Starting phenix.real_space_refine on Wed Jun 18 18:40:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo9_43368/06_2025/8vo9_43368_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo9_43368/06_2025/8vo9_43368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vo9_43368/06_2025/8vo9_43368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo9_43368/06_2025/8vo9_43368.map" model { file = "/net/cci-nas-00/data/ceres_data/8vo9_43368/06_2025/8vo9_43368_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo9_43368/06_2025/8vo9_43368_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 140 5.16 5 C 13504 2.51 5 N 3654 2.21 5 O 4143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21459 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3789 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 469} Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.36, per 1000 atoms: 0.67 Number of scatterers: 21459 At special positions: 0 Unit cell: (217.33, 108.15, 158.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 140 16.00 P 12 15.00 Mg 6 11.99 O 4143 8.00 N 3654 7.00 C 13504 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: 5.31 Conformation dependent library (CDL) restraints added in 3.1 seconds 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5034 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 55 sheets defined 42.9% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 86 through 89 Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.661A pdb=" N LEU A 119 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.936A pdb=" N LYS A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.590A pdb=" N LEU A 375 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.575A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.742A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.645A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.860A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 296 removed outlier: 4.017A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.525A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.573A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.555A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.803A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.784A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.560A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.683A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.594A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.753A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.650A pdb=" N MET C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.589A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.686A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.704A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.587A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.590A pdb=" N LEU D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.990A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.501A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 352 through 356 removed outlier: 3.676A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.339A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.506A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.857A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.778A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.587A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.572A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 removed outlier: 3.687A pdb=" N LEU E 261 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 286 through 296 removed outlier: 4.043A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.510A pdb=" N MET E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 356 removed outlier: 4.499A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.873A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 removed outlier: 3.597A pdb=" N GLN F 59 " --> pdb=" O GLY F 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 55 through 59' Processing helix chain 'F' and resid 60 through 63 removed outlier: 5.489A pdb=" N GLY F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 60 through 63' Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.706A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.817A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 146 removed outlier: 3.579A pdb=" N LEU F 140 " --> pdb=" O ILE F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 231 removed outlier: 3.691A pdb=" N GLU F 226 " --> pdb=" O ASP F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.805A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 removed outlier: 3.515A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 352 through 356 removed outlier: 3.813A pdb=" N TRP F 356 " --> pdb=" O GLN F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.285A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 removed outlier: 3.538A pdb=" N GLN G 59 " --> pdb=" O GLY G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 91 Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.870A pdb=" N GLU G 100 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 97 through 101' Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.624A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 194 removed outlier: 3.996A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.768A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 262 Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 286 through 296 removed outlier: 3.842A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 348 Processing helix chain 'G' and resid 350 through 355 removed outlier: 3.916A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 5.537A pdb=" N TYR A 23 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 36 " --> pdb=" O TYR A 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 72 removed outlier: 4.009A pdb=" N ARG A 82 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA A 71 " --> pdb=" O CYS A 80 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N CYS A 80 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 156 removed outlier: 4.143A pdb=" N GLU A 162 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA8, first strand: chain 'A' and resid 231 through 234 Processing sheet with id=AA9, first strand: chain 'A' and resid 305 through 308 removed outlier: 4.019A pdb=" N ALA A 261 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.462A pdb=" N ASN A 272 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AB3, first strand: chain 'A' and resid 337 through 340 Processing sheet with id=AB4, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.741A pdb=" N VAL A 367 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A 356 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ALA A 365 " --> pdb=" O THR A 356 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 385 through 386 Processing sheet with id=AB6, first strand: chain 'A' and resid 394 through 396 removed outlier: 5.148A pdb=" N PHE A 394 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 452 through 457 removed outlier: 6.735A pdb=" N LYS A 460 " --> pdb=" O CYS A 456 " (cutoff:3.500A) removed outlier: 13.064A pdb=" N VAL A 461 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N GLY A 472 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE A 463 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TYR A 469 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 452 through 457 removed outlier: 6.735A pdb=" N LYS A 460 " --> pdb=" O CYS A 456 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.692A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 357 " --> pdb=" O MET B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AC2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'B' and resid 41 through 42 removed outlier: 4.320A pdb=" N GLN B 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 41 through 42 removed outlier: 4.320A pdb=" N GLN B 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AC7, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.513A pdb=" N VAL B 152 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.624A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 8 through 9 removed outlier: 6.543A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AD2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AD3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AD4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AD5, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.304A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 135 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 357 " --> pdb=" O MET D 132 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AD8, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AD9, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.581A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 165 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 238 through 241 removed outlier: 3.512A pdb=" N LYS D 238 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.571A pdb=" N ALA E 29 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'E' and resid 41 through 42 removed outlier: 4.255A pdb=" N GLN E 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 41 through 42 removed outlier: 4.255A pdb=" N GLN E 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AE7, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AE8, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.533A pdb=" N VAL E 152 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AF1, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.584A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AF3, first strand: chain 'F' and resid 71 through 72 removed outlier: 3.603A pdb=" N GLU F 72 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 238 through 241 removed outlier: 3.504A pdb=" N LYS F 238 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.603A pdb=" N VAL G 9 " --> pdb=" O GLY G 20 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASN G 12 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AF7, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AF8, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AF9, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.534A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 238 through 241 940 hydrogen bonds defined for protein. 2397 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: 9.41 Time building geometry restraints manager: 6.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7047 1.34 - 1.46: 4940 1.46 - 1.58: 9680 1.58 - 1.70: 18 1.70 - 1.82: 239 Bond restraints: 21924 Sorted by residual: bond pdb=" CE1 HIC G 73 " pdb=" NE2 HIC G 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.97e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.87e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.78e+00 ... (remaining 21919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 28977 1.46 - 2.91: 563 2.91 - 4.37: 148 4.37 - 5.82: 48 5.82 - 7.28: 3 Bond angle restraints: 29739 Sorted by residual: angle pdb=" N VAL B 43 " pdb=" CA VAL B 43 " pdb=" C VAL B 43 " ideal model delta sigma weight residual 113.71 109.61 4.10 9.50e-01 1.11e+00 1.86e+01 angle pdb=" N THR E 148 " pdb=" CA THR E 148 " pdb=" C THR E 148 " ideal model delta sigma weight residual 114.56 109.71 4.85 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N ILE A 381 " pdb=" CA ILE A 381 " pdb=" C ILE A 381 " ideal model delta sigma weight residual 113.42 110.00 3.42 1.17e+00 7.31e-01 8.54e+00 angle pdb=" N HIC G 73 " pdb=" CA HIC G 73 " pdb=" CB HIC G 73 " ideal model delta sigma weight residual 110.50 115.32 -4.82 1.70e+00 3.46e-01 8.04e+00 angle pdb=" CA ASP F 56 " pdb=" C ASP F 56 " pdb=" O ASP F 56 " ideal model delta sigma weight residual 120.90 118.06 2.84 1.03e+00 9.43e-01 7.63e+00 ... (remaining 29734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.53: 12331 22.53 - 45.06: 738 45.06 - 67.60: 62 67.60 - 90.13: 23 90.13 - 112.66: 6 Dihedral angle restraints: 13160 sinusoidal: 5298 harmonic: 7862 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -172.66 112.66 1 2.00e+01 2.50e-03 3.32e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -170.38 110.38 1 2.00e+01 2.50e-03 3.24e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -170.11 110.11 1 2.00e+01 2.50e-03 3.23e+01 ... (remaining 13157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2293 0.039 - 0.077: 645 0.077 - 0.116: 320 0.116 - 0.154: 22 0.154 - 0.193: 1 Chirality restraints: 3281 Sorted by residual: chirality pdb=" CB THR D 5 " pdb=" CA THR D 5 " pdb=" OG1 THR D 5 " pdb=" CG2 THR D 5 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA ILE C 151 " pdb=" N ILE C 151 " pdb=" C ILE C 151 " pdb=" CB ILE C 151 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ILE A 385 " pdb=" N ILE A 385 " pdb=" C ILE A 385 " pdb=" CB ILE A 385 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 3278 not shown) Planarity restraints: 3827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 242 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO E 243 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO C 164 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 111 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO C 112 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " -0.018 5.00e-02 4.00e+02 ... (remaining 3824 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 672 2.71 - 3.26: 21530 3.26 - 3.81: 34238 3.81 - 4.35: 43779 4.35 - 4.90: 74368 Nonbonded interactions: 174587 Sorted by model distance: nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.167 2.170 nonbonded pdb=" OG1 THR D 5 " pdb=" O GLU D 100 " model vdw 2.221 3.040 nonbonded pdb=" O GLY E 156 " pdb=" OG1 THR E 303 " model vdw 2.221 3.040 nonbonded pdb=" O GLY D 301 " pdb=" OG1 THR D 304 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR F 218 " pdb=" OE2 GLU F 226 " model vdw 2.229 3.040 ... (remaining 174582 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 54.110 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.120 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 : 0.003 0.057 21924 Z= 0.143 Angle : 0.571 7.278 29739 Z= 0.299 Chirality : 0.043 0.193 3281 Planarity : 0.003 0.038 3827 Dihedral : 14.003 112.658 8126 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2691 helix: 0.50 (0.18), residues: 954 sheet: 0.23 (0.23), residues: 551 loop : 0.33 (0.19), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 356 HIS 0.003 0.001 HIS G 371 PHE 0.010 0.001 PHE A 455 TYR 0.016 0.001 TYR F 198 ARG 0.006 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.21328 ( 921) hydrogen bonds : angle 7.36352 ( 2397) covalent geometry : bond 0.00293 (21924) covalent geometry : angle 0.57077 (29739) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 2.547 Fit side-chains revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7535 (mp0) cc_final: 0.7166 (mp0) REVERT: A 317 LEU cc_start: 0.8575 (tp) cc_final: 0.8353 (tt) REVERT: A 474 HIS cc_start: 0.5281 (p-80) cc_final: 0.4987 (p-80) REVERT: B 72 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7105 (tp30) REVERT: B 211 ASP cc_start: 0.7964 (t0) cc_final: 0.7654 (m-30) REVERT: B 327 ILE cc_start: 0.8845 (mp) cc_final: 0.8609 (mm) REVERT: B 355 MET cc_start: 0.7937 (mmp) cc_final: 0.7686 (mmm) REVERT: C 24 ASP cc_start: 0.6896 (m-30) cc_final: 0.6537 (m-30) REVERT: C 53 TYR cc_start: 0.8682 (m-80) cc_final: 0.8284 (m-80) REVERT: C 123 MET cc_start: 0.8188 (tpp) cc_final: 0.7863 (tpt) REVERT: C 221 LEU cc_start: 0.8840 (tp) cc_final: 0.8564 (mm) REVERT: D 159 VAL cc_start: 0.8877 (p) cc_final: 0.8659 (m) REVERT: D 176 MET cc_start: 0.7985 (mmm) cc_final: 0.7512 (mtt) REVERT: D 206 ARG cc_start: 0.7279 (ttm-80) cc_final: 0.7045 (ttt180) REVERT: D 212 ILE cc_start: 0.7484 (mt) cc_final: 0.7237 (mt) REVERT: E 113 LYS cc_start: 0.5741 (mptt) cc_final: 0.4954 (mttt) REVERT: G 59 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8034 (tp40) REVERT: G 82 MET cc_start: 0.7707 (tpt) cc_final: 0.7143 (tpt) REVERT: G 207 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7042 (mm-30) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.3398 time to fit residues: 225.3896 Evaluate side-chains 262 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 211 optimal weight: 0.0050 chunk 81 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 157 optimal weight: 5.9990 chunk 245 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 87 HIS B 353 GLN C 87 HIS D 87 HIS E 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.143745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119568 restraints weight = 31828.462| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.84 r_work: 0.3312 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21924 Z= 0.127 Angle : 0.591 8.002 29739 Z= 0.296 Chirality : 0.046 0.164 3281 Planarity : 0.004 0.038 3827 Dihedral : 7.404 104.677 3048 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.70 % Allowed : 6.95 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2691 helix: 0.36 (0.18), residues: 924 sheet: 0.26 (0.23), residues: 549 loop : 0.43 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 101 HIS 0.007 0.001 HIS D 87 PHE 0.022 0.001 PHE C 352 TYR 0.019 0.001 TYR F 306 ARG 0.007 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 921) hydrogen bonds : angle 5.59708 ( 2397) covalent geometry : bond 0.00291 (21924) covalent geometry : angle 0.59129 (29739) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 287 time to evaluate : 2.729 Fit side-chains revert: symmetry clash REVERT: A 320 THR cc_start: 0.7867 (m) cc_final: 0.7630 (p) REVERT: A 326 THR cc_start: 0.7794 (p) cc_final: 0.7561 (p) REVERT: A 474 HIS cc_start: 0.4955 (p-80) cc_final: 0.4748 (p-80) REVERT: B 72 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7470 (tp30) REVERT: B 211 ASP cc_start: 0.8524 (t0) cc_final: 0.8233 (m-30) REVERT: B 325 MET cc_start: 0.8454 (mmm) cc_final: 0.8195 (mmp) REVERT: B 327 ILE cc_start: 0.8762 (mp) cc_final: 0.8537 (mm) REVERT: B 360 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: C 24 ASP cc_start: 0.7638 (m-30) cc_final: 0.7198 (m-30) REVERT: C 53 TYR cc_start: 0.9080 (m-80) cc_final: 0.8846 (m-80) REVERT: C 123 MET cc_start: 0.8452 (tpp) cc_final: 0.8004 (tpt) REVERT: C 178 LEU cc_start: 0.8815 (mp) cc_final: 0.8461 (mt) REVERT: C 221 LEU cc_start: 0.8880 (tp) cc_final: 0.8666 (mm) REVERT: D 176 MET cc_start: 0.8887 (mmm) cc_final: 0.8685 (mtt) REVERT: D 212 ILE cc_start: 0.8250 (mt) cc_final: 0.7944 (mt) REVERT: D 373 LYS cc_start: 0.7853 (mtpp) cc_final: 0.7638 (mtpt) REVERT: E 45 VAL cc_start: 0.8582 (t) cc_final: 0.8238 (p) REVERT: E 113 LYS cc_start: 0.6592 (mptt) cc_final: 0.5652 (mttt) REVERT: E 369 ILE cc_start: 0.8582 (pt) cc_final: 0.8328 (tp) REVERT: F 82 MET cc_start: 0.8426 (tpt) cc_final: 0.8120 (tpp) REVERT: G 162 ASN cc_start: 0.8124 (m-40) cc_final: 0.7845 (m110) REVERT: G 372 ARG cc_start: 0.7615 (mtp180) cc_final: 0.6913 (ptm160) outliers start: 16 outliers final: 12 residues processed: 297 average time/residue: 0.3324 time to fit residues: 155.4645 Evaluate side-chains 254 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 241 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 221 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 218 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN B 87 HIS G 296 ASN G 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.145291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.121931 restraints weight = 30777.462| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.63 r_work: 0.3369 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21924 Z= 0.158 Angle : 0.589 8.441 29739 Z= 0.293 Chirality : 0.047 0.172 3281 Planarity : 0.004 0.037 3827 Dihedral : 7.423 104.869 3048 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.05 % Allowed : 9.44 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2691 helix: 0.37 (0.17), residues: 960 sheet: 0.07 (0.23), residues: 563 loop : 0.36 (0.20), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 101 HIS 0.007 0.001 HIS D 87 PHE 0.014 0.001 PHE C 352 TYR 0.019 0.001 TYR E 362 ARG 0.008 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 921) hydrogen bonds : angle 5.30213 ( 2397) covalent geometry : bond 0.00379 (21924) covalent geometry : angle 0.58937 (29739) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 259 time to evaluate : 2.365 Fit side-chains REVERT: A 317 LEU cc_start: 0.8683 (tp) cc_final: 0.8426 (tt) REVERT: A 320 THR cc_start: 0.8052 (m) cc_final: 0.7787 (p) REVERT: A 474 HIS cc_start: 0.5272 (p-80) cc_final: 0.5033 (p90) REVERT: B 72 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7500 (tp30) REVERT: B 211 ASP cc_start: 0.8391 (t0) cc_final: 0.8159 (m-30) REVERT: B 325 MET cc_start: 0.8454 (mmm) cc_final: 0.8243 (mmp) REVERT: C 24 ASP cc_start: 0.7648 (m-30) cc_final: 0.7444 (m-30) REVERT: C 53 TYR cc_start: 0.9149 (m-80) cc_final: 0.8902 (m-80) REVERT: C 123 MET cc_start: 0.8378 (tpp) cc_final: 0.7936 (tpt) REVERT: C 151 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8161 (tt) REVERT: C 178 LEU cc_start: 0.8766 (mp) cc_final: 0.8407 (mt) REVERT: C 215 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7928 (mtmm) REVERT: C 221 LEU cc_start: 0.8874 (tp) cc_final: 0.8657 (mm) REVERT: D 176 MET cc_start: 0.8609 (mmm) cc_final: 0.8339 (mtt) REVERT: E 45 VAL cc_start: 0.8743 (t) cc_final: 0.8447 (p) REVERT: E 113 LYS cc_start: 0.6253 (mptt) cc_final: 0.5347 (mttm) REVERT: E 249 THR cc_start: 0.8983 (m) cc_final: 0.8736 (p) REVERT: E 369 ILE cc_start: 0.8633 (pt) cc_final: 0.8398 (tp) REVERT: F 82 MET cc_start: 0.8435 (tpt) cc_final: 0.8199 (tpp) REVERT: F 128 ASN cc_start: 0.7184 (t0) cc_final: 0.6946 (t0) REVERT: F 215 LYS cc_start: 0.7543 (ttmt) cc_final: 0.7122 (ttpt) REVERT: G 372 ARG cc_start: 0.7732 (mtp180) cc_final: 0.7028 (ptm160) outliers start: 24 outliers final: 11 residues processed: 276 average time/residue: 0.3209 time to fit residues: 139.5021 Evaluate side-chains 245 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 232 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 140 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 0.0060 chunk 66 optimal weight: 0.9990 chunk 150 optimal weight: 0.3980 chunk 266 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS C 353 GLN G 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.145682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122327 restraints weight = 31198.012| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.63 r_work: 0.3372 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21924 Z= 0.133 Angle : 0.566 7.398 29739 Z= 0.279 Chirality : 0.046 0.162 3281 Planarity : 0.004 0.037 3827 Dihedral : 7.316 103.743 3048 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.40 % Allowed : 11.01 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2691 helix: 0.40 (0.17), residues: 960 sheet: 0.04 (0.23), residues: 563 loop : 0.35 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 101 HIS 0.007 0.001 HIS D 87 PHE 0.012 0.001 PHE G 266 TYR 0.021 0.001 TYR E 362 ARG 0.007 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 921) hydrogen bonds : angle 5.08286 ( 2397) covalent geometry : bond 0.00317 (21924) covalent geometry : angle 0.56637 (29739) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 2.651 Fit side-chains REVERT: A 303 LYS cc_start: 0.8033 (mmpt) cc_final: 0.7694 (tmtt) REVERT: A 317 LEU cc_start: 0.8687 (tp) cc_final: 0.8439 (tt) REVERT: A 320 THR cc_start: 0.8033 (m) cc_final: 0.7807 (p) REVERT: A 474 HIS cc_start: 0.5286 (p-80) cc_final: 0.5008 (p90) REVERT: B 72 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7588 (tp30) REVERT: B 211 ASP cc_start: 0.8412 (t0) cc_final: 0.8148 (m-30) REVERT: B 325 MET cc_start: 0.8441 (mmm) cc_final: 0.8149 (mmp) REVERT: C 24 ASP cc_start: 0.7626 (m-30) cc_final: 0.7390 (m-30) REVERT: C 123 MET cc_start: 0.8389 (tpp) cc_final: 0.7938 (tpt) REVERT: C 178 LEU cc_start: 0.8748 (mp) cc_final: 0.8434 (mt) REVERT: C 215 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7910 (mtmm) REVERT: C 221 LEU cc_start: 0.8897 (tp) cc_final: 0.8642 (mm) REVERT: D 176 MET cc_start: 0.8653 (mmm) cc_final: 0.8377 (mtt) REVERT: E 45 VAL cc_start: 0.8808 (t) cc_final: 0.8495 (p) REVERT: E 113 LYS cc_start: 0.6302 (mptt) cc_final: 0.5375 (mttt) REVERT: E 179 ASP cc_start: 0.8576 (m-30) cc_final: 0.8301 (m-30) REVERT: E 249 THR cc_start: 0.8976 (m) cc_final: 0.8734 (p) REVERT: E 369 ILE cc_start: 0.8620 (pt) cc_final: 0.8395 (tp) REVERT: F 82 MET cc_start: 0.8432 (tpt) cc_final: 0.8185 (tpp) REVERT: F 128 ASN cc_start: 0.7193 (t0) cc_final: 0.6873 (t0) REVERT: G 372 ARG cc_start: 0.7760 (mtp180) cc_final: 0.7053 (ptm160) outliers start: 32 outliers final: 19 residues processed: 271 average time/residue: 0.3461 time to fit residues: 149.8804 Evaluate side-chains 255 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 221 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 101 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 0.0470 chunk 81 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS B 87 HIS D 87 HIS ** G 296 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 = 0.3739 r_free = 0.3739 target = 0.141390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116895 restraints weight = 31347.665| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.70 r_work: 0.3268 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 21924 Z= 0.240 Angle : 0.653 9.734 29739 Z= 0.326 Chirality : 0.049 0.189 3281 Planarity : 0.004 0.038 3827 Dihedral : 7.684 108.679 3048 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.83 % Allowed : 11.75 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2691 helix: 0.10 (0.17), residues: 960 sheet: -0.16 (0.23), residues: 563 loop : 0.21 (0.20), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 101 HIS 0.007 0.001 HIS D 87 PHE 0.014 0.002 PHE A 336 TYR 0.015 0.002 TYR G 166 ARG 0.006 0.001 ARG F 196 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 921) hydrogen bonds : angle 5.27091 ( 2397) covalent geometry : bond 0.00587 (21924) covalent geometry : angle 0.65315 (29739) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 2.379 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8696 (tp) cc_final: 0.8422 (tt) REVERT: A 320 THR cc_start: 0.8205 (m) cc_final: 0.7800 (t) REVERT: A 326 THR cc_start: 0.7687 (p) cc_final: 0.7375 (p) REVERT: A 474 HIS cc_start: 0.5845 (p-80) cc_final: 0.5515 (p90) REVERT: B 72 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7656 (tp30) REVERT: B 211 ASP cc_start: 0.8503 (t0) cc_final: 0.8213 (m-30) REVERT: B 325 MET cc_start: 0.8516 (mmm) cc_final: 0.8091 (mmp) REVERT: C 24 ASP cc_start: 0.7747 (m-30) cc_final: 0.7501 (m-30) REVERT: C 123 MET cc_start: 0.8392 (tpp) cc_final: 0.8035 (tpt) REVERT: C 215 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7984 (mtmm) REVERT: D 123 MET cc_start: 0.8033 (tpp) cc_final: 0.7810 (tpp) REVERT: D 176 MET cc_start: 0.8669 (mmm) cc_final: 0.8400 (mtt) REVERT: E 65 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8750 (pp) REVERT: E 113 LYS cc_start: 0.5787 (mptt) cc_final: 0.4701 (mttt) REVERT: E 369 ILE cc_start: 0.8681 (pt) cc_final: 0.8437 (tp) REVERT: F 16 LEU cc_start: 0.8487 (mt) cc_final: 0.8262 (mp) REVERT: F 57 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: F 82 MET cc_start: 0.8493 (tpt) cc_final: 0.8230 (tpp) REVERT: F 107 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: F 128 ASN cc_start: 0.7301 (t0) cc_final: 0.6907 (t0) REVERT: G 276 GLU cc_start: 0.8021 (tp30) cc_final: 0.7645 (mm-30) REVERT: G 372 ARG cc_start: 0.7693 (mtp180) cc_final: 0.7003 (ptm160) outliers start: 42 outliers final: 24 residues processed: 268 average time/residue: 0.3216 time to fit residues: 136.4507 Evaluate side-chains 254 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 216 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 184 optimal weight: 0.0870 chunk 8 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS D 59 GLN D 87 HIS F 354 GLN G 162 ASN G 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120180 restraints weight = 30987.628| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.71 r_work: 0.3352 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21924 Z= 0.126 Angle : 0.572 9.292 29739 Z= 0.282 Chirality : 0.045 0.157 3281 Planarity : 0.004 0.038 3827 Dihedral : 7.420 105.199 3048 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.27 % Allowed : 13.28 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2691 helix: 0.27 (0.17), residues: 960 sheet: -0.07 (0.23), residues: 553 loop : 0.24 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 101 HIS 0.026 0.001 HIS D 87 PHE 0.009 0.001 PHE C 31 TYR 0.013 0.001 TYR E 362 ARG 0.006 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 921) hydrogen bonds : angle 5.03026 ( 2397) covalent geometry : bond 0.00298 (21924) covalent geometry : angle 0.57190 (29739) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 3.783 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8677 (tp) cc_final: 0.8456 (tt) REVERT: A 320 THR cc_start: 0.8236 (m) cc_final: 0.7841 (t) REVERT: A 474 HIS cc_start: 0.5558 (p-80) cc_final: 0.5165 (p90) REVERT: B 44 MET cc_start: 0.8619 (mmm) cc_final: 0.8369 (mtt) REVERT: B 211 ASP cc_start: 0.8461 (t0) cc_final: 0.8138 (m-30) REVERT: B 325 MET cc_start: 0.8496 (mmm) cc_final: 0.8038 (mmp) REVERT: C 24 ASP cc_start: 0.7701 (m-30) cc_final: 0.7401 (m-30) REVERT: C 72 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: C 123 MET cc_start: 0.8420 (tpp) cc_final: 0.8021 (tpt) REVERT: C 151 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8419 (tp) REVERT: C 215 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7902 (mtmm) REVERT: D 123 MET cc_start: 0.8073 (tpp) cc_final: 0.7654 (tpp) REVERT: E 45 VAL cc_start: 0.8600 (t) cc_final: 0.8219 (p) REVERT: E 65 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8729 (pp) REVERT: E 113 LYS cc_start: 0.6164 (mptt) cc_final: 0.5007 (mttt) REVERT: E 179 ASP cc_start: 0.8610 (m-30) cc_final: 0.8375 (m-30) REVERT: E 249 THR cc_start: 0.8965 (m) cc_final: 0.8721 (p) REVERT: E 369 ILE cc_start: 0.8631 (pt) cc_final: 0.8418 (tp) REVERT: F 82 MET cc_start: 0.8394 (tpt) cc_final: 0.8159 (tpp) REVERT: F 107 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7070 (tt0) REVERT: F 128 ASN cc_start: 0.7166 (t0) cc_final: 0.6742 (t0) REVERT: F 246 GLN cc_start: 0.7945 (mp10) cc_final: 0.7707 (mp10) REVERT: G 372 ARG cc_start: 0.7700 (mtp180) cc_final: 0.7050 (ptm160) outliers start: 29 outliers final: 19 residues processed: 270 average time/residue: 0.3345 time to fit residues: 144.0135 Evaluate side-chains 255 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 221 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 56 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 226 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 189 optimal weight: 0.0270 chunk 136 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS D 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.142560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118285 restraints weight = 31243.453| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.68 r_work: 0.3296 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 21924 Z= 0.187 Angle : 0.611 9.469 29739 Z= 0.303 Chirality : 0.047 0.162 3281 Planarity : 0.004 0.038 3827 Dihedral : 7.505 106.750 3048 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.57 % Allowed : 14.29 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2691 helix: 0.20 (0.17), residues: 960 sheet: -0.18 (0.22), residues: 563 loop : 0.20 (0.20), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 101 HIS 0.004 0.001 HIS C 87 PHE 0.012 0.001 PHE A 195 TYR 0.019 0.001 TYR F 166 ARG 0.007 0.001 ARG F 196 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 921) hydrogen bonds : angle 5.08861 ( 2397) covalent geometry : bond 0.00458 (21924) covalent geometry : angle 0.61089 (29739) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 2.504 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8693 (tp) cc_final: 0.8457 (tt) REVERT: A 320 THR cc_start: 0.8304 (m) cc_final: 0.7917 (t) REVERT: A 474 HIS cc_start: 0.5830 (p-80) cc_final: 0.5327 (p90) REVERT: B 44 MET cc_start: 0.8619 (mmm) cc_final: 0.8357 (mtt) REVERT: B 211 ASP cc_start: 0.8471 (t0) cc_final: 0.8150 (m-30) REVERT: C 24 ASP cc_start: 0.7730 (m-30) cc_final: 0.7443 (m-30) REVERT: C 72 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: C 123 MET cc_start: 0.8407 (tpp) cc_final: 0.8040 (tpt) REVERT: C 215 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7921 (mtmm) REVERT: D 24 ASP cc_start: 0.6923 (m-30) cc_final: 0.6685 (m-30) REVERT: D 123 MET cc_start: 0.8135 (tpp) cc_final: 0.7685 (tpp) REVERT: E 45 VAL cc_start: 0.8632 (t) cc_final: 0.8263 (p) REVERT: E 65 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8735 (pp) REVERT: E 113 LYS cc_start: 0.5888 (mptt) cc_final: 0.4663 (mttt) REVERT: E 249 THR cc_start: 0.8987 (m) cc_final: 0.8775 (p) REVERT: E 369 ILE cc_start: 0.8648 (pt) cc_final: 0.8431 (tp) REVERT: F 57 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: F 82 MET cc_start: 0.8422 (tpt) cc_final: 0.8185 (tpp) REVERT: F 107 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: F 128 ASN cc_start: 0.7266 (t0) cc_final: 0.6811 (t0) REVERT: F 246 GLN cc_start: 0.7940 (mp10) cc_final: 0.7675 (mp10) REVERT: G 372 ARG cc_start: 0.7697 (mtp180) cc_final: 0.7012 (ptm160) outliers start: 36 outliers final: 26 residues processed: 262 average time/residue: 0.3173 time to fit residues: 132.1747 Evaluate side-chains 259 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 19 optimal weight: 5.9990 chunk 265 optimal weight: 3.9990 chunk 219 optimal weight: 0.0970 chunk 66 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 256 optimal weight: 5.9990 chunk 257 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 209 optimal weight: 0.9990 chunk 212 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.145238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120597 restraints weight = 31277.038| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.74 r_work: 0.3310 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21924 Z= 0.116 Angle : 0.569 8.935 29739 Z= 0.279 Chirality : 0.045 0.162 3281 Planarity : 0.004 0.038 3827 Dihedral : 7.296 103.936 3048 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.49 % Allowed : 14.59 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2691 helix: 0.36 (0.17), residues: 960 sheet: -0.04 (0.23), residues: 553 loop : 0.23 (0.20), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.021 0.001 HIS D 87 PHE 0.012 0.001 PHE A 195 TYR 0.014 0.001 TYR E 166 ARG 0.006 0.000 ARG F 196 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 921) hydrogen bonds : angle 4.94581 ( 2397) covalent geometry : bond 0.00275 (21924) covalent geometry : angle 0.56921 (29739) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 2.376 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8681 (tp) cc_final: 0.8441 (tt) REVERT: A 320 THR cc_start: 0.8264 (m) cc_final: 0.7895 (t) REVERT: A 474 HIS cc_start: 0.5619 (p-80) cc_final: 0.5117 (p90) REVERT: B 44 MET cc_start: 0.8650 (mmm) cc_final: 0.8411 (mtt) REVERT: B 211 ASP cc_start: 0.8469 (t0) cc_final: 0.8076 (m-30) REVERT: B 325 MET cc_start: 0.8509 (mmm) cc_final: 0.7988 (mmt) REVERT: C 24 ASP cc_start: 0.7695 (m-30) cc_final: 0.7347 (m-30) REVERT: C 72 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: C 123 MET cc_start: 0.8420 (tpp) cc_final: 0.7997 (tpt) REVERT: C 151 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8397 (tp) REVERT: C 325 MET cc_start: 0.7108 (ptt) cc_final: 0.6723 (ptt) REVERT: D 24 ASP cc_start: 0.6836 (m-30) cc_final: 0.6633 (m-30) REVERT: D 123 MET cc_start: 0.8128 (tpp) cc_final: 0.7609 (tpp) REVERT: E 45 VAL cc_start: 0.8612 (t) cc_final: 0.8256 (p) REVERT: E 65 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8699 (pp) REVERT: E 113 LYS cc_start: 0.5829 (mptt) cc_final: 0.4693 (mttt) REVERT: E 179 ASP cc_start: 0.8564 (m-30) cc_final: 0.8315 (m-30) REVERT: E 249 THR cc_start: 0.8941 (m) cc_final: 0.8728 (p) REVERT: E 369 ILE cc_start: 0.8626 (pt) cc_final: 0.8408 (tp) REVERT: F 107 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: F 128 ASN cc_start: 0.7216 (t0) cc_final: 0.6757 (t0) REVERT: F 246 GLN cc_start: 0.7933 (mp10) cc_final: 0.7662 (mp10) REVERT: G 372 ARG cc_start: 0.7704 (mtp180) cc_final: 0.7025 (ptm160) outliers start: 34 outliers final: 25 residues processed: 272 average time/residue: 0.3103 time to fit residues: 134.8783 Evaluate side-chains 259 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 491 TRP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 57 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 9 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 118 optimal weight: 0.0050 chunk 262 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 168 optimal weight: 0.4980 chunk 174 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS D 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121611 restraints weight = 30922.892| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.74 r_work: 0.3361 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21924 Z= 0.111 Angle : 0.569 8.433 29739 Z= 0.277 Chirality : 0.045 0.166 3281 Planarity : 0.004 0.040 3827 Dihedral : 7.093 100.413 3048 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.27 % Allowed : 15.20 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2691 helix: 0.42 (0.17), residues: 960 sheet: 0.00 (0.23), residues: 558 loop : 0.27 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 101 HIS 0.011 0.001 HIS D 87 PHE 0.017 0.001 PHE C 352 TYR 0.014 0.001 TYR E 166 ARG 0.007 0.000 ARG F 196 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 921) hydrogen bonds : angle 4.83658 ( 2397) covalent geometry : bond 0.00262 (21924) covalent geometry : angle 0.56869 (29739) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 2.447 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8694 (tp) cc_final: 0.8442 (tt) REVERT: A 320 THR cc_start: 0.8259 (m) cc_final: 0.7915 (t) REVERT: A 474 HIS cc_start: 0.5635 (p-80) cc_final: 0.5058 (p90) REVERT: B 12 ASN cc_start: 0.8004 (p0) cc_final: 0.7692 (p0) REVERT: B 44 MET cc_start: 0.8637 (mmm) cc_final: 0.8373 (mtt) REVERT: B 211 ASP cc_start: 0.8467 (t0) cc_final: 0.8076 (m-30) REVERT: B 325 MET cc_start: 0.8462 (mmm) cc_final: 0.8004 (mmt) REVERT: C 24 ASP cc_start: 0.7611 (m-30) cc_final: 0.7281 (m-30) REVERT: C 72 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: C 123 MET cc_start: 0.8432 (tpp) cc_final: 0.7985 (tpt) REVERT: C 325 MET cc_start: 0.7179 (ptt) cc_final: 0.6845 (ptt) REVERT: D 24 ASP cc_start: 0.6813 (m-30) cc_final: 0.6568 (m-30) REVERT: D 28 ARG cc_start: 0.7741 (ptt180) cc_final: 0.7439 (ttp80) REVERT: D 123 MET cc_start: 0.8130 (tpp) cc_final: 0.7735 (tpp) REVERT: E 45 VAL cc_start: 0.8607 (t) cc_final: 0.8283 (p) REVERT: E 113 LYS cc_start: 0.6101 (mptt) cc_final: 0.4964 (mttt) REVERT: E 179 ASP cc_start: 0.8591 (m-30) cc_final: 0.8353 (m-30) REVERT: E 249 THR cc_start: 0.8987 (m) cc_final: 0.8761 (p) REVERT: E 369 ILE cc_start: 0.8627 (pt) cc_final: 0.8418 (tp) REVERT: F 107 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: F 128 ASN cc_start: 0.7054 (t0) cc_final: 0.6624 (t0) REVERT: F 246 GLN cc_start: 0.7906 (mp10) cc_final: 0.7618 (mp10) REVERT: G 372 ARG cc_start: 0.7732 (mtp180) cc_final: 0.7087 (ptm160) outliers start: 29 outliers final: 22 residues processed: 265 average time/residue: 0.3339 time to fit residues: 141.3902 Evaluate side-chains 265 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 491 TRP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 173 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 137 optimal weight: 0.2980 chunk 185 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 HIS B 87 HIS C 353 GLN D 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.143274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119000 restraints weight = 31357.306| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.68 r_work: 0.3333 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21924 Z= 0.184 Angle : 0.623 11.126 29739 Z= 0.305 Chirality : 0.048 0.212 3281 Planarity : 0.004 0.041 3827 Dihedral : 7.282 102.917 3048 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.40 % Allowed : 15.38 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2691 helix: 0.34 (0.17), residues: 960 sheet: -0.09 (0.23), residues: 562 loop : 0.22 (0.20), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 171 HIS 0.039 0.001 HIS D 87 PHE 0.018 0.001 PHE C 352 TYR 0.020 0.001 TYR E 166 ARG 0.006 0.001 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 921) hydrogen bonds : angle 4.97964 ( 2397) covalent geometry : bond 0.00449 (21924) covalent geometry : angle 0.62302 (29739) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 4.118 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8713 (tp) cc_final: 0.8451 (tt) REVERT: A 320 THR cc_start: 0.8279 (m) cc_final: 0.7928 (t) REVERT: B 12 ASN cc_start: 0.8061 (p0) cc_final: 0.7725 (p0) REVERT: B 211 ASP cc_start: 0.8462 (t0) cc_final: 0.8069 (m-30) REVERT: B 325 MET cc_start: 0.8482 (mmm) cc_final: 0.8020 (mmt) REVERT: C 72 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: C 123 MET cc_start: 0.8419 (tpp) cc_final: 0.8039 (tpt) REVERT: C 325 MET cc_start: 0.7281 (ptt) cc_final: 0.6829 (ptm) REVERT: D 28 ARG cc_start: 0.7871 (ptt180) cc_final: 0.7528 (ttp80) REVERT: D 123 MET cc_start: 0.8138 (tpp) cc_final: 0.7686 (tpp) REVERT: E 45 VAL cc_start: 0.8648 (t) cc_final: 0.8319 (p) REVERT: E 113 LYS cc_start: 0.5846 (mptt) cc_final: 0.4647 (mttt) REVERT: E 179 ASP cc_start: 0.8574 (m-30) cc_final: 0.8334 (m-30) REVERT: E 249 THR cc_start: 0.9048 (m) cc_final: 0.8819 (p) REVERT: E 369 ILE cc_start: 0.8660 (pt) cc_final: 0.8441 (tp) REVERT: F 107 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: F 128 ASN cc_start: 0.7109 (t0) cc_final: 0.6676 (t0) REVERT: F 246 GLN cc_start: 0.7932 (mp10) cc_final: 0.7634 (mp10) REVERT: G 276 GLU cc_start: 0.7996 (tp30) cc_final: 0.7652 (mm-30) REVERT: G 372 ARG cc_start: 0.7738 (mtp180) cc_final: 0.7230 (ttp-170) outliers start: 32 outliers final: 23 residues processed: 266 average time/residue: 0.4418 time to fit residues: 189.2080 Evaluate side-chains 259 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 138 optimal weight: 0.4980 chunk 199 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 157 optimal weight: 0.5980 chunk 247 optimal weight: 0.9990 chunk 111 optimal weight: 0.0870 chunk 68 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS B 87 HIS D 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.146051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.121824 restraints weight = 31011.598| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.69 r_work: 0.3373 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21924 Z= 0.111 Angle : 0.584 11.610 29739 Z= 0.283 Chirality : 0.045 0.200 3281 Planarity : 0.004 0.041 3827 Dihedral : 7.108 100.857 3048 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.14 % Allowed : 15.95 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2691 helix: 0.42 (0.17), residues: 960 sheet: 0.03 (0.23), residues: 552 loop : 0.25 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 132 HIS 0.006 0.001 HIS A 198 PHE 0.020 0.001 PHE C 352 TYR 0.014 0.001 TYR E 166 ARG 0.006 0.000 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.03108 ( 921) hydrogen bonds : angle 4.85801 ( 2397) covalent geometry : bond 0.00263 (21924) covalent geometry : angle 0.58352 (29739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12117.82 seconds wall clock time: 213 minutes 12.27 seconds (12792.27 seconds total)