Starting phenix.real_space_refine on Thu Feb 5 10:55:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kej_62291/02_2026/9kej_62291.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kej_62291/02_2026/9kej_62291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kej_62291/02_2026/9kej_62291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kej_62291/02_2026/9kej_62291.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kej_62291/02_2026/9kej_62291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kej_62291/02_2026/9kej_62291.map" } resolution = 3.04 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= 0.001 sd= 0.008 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 12 5.49 5 S 72 5.16 5 C 10602 2.51 5 N 2808 2.21 5 O 3144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16638 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2728 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain: "B" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2728 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain: "C" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2728 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain: "D" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2728 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain: "E" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2728 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain: "F" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2728 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.32, per 1000 atoms: 0.20 Number of scatterers: 16638 At special positions: 0 Unit cell: (83.88, 83.88, 168.692, 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 72 16.00 P 12 15.00 O 3144 8.00 N 2808 7.00 C 10602 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: 1.19 Conformation dependent library (CDL) restraints added in 522.5 milliseconds 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3852 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 12 sheets defined 55.2% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 21 through 41 removed outlier: 3.951A pdb=" N THR A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.913A pdb=" N TYR A 50 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 69 Processing helix chain 'A' and resid 72 through 88 removed outlier: 4.063A pdb=" N THR A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 109 through 121 removed outlier: 3.587A pdb=" N MET A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.993A pdb=" N ASN A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 211 removed outlier: 3.601A pdb=" N VAL A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 258 through 284 Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.057A pdb=" N ALA A 303 " --> pdb=" O ASN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 333 removed outlier: 3.805A pdb=" N LYS A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 removed outlier: 3.645A pdb=" N ARG A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 21 through 41 removed outlier: 3.792A pdb=" N THR B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.838A pdb=" N TYR B 50 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.535A pdb=" N GLY B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 88 removed outlier: 3.641A pdb=" N ILE B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 108 through 121 removed outlier: 4.231A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 163 through 172 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 201 through 211 removed outlier: 3.657A pdb=" N VAL B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.537A pdb=" N SER B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.631A pdb=" N ALA B 303 " --> pdb=" O ASN B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 333 Processing helix chain 'B' and resid 333 through 338 removed outlier: 3.649A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 21 through 41 removed outlier: 3.604A pdb=" N THR C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 removed outlier: 3.647A pdb=" N TYR C 50 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE C 51 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 69 Processing helix chain 'C' and resid 72 through 88 removed outlier: 3.507A pdb=" N LEU C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR C 85 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 109 through 121 removed outlier: 3.620A pdb=" N MET C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.961A pdb=" N LEU C 129 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 192 through 196 removed outlier: 3.532A pdb=" N LEU C 195 " --> pdb=" O ASP C 192 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 196 " --> pdb=" O GLY C 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 192 through 196' Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 239 through 247 Processing helix chain 'C' and resid 258 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.774A pdb=" N ALA C 303 " --> pdb=" O ASN C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 333 removed outlier: 3.580A pdb=" N ALA C 327 " --> pdb=" O LYS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 340 removed outlier: 3.539A pdb=" N ARG C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 21 through 41 removed outlier: 4.016A pdb=" N THR D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.749A pdb=" N TYR D 50 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE D 51 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 70 removed outlier: 3.539A pdb=" N GLY D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 88 removed outlier: 3.543A pdb=" N ILE D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 95 Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 108 through 121 removed outlier: 4.428A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 172 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 201 through 211 removed outlier: 3.662A pdb=" N VAL D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'D' and resid 258 through 284 removed outlier: 3.540A pdb=" N LEU D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 298 through 303 removed outlier: 3.557A pdb=" N ALA D 303 " --> pdb=" O ASN D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 333 removed outlier: 3.508A pdb=" N ALA D 327 " --> pdb=" O LYS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 340 removed outlier: 4.218A pdb=" N PHE D 340 " --> pdb=" O LEU D 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 20 No H-bonds generated for 'chain 'E' and resid 18 through 20' Processing helix chain 'E' and resid 21 through 41 removed outlier: 4.067A pdb=" N THR E 25 " --> pdb=" O ARG E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 51 removed outlier: 3.737A pdb=" N TYR E 50 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE E 51 " --> pdb=" O GLY E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 70 removed outlier: 3.755A pdb=" N GLY E 70 " --> pdb=" O GLY E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 88 removed outlier: 4.161A pdb=" N THR E 85 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 104 removed outlier: 3.602A pdb=" N ARG E 104 " --> pdb=" O ASN E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 121 removed outlier: 3.640A pdb=" N MET E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 172 Processing helix chain 'E' and resid 192 through 196 removed outlier: 3.562A pdb=" N LEU E 195 " --> pdb=" O ASP E 192 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL E 196 " --> pdb=" O GLY E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 192 through 196' Processing helix chain 'E' and resid 200 through 211 removed outlier: 3.535A pdb=" N ILE E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG E 206 " --> pdb=" O TYR E 202 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 209 " --> pdb=" O ILE E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 222 No H-bonds generated for 'chain 'E' and resid 220 through 222' Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 258 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 300 through 304 removed outlier: 3.629A pdb=" N ALA E 303 " --> pdb=" O GLU E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 333 Processing helix chain 'E' and resid 333 through 340 removed outlier: 3.654A pdb=" N ARG E 337 " --> pdb=" O ASN E 333 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE E 339 " --> pdb=" O GLU E 335 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE E 340 " --> pdb=" O LEU E 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 20 No H-bonds generated for 'chain 'F' and resid 18 through 20' Processing helix chain 'F' and resid 21 through 41 removed outlier: 3.795A pdb=" N THR F 25 " --> pdb=" O ARG F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 51 removed outlier: 3.801A pdb=" N PHE F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 70 Processing helix chain 'F' and resid 72 through 88 removed outlier: 4.601A pdb=" N THR F 85 " --> pdb=" O GLU F 81 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS F 86 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 104 Processing helix chain 'F' and resid 108 through 120 removed outlier: 4.271A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 129 removed outlier: 3.539A pdb=" N LEU F 129 " --> pdb=" O PHE F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 172 Processing helix chain 'F' and resid 192 through 196 removed outlier: 3.551A pdb=" N LEU F 195 " --> pdb=" O ASP F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 211 Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'F' and resid 258 through 285 Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 298 through 303 removed outlier: 4.203A pdb=" N ALA F 303 " --> pdb=" O ASN F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 333 Processing helix chain 'F' and resid 333 through 339 removed outlier: 3.589A pdb=" N ARG F 337 " --> pdb=" O ASN F 333 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 145 through 149 removed outlier: 3.576A pdb=" N VAL A 138 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 149 removed outlier: 3.640A pdb=" N THR A 136 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS A 11 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR A 55 " --> pdb=" O LYS A 11 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU A 13 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE A 10 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU A 227 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 12 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE A 229 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER A 14 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL A 291 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 226 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE A 293 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN A 228 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 145 through 149 removed outlier: 3.571A pdb=" N ASN B 188 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 149 removed outlier: 3.555A pdb=" N THR B 136 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS B 11 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR B 55 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU B 13 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 10 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU B 227 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE B 12 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE B 229 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER B 14 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 291 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL B 226 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE B 293 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN B 228 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 144 through 149 removed outlier: 3.680A pdb=" N VAL C 138 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN C 188 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 144 through 149 removed outlier: 3.629A pdb=" N THR C 136 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS C 11 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N THR C 55 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU C 13 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE C 10 " --> pdb=" O LYS C 225 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU C 227 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 12 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE C 229 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER C 14 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL C 291 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL C 226 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE C 293 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN C 228 " --> pdb=" O ILE C 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.755A pdb=" N LYS D 11 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR D 55 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU D 13 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE D 10 " --> pdb=" O LYS D 225 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU D 227 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE D 12 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE D 229 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER D 14 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL D 291 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL D 226 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE D 293 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN D 228 " --> pdb=" O ILE D 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 145 through 149 removed outlier: 3.786A pdb=" N ASN D 188 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 145 through 149 removed outlier: 3.661A pdb=" N VAL E 138 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN E 188 " --> pdb=" O ILE E 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 145 through 149 removed outlier: 6.621A pdb=" N ILE E 54 " --> pdb=" O MET E 134 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N THR E 136 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLY E 56 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 9.755A pdb=" N VAL E 138 " --> pdb=" O GLY E 56 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS E 11 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N THR E 55 " --> pdb=" O LYS E 11 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU E 13 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE E 10 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU E 227 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE E 12 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE E 229 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER E 14 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL E 291 " --> pdb=" O ILE E 224 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL E 226 " --> pdb=" O VAL E 291 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE E 293 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN E 228 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 144 through 149 removed outlier: 3.875A pdb=" N VAL F 138 " --> pdb=" O ALA F 191 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN F 188 " --> pdb=" O ILE F 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 144 through 149 removed outlier: 6.631A pdb=" N ILE F 54 " --> pdb=" O MET F 134 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N THR F 136 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLY F 56 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 9.817A pdb=" N VAL F 138 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS F 11 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR F 55 " --> pdb=" O LYS F 11 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU F 13 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE F 10 " --> pdb=" O LYS F 225 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU F 227 " --> pdb=" O ILE F 10 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE F 12 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE F 229 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER F 14 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL F 291 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL F 226 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE F 293 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN F 228 " --> pdb=" O ILE F 293 " (cutoff:3.500A) 739 hydrogen bonds defined for protein. 2148 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: 2.38 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5354 1.35 - 1.46: 3796 1.46 - 1.58: 7680 1.58 - 1.70: 24 1.70 - 1.82: 126 Bond restraints: 16980 Sorted by residual: bond pdb=" CB GLN A 97 " pdb=" CG GLN A 97 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.32e+00 bond pdb=" N MET B 257 " pdb=" CA MET B 257 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.21e+00 bond pdb=" CA MET B 257 " pdb=" CB MET B 257 " ideal model delta sigma weight residual 1.530 1.512 0.018 1.69e-02 3.50e+03 1.19e+00 bond pdb=" CB GLU E 287 " pdb=" CG GLU E 287 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CA THR D 231 " pdb=" C THR D 231 " ideal model delta sigma weight residual 1.521 1.536 -0.015 1.54e-02 4.22e+03 9.87e-01 ... (remaining 16975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 22738 2.33 - 4.66: 173 4.66 - 6.99: 21 6.99 - 9.32: 11 9.32 - 11.65: 1 Bond angle restraints: 22944 Sorted by residual: angle pdb=" C ILE B 162 " pdb=" N ARG B 163 " pdb=" CA ARG B 163 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 angle pdb=" C ILE C 106 " pdb=" N TYR C 107 " pdb=" CA TYR C 107 " ideal model delta sigma weight residual 121.54 129.16 -7.62 1.91e+00 2.74e-01 1.59e+01 angle pdb=" CB MET F 155 " pdb=" CG MET F 155 " pdb=" SD MET F 155 " ideal model delta sigma weight residual 112.70 124.35 -11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" CA ILE A 286 " pdb=" CB ILE A 286 " pdb=" CG1 ILE A 286 " ideal model delta sigma weight residual 110.40 116.62 -6.22 1.70e+00 3.46e-01 1.34e+01 angle pdb=" CA GLU B 287 " pdb=" CB GLU B 287 " pdb=" CG GLU B 287 " ideal model delta sigma weight residual 114.10 120.79 -6.69 2.00e+00 2.50e-01 1.12e+01 ... (remaining 22939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 10145 35.77 - 71.53: 378 71.53 - 107.30: 25 107.30 - 143.06: 4 143.06 - 178.83: 38 Dihedral angle restraints: 10590 sinusoidal: 4614 harmonic: 5976 Sorted by residual: dihedral pdb=" CAN 4BW C 401 " pdb=" OAV 4BW C 401 " pdb=" PBR 4BW C 401 " pdb=" OAH 4BW C 401 " ideal model delta sinusoidal sigma weight residual -29.82 149.01 -178.83 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CAN 4BW D 401 " pdb=" OAV 4BW D 401 " pdb=" PBR 4BW D 401 " pdb=" OAH 4BW D 401 " ideal model delta sinusoidal sigma weight residual 330.18 153.38 176.80 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CAN 4BW B 401 " pdb=" OAV 4BW B 401 " pdb=" PBR 4BW B 401 " pdb=" OAH 4BW B 401 " ideal model delta sinusoidal sigma weight residual 330.18 156.21 173.97 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 10587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1605 0.031 - 0.062: 673 0.062 - 0.094: 159 0.094 - 0.125: 105 0.125 - 0.156: 8 Chirality restraints: 2550 Sorted by residual: chirality pdb=" CB THR C 231 " pdb=" CA THR C 231 " pdb=" OG1 THR C 231 " pdb=" CG2 THR C 231 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA ILE E 297 " pdb=" N ILE E 297 " pdb=" C ILE E 297 " pdb=" CB ILE E 297 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE D 297 " pdb=" N ILE D 297 " pdb=" C ILE D 297 " pdb=" CB ILE D 297 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 2547 not shown) Planarity restraints: 2886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 231 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C THR E 231 " -0.034 2.00e-02 2.50e+03 pdb=" O THR E 231 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU E 232 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 286 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ILE A 286 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 286 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 287 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 287 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C GLU B 287 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU B 287 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS B 288 " -0.009 2.00e-02 2.50e+03 ... (remaining 2883 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 613 2.71 - 3.26: 16824 3.26 - 3.81: 27547 3.81 - 4.35: 37367 4.35 - 4.90: 62079 Nonbonded interactions: 144430 Sorted by model distance: nonbonded pdb=" OG SER C 105 " pdb=" O TYR C 177 " model vdw 2.168 3.040 nonbonded pdb=" O PRO E 145 " pdb=" O2' 4BW E 401 " model vdw 2.188 3.040 nonbonded pdb=" O ILE A 261 " pdb=" OG1 THR A 265 " model vdw 2.195 3.040 nonbonded pdb=" O PRO C 145 " pdb=" O2' 4BW C 401 " model vdw 2.196 3.040 nonbonded pdb=" O ARG C 260 " pdb=" OG SER C 264 " model vdw 2.209 3.040 ... (remaining 144425 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 13.560 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 0.002 0.035 16980 Z= 0.113 Angle : 0.538 11.652 22944 Z= 0.270 Chirality : 0.040 0.156 2550 Planarity : 0.003 0.039 2886 Dihedral : 21.246 178.828 6738 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.20 % Favored : 95.45 % Rotamer: Outliers : 1.92 % Allowed : 27.29 % Favored : 70.79 % 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: -0.36 (0.19), residues: 2046 helix: 0.33 (0.17), residues: 972 sheet: -0.28 (0.32), residues: 264 loop : -0.79 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 279 TYR 0.012 0.001 TYR B 182 PHE 0.020 0.001 PHE F 93 TRP 0.018 0.002 TRP F 255 HIS 0.004 0.001 HIS D 152 Details of bonding type rmsd covalent geometry : bond 0.00248 (16980) covalent geometry : angle 0.53784 (22944) hydrogen bonds : bond 0.23232 ( 715) hydrogen bonds : angle 8.03364 ( 2148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 301 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 MET cc_start: 0.8894 (mmm) cc_final: 0.8483 (tmm) REVERT: B 187 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7649 (tt0) REVERT: B 251 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: E 152 HIS cc_start: 0.8634 (OUTLIER) cc_final: 0.8198 (p-80) REVERT: E 325 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8364 (mm) outliers start: 34 outliers final: 11 residues processed: 322 average time/residue: 0.1098 time to fit residues: 55.5006 Evaluate side-chains 218 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 0.0030 chunk 122 optimal weight: 0.0570 overall best weight: 1.3310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN B 223 ASN C 188 ASN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 ASN F 44 ASN F 188 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.074728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.062938 restraints weight = 50821.470| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 4.05 r_work: 0.3115 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16980 Z= 0.127 Angle : 0.598 8.774 22944 Z= 0.306 Chirality : 0.043 0.149 2550 Planarity : 0.004 0.037 2886 Dihedral : 22.025 176.943 2622 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.42 % Favored : 96.29 % Rotamer: Outliers : 2.88 % Allowed : 22.94 % Favored : 74.18 % 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: 0.27 (0.18), residues: 2046 helix: 0.92 (0.17), residues: 978 sheet: 0.24 (0.36), residues: 204 loop : -0.62 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 163 TYR 0.015 0.001 TYR B 350 PHE 0.015 0.001 PHE F 156 TRP 0.018 0.002 TRP F 255 HIS 0.004 0.001 HIS F 152 Details of bonding type rmsd covalent geometry : bond 0.00267 (16980) covalent geometry : angle 0.59821 (22944) hydrogen bonds : bond 0.04436 ( 715) hydrogen bonds : angle 5.49414 ( 2148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8462 (tpp) cc_final: 0.8099 (ttt) REVERT: A 155 MET cc_start: 0.9379 (mmm) cc_final: 0.9171 (mmp) REVERT: A 202 TYR cc_start: 0.8201 (t80) cc_final: 0.7992 (t80) REVERT: B 155 MET cc_start: 0.9350 (mmm) cc_final: 0.8383 (tmm) REVERT: B 187 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7897 (tt0) REVERT: B 236 TYR cc_start: 0.9016 (t80) cc_final: 0.8792 (t80) REVERT: C 187 GLU cc_start: 0.8445 (mp0) cc_final: 0.8236 (mp0) REVERT: C 295 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8141 (mm-30) REVERT: D 55 THR cc_start: 0.8779 (m) cc_final: 0.8471 (p) REVERT: D 110 GLU cc_start: 0.8577 (mp0) cc_final: 0.8325 (mp0) REVERT: D 158 MET cc_start: 0.7929 (ttt) cc_final: 0.7698 (tpp) REVERT: D 213 LYS cc_start: 0.9140 (mtpm) cc_final: 0.8707 (mmmt) REVERT: D 295 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7915 (mm-30) REVERT: E 119 MET cc_start: 0.8815 (tpp) cc_final: 0.8557 (tpp) REVERT: E 152 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.8429 (p-80) REVERT: E 155 MET cc_start: 0.9325 (mmp) cc_final: 0.9087 (mmp) REVERT: E 334 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: F 159 ASP cc_start: 0.8175 (m-30) cc_final: 0.7273 (p0) outliers start: 51 outliers final: 15 residues processed: 261 average time/residue: 0.1099 time to fit residues: 46.0437 Evaluate side-chains 215 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 277 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 163 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 182 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 188 ASN C 188 ASN C 269 ASN D 270 GLN E 16 ASN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.072138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.060483 restraints weight = 53038.168| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.03 r_work: 0.3049 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16980 Z= 0.181 Angle : 0.603 9.748 22944 Z= 0.304 Chirality : 0.043 0.194 2550 Planarity : 0.004 0.041 2886 Dihedral : 22.275 177.525 2608 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.40 % Favored : 95.31 % Rotamer: Outliers : 3.16 % Allowed : 23.16 % Favored : 73.67 % 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: 0.36 (0.19), residues: 2046 helix: 0.77 (0.17), residues: 1026 sheet: 0.11 (0.37), residues: 204 loop : -0.26 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 279 TYR 0.010 0.001 TYR B 177 PHE 0.013 0.001 PHE F 156 TRP 0.019 0.002 TRP F 255 HIS 0.003 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00393 (16980) covalent geometry : angle 0.60335 (22944) hydrogen bonds : bond 0.04066 ( 715) hydrogen bonds : angle 5.07973 ( 2148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8746 (tpp) cc_final: 0.8375 (ttt) REVERT: A 155 MET cc_start: 0.9431 (mmm) cc_final: 0.9214 (mmp) REVERT: A 169 MET cc_start: 0.8590 (mmm) cc_final: 0.8369 (mmm) REVERT: B 155 MET cc_start: 0.9375 (mmm) cc_final: 0.8359 (tmm) REVERT: B 187 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7967 (tt0) REVERT: B 236 TYR cc_start: 0.9157 (t80) cc_final: 0.8834 (t80) REVERT: B 241 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: C 40 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8470 (tp30) REVERT: C 67 LEU cc_start: 0.9368 (mp) cc_final: 0.9121 (mp) REVERT: C 187 GLU cc_start: 0.8526 (mp0) cc_final: 0.8227 (mp0) REVERT: C 295 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8035 (mm-30) REVERT: D 55 THR cc_start: 0.8845 (m) cc_final: 0.8430 (p) REVERT: D 110 GLU cc_start: 0.8732 (mp0) cc_final: 0.8350 (mp0) REVERT: D 251 TYR cc_start: 0.7086 (OUTLIER) cc_final: 0.6697 (t80) REVERT: D 295 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7959 (mm-30) REVERT: E 263 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9355 (mt) REVERT: E 282 GLU cc_start: 0.9455 (pt0) cc_final: 0.9087 (pp20) REVERT: E 334 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: F 152 HIS cc_start: 0.9046 (OUTLIER) cc_final: 0.8618 (p-80) REVERT: F 159 ASP cc_start: 0.8289 (m-30) cc_final: 0.7640 (p0) REVERT: F 325 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8917 (mm) outliers start: 56 outliers final: 30 residues processed: 243 average time/residue: 0.1052 time to fit residues: 42.0475 Evaluate side-chains 219 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 104 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 139 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 185 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN ** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN E 16 ASN E 299 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.073376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.061635 restraints weight = 51541.643| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 4.02 r_work: 0.3099 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16980 Z= 0.109 Angle : 0.569 10.430 22944 Z= 0.282 Chirality : 0.042 0.160 2550 Planarity : 0.003 0.038 2886 Dihedral : 22.066 177.964 2604 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.91 % Favored : 95.80 % Rotamer: Outliers : 2.20 % Allowed : 23.73 % Favored : 74.07 % 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: 0.45 (0.19), residues: 2046 helix: 0.85 (0.17), residues: 1026 sheet: 0.32 (0.37), residues: 204 loop : -0.29 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 206 TYR 0.010 0.001 TYR A 350 PHE 0.012 0.001 PHE F 156 TRP 0.020 0.002 TRP F 255 HIS 0.002 0.001 HIS E 181 Details of bonding type rmsd covalent geometry : bond 0.00237 (16980) covalent geometry : angle 0.56865 (22944) hydrogen bonds : bond 0.03557 ( 715) hydrogen bonds : angle 4.88719 ( 2148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 134 MET cc_start: 0.8732 (tpp) cc_final: 0.8384 (ttt) REVERT: A 155 MET cc_start: 0.9421 (mmm) cc_final: 0.9179 (mmp) REVERT: A 169 MET cc_start: 0.8536 (mmm) cc_final: 0.8270 (mmm) REVERT: B 155 MET cc_start: 0.9332 (mmm) cc_final: 0.8335 (tmm) REVERT: B 187 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7942 (tt0) REVERT: B 300 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8027 (mm-30) REVERT: C 67 LEU cc_start: 0.9395 (mp) cc_final: 0.9138 (mp) REVERT: C 187 GLU cc_start: 0.8601 (mp0) cc_final: 0.8265 (mp0) REVERT: C 295 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8130 (mm-30) REVERT: D 110 GLU cc_start: 0.8734 (mp0) cc_final: 0.8285 (mp0) REVERT: D 213 LYS cc_start: 0.9110 (mtpm) cc_final: 0.8692 (mmmt) REVERT: D 257 MET cc_start: 0.7152 (mmp) cc_final: 0.6929 (mmp) REVERT: D 295 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7966 (mm-30) REVERT: E 76 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8693 (mm) REVERT: E 282 GLU cc_start: 0.9390 (pt0) cc_final: 0.9039 (pp20) REVERT: E 295 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: E 334 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7878 (tm-30) REVERT: F 152 HIS cc_start: 0.9051 (OUTLIER) cc_final: 0.8341 (p-80) REVERT: F 159 ASP cc_start: 0.8176 (m-30) cc_final: 0.7603 (p0) REVERT: F 325 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8904 (mm) outliers start: 39 outliers final: 20 residues processed: 228 average time/residue: 0.1027 time to fit residues: 38.0338 Evaluate side-chains 210 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 198 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 309 ASN C 269 ASN E 228 ASN E 271 HIS ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 269 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.071867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.060268 restraints weight = 52485.011| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 4.06 r_work: 0.3065 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16980 Z= 0.152 Angle : 0.577 8.702 22944 Z= 0.290 Chirality : 0.042 0.152 2550 Planarity : 0.003 0.042 2886 Dihedral : 22.190 179.298 2604 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.35 % Favored : 95.45 % Rotamer: Outliers : 2.54 % Allowed : 23.95 % Favored : 73.50 % 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: 0.48 (0.19), residues: 2046 helix: 0.87 (0.17), residues: 1026 sheet: 0.27 (0.37), residues: 204 loop : -0.25 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 279 TYR 0.011 0.001 TYR B 350 PHE 0.015 0.001 PHE F 156 TRP 0.018 0.002 TRP F 255 HIS 0.002 0.001 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00332 (16980) covalent geometry : angle 0.57736 (22944) hydrogen bonds : bond 0.03558 ( 715) hydrogen bonds : angle 4.83527 ( 2148) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 134 MET cc_start: 0.8749 (tpp) cc_final: 0.8458 (ttt) REVERT: A 155 MET cc_start: 0.9454 (mmm) cc_final: 0.9202 (mmp) REVERT: A 169 MET cc_start: 0.8648 (mmm) cc_final: 0.8349 (mmm) REVERT: B 155 MET cc_start: 0.9313 (mmm) cc_final: 0.8378 (tmm) REVERT: B 187 GLU cc_start: 0.8552 (mm-30) cc_final: 0.7957 (tt0) REVERT: B 251 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: C 40 GLU cc_start: 0.8427 (tp30) cc_final: 0.8163 (tp30) REVERT: C 67 LEU cc_start: 0.9382 (mp) cc_final: 0.9116 (mp) REVERT: C 187 GLU cc_start: 0.8620 (mp0) cc_final: 0.8251 (mp0) REVERT: C 295 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8133 (mm-30) REVERT: D 41 LYS cc_start: 0.9366 (mtmt) cc_final: 0.9130 (mtmm) REVERT: D 110 GLU cc_start: 0.8807 (mp0) cc_final: 0.8358 (mp0) REVERT: D 213 LYS cc_start: 0.9138 (mtpm) cc_final: 0.8702 (mmmt) REVERT: D 295 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7973 (mm-30) REVERT: E 76 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8848 (mm) REVERT: E 257 MET cc_start: 0.7986 (mmm) cc_final: 0.6360 (mtm) REVERT: E 282 GLU cc_start: 0.9406 (pt0) cc_final: 0.9067 (pp20) REVERT: E 295 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8108 (tm-30) REVERT: E 325 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8974 (mm) REVERT: E 334 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: F 152 HIS cc_start: 0.9101 (OUTLIER) cc_final: 0.8594 (p-80) REVERT: F 159 ASP cc_start: 0.8294 (m-30) cc_final: 0.7712 (p0) REVERT: F 234 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7515 (tm-30) REVERT: F 325 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8904 (mm) outliers start: 45 outliers final: 24 residues processed: 219 average time/residue: 0.1013 time to fit residues: 36.0766 Evaluate side-chains 206 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 269 ASN D 270 GLN E 269 ASN E 299 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.072358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.060722 restraints weight = 51900.384| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 4.06 r_work: 0.3088 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16980 Z= 0.113 Angle : 0.572 10.814 22944 Z= 0.283 Chirality : 0.042 0.291 2550 Planarity : 0.003 0.039 2886 Dihedral : 22.092 179.215 2604 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.06 % Favored : 95.75 % Rotamer: Outliers : 2.26 % Allowed : 24.29 % Favored : 73.45 % 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: 0.51 (0.19), residues: 2046 helix: 0.92 (0.17), residues: 1026 sheet: 0.37 (0.37), residues: 204 loop : -0.29 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 21 TYR 0.009 0.001 TYR B 177 PHE 0.013 0.001 PHE F 156 TRP 0.019 0.002 TRP F 255 HIS 0.002 0.001 HIS E 181 Details of bonding type rmsd covalent geometry : bond 0.00246 (16980) covalent geometry : angle 0.57231 (22944) hydrogen bonds : bond 0.03370 ( 715) hydrogen bonds : angle 4.72966 ( 2148) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8761 (tpp) cc_final: 0.8467 (ttt) REVERT: A 155 MET cc_start: 0.9441 (mmm) cc_final: 0.9178 (mmp) REVERT: A 169 MET cc_start: 0.8617 (mmm) cc_final: 0.8312 (mmm) REVERT: A 212 MET cc_start: 0.8339 (ttm) cc_final: 0.7729 (mtp) REVERT: B 155 MET cc_start: 0.9307 (mmm) cc_final: 0.8360 (tmm) REVERT: B 187 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7942 (tm-30) REVERT: B 251 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7992 (m-10) REVERT: C 21 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8301 (mtm-85) REVERT: C 187 GLU cc_start: 0.8641 (mp0) cc_final: 0.8241 (mp0) REVERT: C 295 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8137 (mm-30) REVERT: D 41 LYS cc_start: 0.9365 (mtmt) cc_final: 0.9126 (mtmm) REVERT: D 110 GLU cc_start: 0.8762 (mp0) cc_final: 0.8256 (mp0) REVERT: D 213 LYS cc_start: 0.9159 (mtpm) cc_final: 0.8695 (mmmt) REVERT: D 276 MET cc_start: 0.9172 (ptp) cc_final: 0.8870 (mtm) REVERT: D 295 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7982 (mm-30) REVERT: E 76 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8832 (mm) REVERT: E 325 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.8900 (mm) REVERT: E 334 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: F 152 HIS cc_start: 0.9052 (OUTLIER) cc_final: 0.8568 (p-80) REVERT: F 159 ASP cc_start: 0.8245 (m-30) cc_final: 0.7642 (p0) REVERT: F 234 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7555 (tm-30) REVERT: F 269 ASN cc_start: 0.9236 (t160) cc_final: 0.9013 (m-40) REVERT: F 325 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8922 (mm) outliers start: 40 outliers final: 22 residues processed: 217 average time/residue: 0.1072 time to fit residues: 37.2719 Evaluate side-chains 206 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 67 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 116 optimal weight: 0.0980 chunk 103 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 ASN D 270 GLN E 271 HIS ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.073020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.061366 restraints weight = 51798.868| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 4.06 r_work: 0.3106 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16980 Z= 0.107 Angle : 0.580 9.921 22944 Z= 0.284 Chirality : 0.042 0.213 2550 Planarity : 0.003 0.037 2886 Dihedral : 22.048 179.498 2604 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.11 % Favored : 95.75 % Rotamer: Outliers : 2.26 % Allowed : 24.18 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 2046 helix: 0.98 (0.17), residues: 1026 sheet: 0.37 (0.37), residues: 204 loop : -0.29 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 274 TYR 0.010 0.001 TYR E 350 PHE 0.013 0.001 PHE F 156 TRP 0.020 0.002 TRP F 255 HIS 0.002 0.001 HIS E 271 Details of bonding type rmsd covalent geometry : bond 0.00234 (16980) covalent geometry : angle 0.58012 (22944) hydrogen bonds : bond 0.03293 ( 715) hydrogen bonds : angle 4.66127 ( 2148) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8741 (tpp) cc_final: 0.8440 (ttt) REVERT: A 155 MET cc_start: 0.9417 (mmm) cc_final: 0.9152 (mmp) REVERT: A 169 MET cc_start: 0.8608 (mmm) cc_final: 0.8318 (mmm) REVERT: B 155 MET cc_start: 0.9304 (mmm) cc_final: 0.8339 (tmm) REVERT: B 187 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7936 (tm-30) REVERT: B 251 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7969 (m-10) REVERT: C 21 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8283 (mtm-85) REVERT: C 187 GLU cc_start: 0.8647 (mp0) cc_final: 0.8221 (mp0) REVERT: C 295 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8104 (mm-30) REVERT: D 40 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8591 (tm-30) REVERT: D 110 GLU cc_start: 0.8782 (mp0) cc_final: 0.8308 (mp0) REVERT: D 213 LYS cc_start: 0.9140 (mtpm) cc_final: 0.8738 (mmmt) REVERT: D 276 MET cc_start: 0.9138 (ptp) cc_final: 0.8923 (mtm) REVERT: D 295 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8033 (mm-30) REVERT: E 76 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8842 (mm) REVERT: E 257 MET cc_start: 0.8046 (mmm) cc_final: 0.6483 (mtm) REVERT: E 325 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8902 (mm) REVERT: E 334 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7944 (tm-30) REVERT: F 152 HIS cc_start: 0.9007 (OUTLIER) cc_final: 0.8286 (p-80) REVERT: F 159 ASP cc_start: 0.8241 (m-30) cc_final: 0.7687 (p0) REVERT: F 234 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7588 (tm-30) REVERT: F 269 ASN cc_start: 0.9191 (t160) cc_final: 0.8873 (m110) REVERT: F 325 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8932 (mm) outliers start: 40 outliers final: 26 residues processed: 222 average time/residue: 0.0985 time to fit residues: 35.4026 Evaluate side-chains 208 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN D 270 GLN E 271 HIS ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.069669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.058212 restraints weight = 53717.816| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 4.03 r_work: 0.3015 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16980 Z= 0.228 Angle : 0.670 11.486 22944 Z= 0.330 Chirality : 0.044 0.146 2550 Planarity : 0.004 0.042 2886 Dihedral : 22.439 179.938 2604 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.59 % Favored : 95.26 % Rotamer: Outliers : 2.49 % Allowed : 24.12 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 2046 helix: 0.83 (0.17), residues: 1026 sheet: 0.14 (0.37), residues: 204 loop : -0.24 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 279 TYR 0.012 0.001 TYR C 177 PHE 0.018 0.001 PHE F 156 TRP 0.016 0.002 TRP F 255 HIS 0.004 0.001 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00495 (16980) covalent geometry : angle 0.67027 (22944) hydrogen bonds : bond 0.03778 ( 715) hydrogen bonds : angle 4.80651 ( 2148) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.9298 (tpp) cc_final: 0.8845 (tpp) REVERT: A 125 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8302 (mtmm) REVERT: A 134 MET cc_start: 0.8732 (tpp) cc_final: 0.8512 (ttt) REVERT: A 155 MET cc_start: 0.9499 (mmm) cc_final: 0.9266 (mmp) REVERT: A 169 MET cc_start: 0.8784 (mmm) cc_final: 0.8492 (mmm) REVERT: A 259 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6007 (mm-30) REVERT: B 155 MET cc_start: 0.9350 (mmm) cc_final: 0.8402 (tmm) REVERT: B 187 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7890 (tm-30) REVERT: B 251 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: C 187 GLU cc_start: 0.8703 (mp0) cc_final: 0.8272 (mp0) REVERT: C 295 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8136 (mm-30) REVERT: D 40 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8543 (tm-30) REVERT: D 110 GLU cc_start: 0.8915 (mp0) cc_final: 0.8444 (mp0) REVERT: D 213 LYS cc_start: 0.9144 (mtpm) cc_final: 0.8712 (mmmt) REVERT: D 295 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8005 (mm-30) REVERT: E 76 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8939 (mm) REVERT: E 257 MET cc_start: 0.8027 (mmm) cc_final: 0.6501 (mtm) REVERT: E 325 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.8869 (mm) REVERT: F 159 ASP cc_start: 0.8434 (m-30) cc_final: 0.7842 (p0) REVERT: F 234 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7504 (tm-30) REVERT: F 325 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8952 (mm) outliers start: 44 outliers final: 26 residues processed: 206 average time/residue: 0.1015 time to fit residues: 34.0475 Evaluate side-chains 202 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 237 CYS Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 180 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 54 optimal weight: 0.0070 chunk 192 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.070959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059478 restraints weight = 52741.945| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.04 r_work: 0.3049 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16980 Z= 0.153 Angle : 0.640 11.835 22944 Z= 0.310 Chirality : 0.043 0.294 2550 Planarity : 0.003 0.041 2886 Dihedral : 22.255 179.788 2604 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.91 % Favored : 95.94 % Rotamer: Outliers : 1.81 % Allowed : 25.20 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.29 (0.19), residues: 2046 helix: 0.79 (0.16), residues: 1032 sheet: -0.31 (0.32), residues: 264 loop : -0.29 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 21 TYR 0.009 0.001 TYR C 177 PHE 0.015 0.001 PHE F 156 TRP 0.019 0.002 TRP F 255 HIS 0.002 0.001 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00338 (16980) covalent geometry : angle 0.63968 (22944) hydrogen bonds : bond 0.03567 ( 715) hydrogen bonds : angle 4.74352 ( 2148) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.9314 (tpp) cc_final: 0.8897 (tpp) REVERT: A 125 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8244 (mtmm) REVERT: A 134 MET cc_start: 0.8755 (tpp) cc_final: 0.8492 (ttt) REVERT: A 155 MET cc_start: 0.9471 (mmm) cc_final: 0.9227 (mmp) REVERT: A 169 MET cc_start: 0.8711 (mmm) cc_final: 0.8425 (mmm) REVERT: A 259 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.5904 (mm-30) REVERT: B 155 MET cc_start: 0.9344 (mmm) cc_final: 0.8387 (tmm) REVERT: B 187 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7923 (tm-30) REVERT: B 251 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: C 187 GLU cc_start: 0.8698 (mp0) cc_final: 0.8225 (mp0) REVERT: C 295 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8183 (mm-30) REVERT: D 40 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8560 (tm-30) REVERT: D 110 GLU cc_start: 0.8904 (mp0) cc_final: 0.8428 (mp0) REVERT: D 213 LYS cc_start: 0.9124 (mtpm) cc_final: 0.8812 (mttp) REVERT: D 295 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7997 (mm-30) REVERT: E 76 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8872 (mm) REVERT: E 257 MET cc_start: 0.7982 (mmm) cc_final: 0.6433 (mtm) REVERT: E 271 HIS cc_start: 0.9228 (m90) cc_final: 0.8874 (m90) REVERT: E 325 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8852 (mm) REVERT: F 159 ASP cc_start: 0.8363 (m-30) cc_final: 0.7804 (p0) REVERT: F 234 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7492 (tm-30) REVERT: F 325 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8942 (mm) outliers start: 32 outliers final: 24 residues processed: 201 average time/residue: 0.1015 time to fit residues: 33.5962 Evaluate side-chains 204 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 202 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 51 optimal weight: 0.0040 chunk 110 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN D 270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.071652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.060125 restraints weight = 52392.299| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 4.06 r_work: 0.3082 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16980 Z= 0.131 Angle : 0.642 12.689 22944 Z= 0.306 Chirality : 0.044 0.313 2550 Planarity : 0.003 0.040 2886 Dihedral : 22.117 179.398 2604 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.20 % Favored : 95.65 % Rotamer: Outliers : 1.75 % Allowed : 24.92 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 2046 helix: 0.81 (0.16), residues: 1032 sheet: -0.27 (0.32), residues: 264 loop : -0.29 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 21 TYR 0.009 0.001 TYR A 350 PHE 0.014 0.001 PHE F 156 TRP 0.021 0.002 TRP F 255 HIS 0.003 0.001 HIS E 181 Details of bonding type rmsd covalent geometry : bond 0.00291 (16980) covalent geometry : angle 0.64208 (22944) hydrogen bonds : bond 0.03505 ( 715) hydrogen bonds : angle 4.70926 ( 2148) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.9309 (tpp) cc_final: 0.8902 (tpp) REVERT: A 125 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8208 (mtmm) REVERT: A 134 MET cc_start: 0.8732 (tpp) cc_final: 0.8488 (ttt) REVERT: A 155 MET cc_start: 0.9463 (mmm) cc_final: 0.9221 (mmp) REVERT: A 169 MET cc_start: 0.8664 (mmm) cc_final: 0.8333 (mmm) REVERT: A 257 MET cc_start: 0.7542 (mmm) cc_final: 0.5801 (mtm) REVERT: B 155 MET cc_start: 0.9336 (mmm) cc_final: 0.8372 (tmm) REVERT: B 187 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7918 (tm-30) REVERT: B 234 GLU cc_start: 0.8863 (pt0) cc_final: 0.8527 (tm-30) REVERT: B 251 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7948 (m-10) REVERT: C 187 GLU cc_start: 0.8695 (mp0) cc_final: 0.8211 (mp0) REVERT: C 295 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8234 (mm-30) REVERT: D 110 GLU cc_start: 0.8929 (mp0) cc_final: 0.8444 (mp0) REVERT: D 213 LYS cc_start: 0.9105 (mtpm) cc_final: 0.8786 (mttp) REVERT: D 295 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8043 (mm-30) REVERT: E 257 MET cc_start: 0.7989 (mmm) cc_final: 0.6432 (mtm) REVERT: E 271 HIS cc_start: 0.9228 (m90) cc_final: 0.8896 (m90) REVERT: E 325 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8928 (mm) REVERT: F 159 ASP cc_start: 0.8344 (m-30) cc_final: 0.7849 (p0) REVERT: F 184 GLU cc_start: 0.9416 (tt0) cc_final: 0.8792 (tp30) REVERT: F 234 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7487 (tm-30) REVERT: F 269 ASN cc_start: 0.9234 (t160) cc_final: 0.9009 (m-40) REVERT: F 325 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8952 (mm) outliers start: 31 outliers final: 22 residues processed: 201 average time/residue: 0.1061 time to fit residues: 34.8228 Evaluate side-chains 200 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 112 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 185 optimal weight: 7.9990 chunk 152 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.075281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.063796 restraints weight = 52413.415| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 4.01 r_work: 0.3110 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16980 Z= 0.108 Angle : 0.632 12.379 22944 Z= 0.300 Chirality : 0.043 0.319 2550 Planarity : 0.003 0.040 2886 Dihedral : 21.950 179.892 2604 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.86 % Favored : 95.99 % Rotamer: Outliers : 1.30 % Allowed : 25.65 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.19), residues: 2046 helix: 0.80 (0.16), residues: 1038 sheet: 0.29 (0.37), residues: 204 loop : -0.24 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 21 TYR 0.007 0.001 TYR C 177 PHE 0.012 0.001 PHE F 156 TRP 0.022 0.002 TRP F 255 HIS 0.002 0.000 HIS D 271 Details of bonding type rmsd covalent geometry : bond 0.00238 (16980) covalent geometry : angle 0.63171 (22944) hydrogen bonds : bond 0.03379 ( 715) hydrogen bonds : angle 4.64030 ( 2148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3614.79 seconds wall clock time: 62 minutes 51.13 seconds (3771.13 seconds total)