (14805) covalent geometry : angle 1.28803 (20013) hydrogen bonds : bond 0.03299 ( 895) hydrogen bonds : angle 4.36128 ( 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 269 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 252 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8172 (mtt180) cc_final: 0.7949 (mtm-85) REVERT: B 74 ARG cc_start: 0.7426 (ttt-90) cc_final: 0.7177 (ttp-110) REVERT: B 134 GLU cc_start: 0.8207 (tt0) cc_final: 0.7990 (tt0) REVERT: C 62 ASP cc_start: 0.7880 (t0) cc_final: 0.7677 (t70) REVERT: C 128 ARG cc_start: 0.8540 (mtt90) cc_final: 0.7991 (mtp-110) REVERT: D 74 ARG cc_start: 0.7666 (ttt-90) cc_final: 0.7134 (ttp80) REVERT: D 204 ILE cc_start: 0.8189 (tp) cc_final: 0.7948 (mt) REVERT: E 47 MET cc_start: 0.7337 (ptm) cc_final: 0.7088 (ptt) REVERT: E 55 LEU cc_start: 0.7096 (mp) cc_final: 0.6857 (mp) REVERT: E 88 ARG cc_start: 0.8819 (tpm170) cc_final: 0.8020 (mmm160) REVERT: E 279 ARG cc_start: 0.7298 (tpp-160) cc_final: 0.6772 (tpt-90) REVERT: F 35 LEU cc_start: 0.9021 (mm) cc_final: 0.8697 (mm) REVERT: F 74 ARG cc_start: 0.7719 (ttt-90) cc_final: 0.7227 (ttp-110) REVERT: F 131 ARG cc_start: 0.7525 (mtm-85) cc_final: 0.7224 (ptp90) REVERT: F 189 ILE cc_start: 0.9235 (mt) cc_final: 0.9003 (mm) REVERT: G 56 MET cc_start: 0.7724 (ttm) cc_final: 0.7436 (ttm) REVERT: G 77 ILE cc_start: 0.8415 (mm) cc_final: 0.8173 (mt) REVERT: G 109 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8107 (mp) REVERT: G 274 ASP cc_start: 0.8595 (m-30) cc_final: 0.8310 (m-30) outliers start: 17 outliers final: 8 residues processed: 263 average time/residue: 0.1411 time to fit residues: 52.9994 Evaluate side-chains 237 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 228 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 F residue 100 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 171 ILE 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: 2.9990 chunk 149 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 78 optimal weight: 0.0060 chunk 81 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN E 149 GLN F 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.137936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.098163 restraints weight = 16792.385| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.73 r_work: 0.2990 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3901 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= 0.104 Angle : 1.261 33.128 20013 Z= 0.457 Chirality : 0.042 0.163 2408 Planarity : 0.003 0.036 2506 Dihedral : 13.313 177.981 2345 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.59 % Allowed : 12.50 % Favored : 85.91 % 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 are not related in a simple way. whole: -0.20 (0.20), residues: 1855 helix: 0.64 (0.17), residues: 1008 sheet: -0.86 (0.34), residues: 245 loop : -0.98 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 59 TYR 0.007 0.001 TYR C 135 PHE 0.011 0.001 PHE F 178 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00235 (14805) covalent geometry : angle 1.26065 (20013) hydrogen bonds : bond 0.02782 ( 895) hydrogen bonds : angle 4.02640 ( 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 282 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7777 (ttm) cc_final: 0.7548 (ttm) REVERT: A 131 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7829 (mtm-85) REVERT: B 31 ILE cc_start: 0.8918 (mt) cc_final: 0.8614 (mp) REVERT: B 74 ARG cc_start: 0.7458 (ttt-90) cc_final: 0.7086 (ttp80) REVERT: B 134 GLU cc_start: 0.8148 (tt0) cc_final: 0.7903 (tt0) REVERT: C 62 ASP cc_start: 0.7962 (t0) cc_final: 0.7699 (t70) REVERT: C 126 MET cc_start: 0.7953 (mtt) cc_final: 0.7725 (mtp) REVERT: C 128 ARG cc_start: 0.8472 (mtt90) cc_final: 0.7940 (mtp-110) REVERT: C 131 ARG cc_start: 0.7880 (ptp90) cc_final: 0.7595 (ptp90) REVERT: D 56 MET cc_start: 0.7757 (ttm) cc_final: 0.7252 (ttm) REVERT: D 74 ARG cc_start: 0.7650 (ttt-90) cc_final: 0.7175 (ttp80) REVERT: D 131 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7832 (mtm-85) REVERT: D 204 ILE cc_start: 0.8183 (tp) cc_final: 0.7960 (mt) REVERT: E 88 ARG cc_start: 0.8745 (tpm170) cc_final: 0.7923 (mmm160) REVERT: E 279 ARG cc_start: 0.7254 (tpp-160) cc_final: 0.6738 (tpt-90) REVERT: F 35 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8752 (mm) REVERT: F 126 MET cc_start: 0.7848 (mtt) cc_final: 0.7634 (mtp) REVERT: F 131 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.7112 (ptp90) REVERT: G 42 LEU cc_start: 0.8808 (mt) cc_final: 0.8597 (mt) REVERT: G 56 MET cc_start: 0.7726 (ttm) cc_final: 0.7434 (ttm) REVERT: G 77 ILE cc_start: 0.8410 (mm) cc_final: 0.8140 (mt) REVERT: G 224 ARG cc_start: 0.8748 (mtp85) cc_final: 0.8499 (mtp180) REVERT: G 250 TYR cc_start: 0.8912 (t80) cc_final: 0.8688 (t80) REVERT: G 274 ASP cc_start: 0.8580 (m-30) cc_final: 0.8289 (m-30) outliers start: 24 outliers final: 8 residues processed: 269 average time/residue: 0.1427 time to fit residues: 54.0917 Evaluate side-chains 256 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 247 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain E residue 69 LEU 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 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: 1.9990 chunk 110 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.135997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.096168 restraints weight = 16886.648| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.74 r_work: 0.2912 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4109 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= 0.116 Angle : 1.262 32.999 20013 Z= 0.457 Chirality : 0.043 0.284 2408 Planarity : 0.003 0.045 2506 Dihedral : 12.840 172.598 2345 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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 are not related in a simple way. whole: 0.12 (0.20), residues: 1855 helix: 0.96 (0.17), residues: 1008 sheet: -0.78 (0.34), residues: 245 loop : -0.91 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 54 TYR 0.008 0.001 TYR F 250 PHE 0.012 0.001 PHE F 178 TRP 0.005 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00265 (14805) covalent geometry : angle 1.26241 (20013) hydrogen bonds : bond 0.02805 ( 895) hydrogen bonds : angle 3.98150 ( 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 273 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7793 (ttm) cc_final: 0.7474 (ttm) REVERT: A 62 ASP cc_start: 0.8071 (t0) cc_final: 0.7863 (t0) REVERT: A 224 ARG cc_start: 0.8657 (mtp85) cc_final: 0.8396 (mtp180) REVERT: B 31 ILE cc_start: 0.8901 (mt) cc_final: 0.8636 (mp) REVERT: B 62 ASP cc_start: 0.8202 (t0) cc_final: 0.7938 (t0) REVERT: B 74 ARG cc_start: 0.7535 (ttt-90) cc_final: 0.7138 (ttp80) REVERT: B 97 ILE cc_start: 0.8657 (mt) cc_final: 0.8411 (mt) REVERT: C 62 ASP cc_start: 0.7989 (t0) cc_final: 0.7737 (t70) REVERT: C 126 MET cc_start: 0.7943 (mtt) cc_final: 0.7731 (mtp) REVERT: C 128 ARG cc_start: 0.8455 (mtt90) cc_final: 0.7905 (mtp-110) REVERT: C 252 ASP cc_start: 0.8793 (m-30) cc_final: 0.8467 (m-30) REVERT: D 56 MET cc_start: 0.7811 (ttm) cc_final: 0.7580 (ttm) REVERT: D 74 ARG cc_start: 0.7727 (ttt-90) cc_final: 0.7239 (ttp80) REVERT: E 42 LEU cc_start: 0.8658 (mt) cc_final: 0.8421 (mt) REVERT: E 88 ARG cc_start: 0.8777 (tpm170) cc_final: 0.7946 (mmm160) REVERT: E 279 ARG cc_start: 0.7461 (tpp-160) cc_final: 0.6943 (tpt-90) REVERT: F 35 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8719 (mm) REVERT: F 131 ARG cc_start: 0.7466 (mtm-85) cc_final: 0.7098 (ptp90) REVERT: G 42 LEU cc_start: 0.8863 (mt) cc_final: 0.8592 (mt) REVERT: G 56 MET cc_start: 0.7736 (ttm) cc_final: 0.7332 (ttm) REVERT: G 77 ILE cc_start: 0.8415 (mm) cc_final: 0.8126 (mt) REVERT: G 224 ARG cc_start: 0.8728 (mtp85) cc_final: 0.8489 (mtp180) REVERT: G 274 ASP cc_start: 0.8562 (m-30) cc_final: 0.8325 (m-30) outliers start: 21 outliers final: 12 residues processed: 261 average time/residue: 0.1355 time to fit residues: 49.7725 Evaluate side-chains 247 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 234 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain E residue 69 LEU 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 155 MET 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: 0.0470 chunk 120 optimal weight: 0.0570 chunk 3 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.139332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.100315 restraints weight = 16734.398| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.72 r_work: 0.2952 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14805 Z= 0.090 Angle : 1.254 33.057 20013 Z= 0.452 Chirality : 0.041 0.137 2408 Planarity : 0.003 0.034 2506 Dihedral : 12.425 169.029 2345 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.59 % Allowed : 13.89 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1855 helix: 1.18 (0.17), residues: 1015 sheet: -0.68 (0.35), residues: 245 loop : -1.00 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 224 TYR 0.005 0.001 TYR A 27 PHE 0.009 0.001 PHE F 178 TRP 0.004 0.000 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00197 (14805) covalent geometry : angle 1.25381 (20013) hydrogen bonds : bond 0.02661 ( 895) hydrogen bonds : angle 3.83205 ( 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 284 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8990 (mt) cc_final: 0.8632 (mt) REVERT: A 128 ARG cc_start: 0.8589 (mtt90) cc_final: 0.8089 (mtp-110) REVERT: A 224 ARG cc_start: 0.8526 (mtp85) cc_final: 0.8246 (mtp180) REVERT: B 31 ILE cc_start: 0.8958 (mt) cc_final: 0.8619 (mp) REVERT: B 62 ASP cc_start: 0.8186 (t0) cc_final: 0.7926 (t0) REVERT: B 74 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7216 (ttp80) REVERT: B 97 ILE cc_start: 0.8682 (mt) cc_final: 0.8478 (mt) REVERT: B 151 PHE cc_start: 0.8971 (m-80) cc_final: 0.8740 (m-80) REVERT: C 62 ASP cc_start: 0.8109 (t0) cc_final: 0.7871 (t70) REVERT: C 128 ARG cc_start: 0.8368 (mtt90) cc_final: 0.7918 (mtp-110) REVERT: D 56 MET cc_start: 0.7796 (ttm) cc_final: 0.7562 (ttm) REVERT: D 74 ARG cc_start: 0.7662 (ttt-90) cc_final: 0.7209 (ttp80) REVERT: E 59 ARG cc_start: 0.7476 (mpt-90) cc_final: 0.7272 (mpt-90) REVERT: E 88 ARG cc_start: 0.8728 (tpm170) cc_final: 0.8011 (mmm160) REVERT: E 149 GLN cc_start: 0.8406 (mt0) cc_final: 0.8193 (mt0) REVERT: E 279 ARG cc_start: 0.7446 (tpp-160) cc_final: 0.6983 (tpt-90) REVERT: F 35 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8660 (mm) REVERT: F 131 ARG cc_start: 0.7480 (mtm-85) cc_final: 0.7060 (ptp90) REVERT: F 161 LYS cc_start: 0.8927 (mttt) cc_final: 0.8659 (mtmt) REVERT: G 77 ILE cc_start: 0.8397 (mm) cc_final: 0.8089 (mt) REVERT: G 278 LYS cc_start: 0.7936 (mttt) cc_final: 0.7660 (mttm) outliers start: 24 outliers final: 13 residues processed: 272 average time/residue: 0.1362 time to fit residues: 52.2809 Evaluate side-chains 274 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 259 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 74 ARG 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 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 155 MET 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: 6.9990 chunk 150 optimal weight: 3.9990 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: 2.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.132838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.092606 restraints weight = 16915.554| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.67 r_work: 0.2794 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14805 Z= 0.258 Angle : 1.299 32.980 20013 Z= 0.485 Chirality : 0.047 0.354 2408 Planarity : 0.003 0.047 2506 Dihedral : 12.864 171.301 2345 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.79 % Allowed : 14.48 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 1855 helix: 0.81 (0.16), residues: 1022 sheet: -1.21 (0.34), residues: 231 loop : -0.88 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 54 TYR 0.014 0.002 TYR C 250 PHE 0.015 0.002 PHE F 178 TRP 0.005 0.001 TRP E 251 Details of bonding type rmsd covalent geometry : bond 0.00614 (14805) covalent geometry : angle 1.29905 (20013) hydrogen bonds : bond 0.03321 ( 895) hydrogen bonds : angle 4.31654 ( 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 269 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 97 ILE cc_start: 0.8662 (mt) cc_final: 0.8377 (mp) REVERT: A 128 ARG cc_start: 0.8731 (mtt90) cc_final: 0.8242 (mtp-110) REVERT: B 31 ILE cc_start: 0.8944 (mt) cc_final: 0.8686 (mp) REVERT: B 74 ARG cc_start: 0.7589 (ttt-90) cc_final: 0.7157 (ttp80) REVERT: B 97 ILE cc_start: 0.8868 (mt) cc_final: 0.8607 (mt) REVERT: C 62 ASP cc_start: 0.8087 (t0) cc_final: 0.7812 (t70) REVERT: C 128 ARG cc_start: 0.8568 (mtt90) cc_final: 0.8126 (mtp-110) REVERT: C 252 ASP cc_start: 0.8821 (m-30) cc_final: 0.8559 (m-30) REVERT: D 56 MET cc_start: 0.7869 (ttm) cc_final: 0.7571 (ttm) REVERT: D 74 ARG cc_start: 0.7719 (ttt-90) cc_final: 0.7207 (ttp80) REVERT: E 59 ARG cc_start: 0.7675 (mpt-90) cc_final: 0.7454 (mpt-90) REVERT: E 62 ASP cc_start: 0.7994 (t0) cc_final: 0.7736 (t70) REVERT: E 127 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6852 (p90) REVERT: E 131 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7427 (mtm-85) REVERT: E 279 ARG cc_start: 0.7571 (tpp-160) cc_final: 0.7103 (tpt-90) REVERT: F 131 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.7168 (ptp90) REVERT: F 161 LYS cc_start: 0.9024 (mttt) cc_final: 0.8776 (mtmt) REVERT: G 77 ILE cc_start: 0.8429 (mm) cc_final: 0.8150 (mt) outliers start: 27 outliers final: 17 residues processed: 259 average time/residue: 0.1418 time to fit residues: 51.4486 Evaluate side-chains 257 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 239 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 171 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 7 optimal weight: 3.9990 chunk 89 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.146185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.104288 restraints weight = 16541.798| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.73 r_work: 0.2938 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14805 Z= 0.109 Angle : 1.269 32.960 20013 Z= 0.462 Chirality : 0.044 0.294 2408 Planarity : 0.003 0.063 2506 Dihedral : 12.344 169.123 2345 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.52 % Allowed : 15.81 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1855 helix: 1.12 (0.17), residues: 1015 sheet: -0.79 (0.35), residues: 245 loop : -0.95 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 54 TYR 0.006 0.001 TYR C 250 PHE 0.011 0.001 PHE F 178 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00247 (14805) covalent geometry : angle 1.26949 (20013) hydrogen bonds : bond 0.02877 ( 895) hydrogen bonds : angle 4.11575 ( 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 268 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 0.467 Fit side-chains REVERT: A 128 ARG cc_start: 0.8716 (mtt90) cc_final: 0.8228 (mtp-110) REVERT: A 224 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8435 (mtp180) REVERT: B 31 ILE cc_start: 0.8979 (mt) cc_final: 0.8739 (mp) REVERT: B 62 ASP cc_start: 0.8337 (t0) cc_final: 0.7886 (t0) REVERT: B 74 ARG cc_start: 0.7692 (ttt-90) cc_final: 0.7350 (ttp80) REVERT: B 97 ILE cc_start: 0.8906 (mt) cc_final: 0.8699 (mt) REVERT: C 62 ASP cc_start: 0.8174 (t0) cc_final: 0.7896 (t70) REVERT: C 128 ARG cc_start: 0.8448 (mtt90) cc_final: 0.7904 (mtp-110) REVERT: C 252 ASP cc_start: 0.8717 (m-30) cc_final: 0.8499 (m-30) REVERT: D 56 MET cc_start: 0.7786 (ttm) cc_final: 0.7478 (ttm) REVERT: D 74 ARG cc_start: 0.7759 (ttt-90) cc_final: 0.7272 (ttp80) REVERT: E 59 ARG cc_start: 0.7624 (mpt-90) cc_final: 0.7419 (mpt-90) REVERT: E 62 ASP cc_start: 0.8084 (t0) cc_final: 0.7815 (t70) REVERT: E 127 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.6603 (p90) REVERT: E 149 GLN cc_start: 0.8370 (mt0) cc_final: 0.8133 (mt0) REVERT: E 279 ARG cc_start: 0.7674 (tpp-160) cc_final: 0.7281 (tpt-90) REVERT: F 131 ARG cc_start: 0.7586 (mtm-85) cc_final: 0.7320 (ptp90) REVERT: G 77 ILE cc_start: 0.8495 (mm) cc_final: 0.8217 (mt) outliers start: 23 outliers final: 18 residues processed: 259 average time/residue: 0.1366 time to fit residues: 49.6804 Evaluate side-chains 260 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU 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 35 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 69 LEU 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: 3.9990 chunk 153 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN F 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.147508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.105799 restraints weight = 16531.795| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.75 r_work: 0.2939 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4726 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= 0.110 Angle : 1.271 32.931 20013 Z= 0.462 Chirality : 0.044 0.346 2408 Planarity : 0.003 0.043 2506 Dihedral : 12.039 168.675 2345 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.59 % Allowed : 15.94 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.20), residues: 1855 helix: 1.24 (0.17), residues: 1015 sheet: -0.62 (0.33), residues: 259 loop : -1.03 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 54 TYR 0.006 0.001 TYR G 250 PHE 0.009 0.001 PHE F 178 TRP 0.004 0.000 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00248 (14805) covalent geometry : angle 1.27143 (20013) hydrogen bonds : bond 0.02849 ( 895) hydrogen bonds : angle 4.08378 ( 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 271 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 247 time to evaluate : 0.559 Fit side-chains REVERT: A 128 ARG cc_start: 0.8699 (mtt90) cc_final: 0.8244 (mtp-110) REVERT: B 31 ILE cc_start: 0.9007 (mt) cc_final: 0.8768 (mp) REVERT: B 62 ASP cc_start: 0.8350 (t0) cc_final: 0.7913 (t0) REVERT: B 74 ARG cc_start: 0.7676 (ttt-90) cc_final: 0.7367 (ttp80) REVERT: B 97 ILE cc_start: 0.8923 (mt) cc_final: 0.8667 (mt) REVERT: B 127 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6338 (p90) REVERT: C 62 ASP cc_start: 0.8221 (t0) cc_final: 0.7949 (t70) REVERT: C 128 ARG cc_start: 0.8400 (mtt90) cc_final: 0.7864 (mtp-110) REVERT: C 252 ASP cc_start: 0.8733 (m-30) cc_final: 0.8432 (m-30) REVERT: D 56 MET cc_start: 0.7791 (ttm) cc_final: 0.7516 (ttm) REVERT: D 74 ARG cc_start: 0.7795 (ttt-90) cc_final: 0.7323 (ttp80) REVERT: E 59 ARG cc_start: 0.7617 (mpt-90) cc_final: 0.7405 (mpt-90) REVERT: E 62 ASP cc_start: 0.8109 (t0) cc_final: 0.7857 (t70) REVERT: E 127 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6630 (p90) REVERT: E 149 GLN cc_start: 0.8365 (mt0) cc_final: 0.8124 (mt0) REVERT: E 279 ARG cc_start: 0.7695 (tpp-160) cc_final: 0.7299 (tpt-90) REVERT: F 131 ARG cc_start: 0.7552 (mtm-85) cc_final: 0.7135 (ptp90) REVERT: G 77 ILE cc_start: 0.8457 (mm) cc_final: 0.8184 (mt) outliers start: 24 outliers final: 21 residues processed: 261 average time/residue: 0.1313 time to fit residues: 48.7918 Evaluate side-chains 256 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 35 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 35 LEU 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 4 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 30.0000 chunk 148 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.145076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.103103 restraints weight = 16505.976| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.74 r_work: 0.2919 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4785 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= 0.135 Angle : 1.279 32.908 20013 Z= 0.467 Chirality : 0.045 0.316 2408 Planarity : 0.003 0.046 2506 Dihedral : 11.856 168.616 2345 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.52 % Allowed : 16.14 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.20), residues: 1855 helix: 1.21 (0.16), residues: 1015 sheet: -0.71 (0.35), residues: 245 loop : -0.88 (0.26), residues: 595 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 0.011 0.001 PHE F 178 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00314 (14805) covalent geometry : angle 1.27887 (20013) hydrogen bonds : bond 0.02939 ( 895) hydrogen bonds : angle 4.14797 ( 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 250 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.527 Fit side-chains REVERT: A 128 ARG cc_start: 0.8703 (mtt90) cc_final: 0.8246 (mtp-110) REVERT: B 31 ILE cc_start: 0.9030 (mt) cc_final: 0.8792 (mp) REVERT: B 74 ARG cc_start: 0.7743 (ttt-90) cc_final: 0.7422 (ttp80) REVERT: B 97 ILE cc_start: 0.8948 (mt) cc_final: 0.8690 (mt) REVERT: B 127 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6440 (p90) REVERT: B 131 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7526 (ptp90) REVERT: C 62 ASP cc_start: 0.8238 (t0) cc_final: 0.7975 (t70) REVERT: C 128 ARG cc_start: 0.8462 (mtt90) cc_final: 0.7952 (mtp-110) REVERT: D 56 MET cc_start: 0.7732 (ttm) cc_final: 0.7446 (ttm) REVERT: D 74 ARG cc_start: 0.7840 (ttt-90) cc_final: 0.7370 (ttp80) REVERT: E 59 ARG cc_start: 0.7672 (mpt-90) cc_final: 0.7464 (mpt-90) REVERT: E 62 ASP cc_start: 0.8234 (t0) cc_final: 0.7983 (t70) REVERT: E 127 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6745 (p90) REVERT: E 279 ARG cc_start: 0.7736 (tpp-160) cc_final: 0.7345 (tpt-90) REVERT: F 131 ARG cc_start: 0.7572 (mtm-85) cc_final: 0.7151 (ptp90) REVERT: G 77 ILE cc_start: 0.8531 (mm) cc_final: 0.8256 (mt) outliers start: 23 outliers final: 20 residues processed: 242 average time/residue: 0.1311 time to fit residues: 44.9787 Evaluate side-chains 254 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 35 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 171 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: 7.9990 chunk 113 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.146010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.104253 restraints weight = 16433.343| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.73 r_work: 0.2932 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14805 Z= 0.116 Angle : 1.278 32.954 20013 Z= 0.465 Chirality : 0.045 0.331 2408 Planarity : 0.003 0.055 2506 Dihedral : 11.515 167.577 2345 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.65 % Allowed : 16.07 % Favored : 82.28 % 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 are not related in a simple way. whole: 0.43 (0.20), residues: 1855 helix: 1.30 (0.17), residues: 1015 sheet: -0.58 (0.33), residues: 259 loop : -1.04 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 54 TYR 0.006 0.001 TYR F 250 PHE 0.010 0.001 PHE F 178 TRP 0.004 0.000 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00266 (14805) covalent geometry : angle 1.27758 (20013) hydrogen bonds : bond 0.02861 ( 895) hydrogen bonds : angle 4.11563 ( 2646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3679.71 seconds wall clock time: 63 minutes 29.90 seconds (3809.90 seconds total)