Starting phenix.real_space_refine on Fri Sep 19 00:28:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo9_43368/09_2025/8vo9_43368_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo9_43368/09_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_43368/09_2025/8vo9_43368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo9_43368/09_2025/8vo9_43368.map" model { file = "/net/cci-nas-00/data/ceres_data/8vo9_43368/09_2025/8vo9_43368_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo9_43368/09_2025/8vo9_43368_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.49, per 1000 atoms: 0.26 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: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.21 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: 4.69 Time building geometry restraints manager: 2.79 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: 8.890 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.660 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.890 ------------------------------------------------------------------------------- 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 : 8.31 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.17), 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 ARG 0.006 0.000 ARG A 118 TYR 0.016 0.001 TYR F 198 PHE 0.010 0.001 PHE A 455 TRP 0.015 0.001 TRP D 356 HIS 0.003 0.001 HIS G 371 Details of bonding type rmsd covalent geometry : bond 0.00293 (21924) covalent geometry : angle 0.57077 (29739) hydrogen bonds : bond 0.21328 ( 921) hydrogen bonds : angle 7.36352 ( 2397) *********************** 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 : 0.869 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: 0.1621 time to fit residues: 108.2264 Evaluate side-chains 261 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.1980 chunk 111 optimal weight: 0.0060 overall best weight: 0.4574 ------------------------------------------------------------------------------- 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 B 353 GLN C 87 HIS D 87 HIS E 296 ASN G 162 ASN G 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.144297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120172 restraints weight = 31921.891| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.84 r_work: 0.3319 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21924 Z= 0.123 Angle : 0.584 7.782 29739 Z= 0.293 Chirality : 0.045 0.164 3281 Planarity : 0.004 0.038 3827 Dihedral : 7.388 104.675 3048 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.61 % Allowed : 7.12 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.17), residues: 2691 helix: 0.39 (0.18), residues: 924 sheet: 0.29 (0.23), residues: 549 loop : 0.45 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 28 TYR 0.019 0.001 TYR F 306 PHE 0.019 0.001 PHE C 352 TRP 0.016 0.001 TRP A 491 HIS 0.007 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00275 (21924) covalent geometry : angle 0.58376 (29739) hydrogen bonds : bond 0.04395 ( 921) hydrogen bonds : angle 5.62620 ( 2397) *********************** 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 311 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 297 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8658 (tp) cc_final: 0.8378 (tt) REVERT: A 320 THR cc_start: 0.7788 (m) cc_final: 0.7563 (p) REVERT: A 474 HIS cc_start: 0.4910 (p-80) cc_final: 0.4709 (p-80) REVERT: B 72 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7476 (tp30) REVERT: B 211 ASP cc_start: 0.8498 (t0) cc_final: 0.8232 (m-30) REVERT: B 325 MET cc_start: 0.8459 (mmm) cc_final: 0.8194 (mmp) REVERT: B 327 ILE cc_start: 0.8752 (mp) cc_final: 0.8527 (mm) REVERT: B 360 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7792 (pm20) REVERT: C 24 ASP cc_start: 0.7623 (m-30) cc_final: 0.7195 (m-30) REVERT: C 53 TYR cc_start: 0.9066 (m-80) cc_final: 0.8790 (m-80) REVERT: C 123 MET cc_start: 0.8435 (tpp) cc_final: 0.7991 (tpt) REVERT: C 178 LEU cc_start: 0.8774 (mp) cc_final: 0.8426 (mt) REVERT: C 221 LEU cc_start: 0.8883 (tp) cc_final: 0.8678 (mm) REVERT: D 212 ILE cc_start: 0.8221 (mt) cc_final: 0.7915 (mt) REVERT: D 353 GLN cc_start: 0.8081 (mp10) cc_final: 0.7860 (mp10) REVERT: E 45 VAL cc_start: 0.8618 (t) cc_final: 0.8289 (p) REVERT: E 113 LYS cc_start: 0.6575 (mptt) cc_final: 0.5652 (mttt) REVERT: E 369 ILE cc_start: 0.8605 (pt) cc_final: 0.8320 (tp) REVERT: F 82 MET cc_start: 0.8409 (tpt) cc_final: 0.8103 (tpp) REVERT: F 336 LYS cc_start: 0.8254 (tttt) cc_final: 0.8026 (tttm) REVERT: G 162 ASN cc_start: 0.8083 (m110) cc_final: 0.7771 (m110) REVERT: G 372 ARG cc_start: 0.7611 (mtp180) cc_final: 0.6909 (ptm160) outliers start: 14 outliers final: 8 residues processed: 306 average time/residue: 0.1622 time to fit residues: 77.5820 Evaluate side-chains 254 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 245 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 121 optimal weight: 0.0050 chunk 43 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 268 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 222 optimal weight: 0.0020 chunk 224 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 185 optimal weight: 0.0870 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.143767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.119408 restraints weight = 31990.975| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.80 r_work: 0.3325 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1728 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= 0.118 Angle : 0.563 7.432 29739 Z= 0.278 Chirality : 0.045 0.163 3281 Planarity : 0.004 0.036 3827 Dihedral : 7.246 101.914 3048 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.00 % Allowed : 8.87 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.17), residues: 2691 helix: 0.37 (0.18), residues: 924 sheet: 0.22 (0.23), residues: 553 loop : 0.40 (0.19), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 37 TYR 0.020 0.001 TYR E 362 PHE 0.015 0.001 PHE C 352 TRP 0.015 0.001 TRP A 101 HIS 0.007 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00274 (21924) covalent geometry : angle 0.56317 (29739) hydrogen bonds : bond 0.03649 ( 921) hydrogen bonds : angle 5.22806 ( 2397) *********************** 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 282 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 259 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7834 (tm-30) REVERT: A 317 LEU cc_start: 0.8640 (tp) cc_final: 0.8371 (tt) REVERT: A 320 THR cc_start: 0.7903 (m) cc_final: 0.7665 (p) REVERT: A 474 HIS cc_start: 0.4925 (p-80) cc_final: 0.4692 (p-80) REVERT: B 72 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7498 (tp30) REVERT: B 211 ASP cc_start: 0.8453 (t0) cc_final: 0.8119 (m-30) REVERT: B 325 MET cc_start: 0.8426 (mmm) cc_final: 0.8191 (mmp) REVERT: B 360 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: C 24 ASP cc_start: 0.7621 (m-30) cc_final: 0.7317 (m-30) REVERT: C 53 TYR cc_start: 0.9127 (m-80) cc_final: 0.8829 (m-80) REVERT: C 123 MET cc_start: 0.8405 (tpp) cc_final: 0.7941 (tpt) REVERT: C 178 LEU cc_start: 0.8825 (mp) cc_final: 0.8488 (mt) REVERT: C 215 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7911 (mtmm) REVERT: C 221 LEU cc_start: 0.8905 (tp) cc_final: 0.8659 (mm) REVERT: D 212 ILE cc_start: 0.8256 (mt) cc_final: 0.7951 (mt) REVERT: E 113 LYS cc_start: 0.6555 (mptt) cc_final: 0.5616 (mttt) REVERT: E 249 THR cc_start: 0.8979 (m) cc_final: 0.8670 (p) REVERT: E 296 ASN cc_start: 0.8267 (m-40) cc_final: 0.8034 (m-40) REVERT: E 369 ILE cc_start: 0.8577 (pt) cc_final: 0.8344 (tp) REVERT: F 82 MET cc_start: 0.8459 (tpt) cc_final: 0.8170 (tpp) REVERT: F 256 ARG cc_start: 0.8169 (ttp-170) cc_final: 0.7938 (ttp80) REVERT: G 372 ARG cc_start: 0.7660 (mtp180) cc_final: 0.6979 (ptm160) outliers start: 23 outliers final: 14 residues processed: 277 average time/residue: 0.1481 time to fit residues: 65.5574 Evaluate side-chains 250 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 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 149 THR 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 65 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 46 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 215 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 E 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121464 restraints weight = 31075.938| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.64 r_work: 0.3364 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21924 Z= 0.158 Angle : 0.585 7.254 29739 Z= 0.289 Chirality : 0.047 0.165 3281 Planarity : 0.004 0.038 3827 Dihedral : 7.365 104.337 3048 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.49 % Allowed : 10.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.17), residues: 2691 helix: 0.41 (0.17), residues: 960 sheet: 0.06 (0.23), residues: 563 loop : 0.35 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 37 TYR 0.017 0.001 TYR F 306 PHE 0.010 0.001 PHE C 352 TRP 0.015 0.002 TRP A 101 HIS 0.007 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00381 (21924) covalent geometry : angle 0.58468 (29739) hydrogen bonds : bond 0.03731 ( 921) hydrogen bonds : angle 5.09720 ( 2397) *********************** 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 285 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 0.845 Fit side-chains REVERT: A 303 LYS cc_start: 0.7934 (mmpt) cc_final: 0.7639 (tmtt) REVERT: A 317 LEU cc_start: 0.8693 (tp) cc_final: 0.8450 (tt) REVERT: A 320 THR cc_start: 0.8011 (m) cc_final: 0.7792 (p) REVERT: A 474 HIS cc_start: 0.5354 (p-80) cc_final: 0.5058 (p90) REVERT: B 72 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7581 (tp30) REVERT: B 211 ASP cc_start: 0.8423 (t0) cc_final: 0.8155 (m-30) REVERT: B 325 MET cc_start: 0.8431 (mmm) cc_final: 0.8137 (mmp) REVERT: B 360 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7826 (pm20) REVERT: C 24 ASP cc_start: 0.7640 (m-30) cc_final: 0.7439 (m-30) REVERT: C 53 TYR cc_start: 0.9144 (m-80) cc_final: 0.8870 (m-80) REVERT: C 123 MET cc_start: 0.8407 (tpp) cc_final: 0.7986 (tpt) REVERT: C 178 LEU cc_start: 0.8772 (mp) cc_final: 0.8445 (mt) REVERT: C 215 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7911 (mtmm) REVERT: C 221 LEU cc_start: 0.8898 (tp) cc_final: 0.8643 (mm) REVERT: E 113 LYS cc_start: 0.6186 (mptt) cc_final: 0.5317 (mttt) REVERT: E 249 THR cc_start: 0.9002 (m) cc_final: 0.8754 (p) REVERT: E 369 ILE cc_start: 0.8645 (pt) cc_final: 0.8406 (tp) REVERT: F 82 MET cc_start: 0.8461 (tpt) cc_final: 0.8219 (tpp) REVERT: G 372 ARG cc_start: 0.7745 (mtp180) cc_final: 0.7036 (ptm160) outliers start: 34 outliers final: 17 residues processed: 278 average time/residue: 0.1477 time to fit residues: 65.5528 Evaluate side-chains 253 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 234 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 B residue 64 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 149 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 F residue 65 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 64 ILE 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 159 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 245 optimal weight: 7.9990 chunk 135 optimal weight: 0.2980 chunk 235 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 C 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.142366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.117496 restraints weight = 31370.794| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.76 r_work: 0.3266 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21924 Z= 0.221 Angle : 0.640 9.669 29739 Z= 0.319 Chirality : 0.049 0.176 3281 Planarity : 0.004 0.041 3827 Dihedral : 7.642 108.013 3048 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.62 % Allowed : 12.01 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.17), residues: 2691 helix: 0.15 (0.17), residues: 960 sheet: -0.11 (0.23), residues: 563 loop : 0.23 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 196 TYR 0.017 0.002 TYR G 166 PHE 0.015 0.002 PHE G 266 TRP 0.017 0.002 TRP A 101 HIS 0.007 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00540 (21924) covalent geometry : angle 0.64017 (29739) hydrogen bonds : bond 0.04210 ( 921) hydrogen bonds : angle 5.23378 ( 2397) *********************** 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 284 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8703 (tp) cc_final: 0.8457 (tt) REVERT: A 320 THR cc_start: 0.8155 (m) cc_final: 0.7760 (t) REVERT: A 326 THR cc_start: 0.7699 (p) cc_final: 0.7391 (p) REVERT: A 474 HIS cc_start: 0.5781 (p-80) cc_final: 0.5458 (p90) REVERT: B 72 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7653 (tp30) REVERT: B 211 ASP cc_start: 0.8506 (t0) cc_final: 0.8214 (m-30) REVERT: B 325 MET cc_start: 0.8516 (mmm) cc_final: 0.8043 (mmp) REVERT: C 24 ASP cc_start: 0.7753 (m-30) cc_final: 0.7505 (m-30) REVERT: C 53 TYR cc_start: 0.9151 (m-80) cc_final: 0.8945 (m-80) REVERT: C 123 MET cc_start: 0.8466 (tpp) cc_final: 0.8065 (tpt) REVERT: C 215 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7952 (mtmm) REVERT: D 123 MET cc_start: 0.8087 (tpp) cc_final: 0.7871 (tpp) REVERT: E 45 VAL cc_start: 0.8631 (t) cc_final: 0.8226 (p) REVERT: E 65 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8747 (pp) REVERT: E 113 LYS cc_start: 0.6118 (mptt) cc_final: 0.5031 (mttt) REVERT: E 179 ASP cc_start: 0.8596 (m-30) cc_final: 0.8339 (m-30) REVERT: E 249 THR cc_start: 0.9036 (m) cc_final: 0.8795 (p) REVERT: E 369 ILE cc_start: 0.8677 (pt) cc_final: 0.8438 (tp) REVERT: F 16 LEU cc_start: 0.8471 (mt) cc_final: 0.8250 (mp) REVERT: F 57 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: F 82 MET cc_start: 0.8512 (tpt) cc_final: 0.8242 (tpp) REVERT: F 107 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7166 (tt0) REVERT: F 196 ARG cc_start: 0.8058 (mtp85) cc_final: 0.7816 (ttm-80) REVERT: G 276 GLU cc_start: 0.8043 (tp30) cc_final: 0.7656 (mm-30) REVERT: G 372 ARG cc_start: 0.7682 (mtp180) cc_final: 0.6999 (ptm160) outliers start: 37 outliers final: 22 residues processed: 273 average time/residue: 0.1454 time to fit residues: 63.1919 Evaluate side-chains 257 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 A residue 485 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 324 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 149 THR 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 287 ILE Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 64 ILE 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 228 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 224 optimal weight: 0.1980 chunk 194 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 267 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 G 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118287 restraints weight = 31315.873| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.64 r_work: 0.3328 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21924 Z= 0.174 Angle : 0.604 9.686 29739 Z= 0.298 Chirality : 0.047 0.158 3281 Planarity : 0.004 0.041 3827 Dihedral : 7.554 107.793 3048 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.53 % Allowed : 13.19 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.17), residues: 2691 helix: 0.17 (0.17), residues: 960 sheet: -0.10 (0.23), residues: 553 loop : 0.17 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 37 TYR 0.013 0.001 TYR E 362 PHE 0.011 0.001 PHE A 336 TRP 0.015 0.002 TRP A 101 HIS 0.007 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00423 (21924) covalent geometry : angle 0.60374 (29739) hydrogen bonds : bond 0.03763 ( 921) hydrogen bonds : angle 5.12792 ( 2397) *********************** 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 272 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8695 (tp) cc_final: 0.8459 (tt) REVERT: A 320 THR cc_start: 0.8212 (m) cc_final: 0.7826 (t) REVERT: A 474 HIS cc_start: 0.5754 (p-80) cc_final: 0.5357 (p90) REVERT: B 44 MET cc_start: 0.8595 (mmm) cc_final: 0.8354 (mtt) REVERT: B 211 ASP cc_start: 0.8425 (t0) cc_final: 0.8138 (m-30) REVERT: C 24 ASP cc_start: 0.7689 (m-30) cc_final: 0.7452 (m-30) REVERT: C 72 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: C 123 MET cc_start: 0.8404 (tpp) cc_final: 0.8016 (tpt) REVERT: C 215 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7928 (mtmm) REVERT: D 123 MET cc_start: 0.8040 (tpp) cc_final: 0.7653 (tpp) REVERT: E 45 VAL cc_start: 0.8586 (t) cc_final: 0.8215 (p) REVERT: E 65 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8730 (pp) REVERT: E 113 LYS cc_start: 0.5831 (mptt) cc_final: 0.4756 (mttt) REVERT: E 369 ILE cc_start: 0.8666 (pt) cc_final: 0.8443 (tp) REVERT: F 82 MET cc_start: 0.8419 (tpt) cc_final: 0.8192 (tpp) REVERT: F 107 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: F 246 GLN cc_start: 0.7963 (mp10) cc_final: 0.7745 (mp10) REVERT: G 372 ARG cc_start: 0.7692 (mtp180) cc_final: 0.7032 (ptm160) outliers start: 35 outliers final: 24 residues processed: 260 average time/residue: 0.1437 time to fit residues: 59.6423 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 : 0.717 ------------------------------------------------------------------------------- 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 132 MET 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 149 THR 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 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 95 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 219 optimal weight: 0.2980 chunk 126 optimal weight: 6.9990 chunk 229 optimal weight: 0.6980 chunk 166 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 0.0770 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120088 restraints weight = 31091.582| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.75 r_work: 0.3316 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21924 Z= 0.127 Angle : 0.574 9.084 29739 Z= 0.283 Chirality : 0.045 0.160 3281 Planarity : 0.004 0.038 3827 Dihedral : 7.384 105.363 3048 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.62 % Allowed : 13.98 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.17), residues: 2691 helix: 0.31 (0.17), residues: 960 sheet: -0.04 (0.23), residues: 553 loop : 0.23 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 37 TYR 0.014 0.001 TYR E 362 PHE 0.009 0.001 PHE A 195 TRP 0.013 0.002 TRP E 340 HIS 0.024 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00305 (21924) covalent geometry : angle 0.57419 (29739) hydrogen bonds : bond 0.03393 ( 921) hydrogen bonds : angle 4.99691 ( 2397) *********************** 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 274 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8685 (tp) cc_final: 0.8440 (tt) REVERT: A 320 THR cc_start: 0.8254 (m) cc_final: 0.7884 (t) REVERT: A 474 HIS cc_start: 0.5591 (p-80) cc_final: 0.5163 (p90) REVERT: B 44 MET cc_start: 0.8622 (mmm) cc_final: 0.8383 (mtt) REVERT: B 211 ASP cc_start: 0.8477 (t0) cc_final: 0.8162 (m-30) REVERT: B 325 MET cc_start: 0.8493 (mmm) cc_final: 0.7995 (mmt) REVERT: C 24 ASP cc_start: 0.7693 (m-30) cc_final: 0.7406 (m-30) REVERT: C 123 MET cc_start: 0.8428 (tpp) cc_final: 0.8030 (tpt) REVERT: D 24 ASP cc_start: 0.6789 (m-30) cc_final: 0.6525 (m-30) REVERT: D 123 MET cc_start: 0.8143 (tpp) cc_final: 0.7706 (tpp) REVERT: E 45 VAL cc_start: 0.8574 (t) cc_final: 0.8226 (p) REVERT: E 65 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8689 (pp) REVERT: E 113 LYS cc_start: 0.5887 (mptt) cc_final: 0.4752 (mttt) REVERT: E 179 ASP cc_start: 0.8569 (m-30) cc_final: 0.8307 (m-30) REVERT: E 249 THR cc_start: 0.8939 (m) cc_final: 0.8725 (p) REVERT: E 369 ILE cc_start: 0.8648 (pt) cc_final: 0.8433 (tp) REVERT: F 107 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7234 (tt0) REVERT: F 196 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7724 (ttm-80) REVERT: F 246 GLN cc_start: 0.7971 (mp10) cc_final: 0.7716 (mp10) REVERT: G 372 ARG cc_start: 0.7712 (mtp180) cc_final: 0.7036 (ptm160) outliers start: 37 outliers final: 27 residues processed: 264 average time/residue: 0.1453 time to fit residues: 61.3311 Evaluate side-chains 258 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 132 MET 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 151 ILE Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 149 THR 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 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 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 90 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 overall best weight: 1.8146 ------------------------------------------------------------------------------- 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 E 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.140547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115923 restraints weight = 31490.567| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.70 r_work: 0.3296 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21924 Z= 0.223 Angle : 0.650 9.922 29739 Z= 0.321 Chirality : 0.049 0.197 3281 Planarity : 0.004 0.039 3827 Dihedral : 7.620 107.539 3048 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.88 % Allowed : 14.07 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.17), residues: 2691 helix: 0.13 (0.17), residues: 960 sheet: -0.23 (0.23), residues: 563 loop : 0.12 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 372 TYR 0.014 0.002 TYR F 166 PHE 0.012 0.002 PHE A 336 TRP 0.016 0.002 TRP A 101 HIS 0.004 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00543 (21924) covalent geometry : angle 0.64989 (29739) hydrogen bonds : bond 0.04178 ( 921) hydrogen bonds : angle 5.19096 ( 2397) *********************** 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 280 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8716 (tp) cc_final: 0.8467 (tt) REVERT: A 320 THR cc_start: 0.8288 (m) cc_final: 0.7923 (t) REVERT: A 474 HIS cc_start: 0.6090 (p-80) cc_final: 0.5580 (p90) REVERT: B 211 ASP cc_start: 0.8493 (t0) cc_final: 0.8177 (m-30) REVERT: B 325 MET cc_start: 0.8515 (mmm) cc_final: 0.8028 (mmp) REVERT: C 24 ASP cc_start: 0.7793 (m-30) cc_final: 0.7522 (m-30) REVERT: C 72 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: C 123 MET cc_start: 0.8410 (tpp) cc_final: 0.8074 (tpt) REVERT: C 215 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7960 (mtmm) REVERT: C 325 MET cc_start: 0.7301 (ptt) cc_final: 0.6934 (ptt) REVERT: D 24 ASP cc_start: 0.6948 (m-30) cc_final: 0.6746 (m-30) REVERT: D 123 MET cc_start: 0.8165 (tpp) cc_final: 0.7678 (tpp) REVERT: E 45 VAL cc_start: 0.8678 (t) cc_final: 0.8310 (p) REVERT: E 113 LYS cc_start: 0.6018 (mptt) cc_final: 0.4611 (mttt) REVERT: E 288 ASP cc_start: 0.6436 (p0) cc_final: 0.6230 (p0) REVERT: E 369 ILE cc_start: 0.8688 (pt) cc_final: 0.8473 (tp) REVERT: F 107 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: F 196 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7792 (ttm-80) REVERT: F 246 GLN cc_start: 0.7985 (mp10) cc_final: 0.7698 (mp10) REVERT: G 227 MET cc_start: 0.7769 (mmm) cc_final: 0.7509 (mmm) REVERT: G 276 GLU cc_start: 0.8071 (tp30) cc_final: 0.7706 (mm-30) REVERT: G 372 ARG cc_start: 0.7759 (mtp180) cc_final: 0.7219 (ttp-170) outliers start: 43 outliers final: 31 residues processed: 268 average time/residue: 0.1489 time to fit residues: 64.1188 Evaluate side-chains 263 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 485 VAL 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 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 139 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR 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 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 198 TYR 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 287 ILE Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 221 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 113 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 249 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 chunk 267 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3774 r_free = 0.3774 target = 0.144319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119976 restraints weight = 31085.301| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.71 r_work: 0.3347 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2542 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= 0.127 Angle : 0.588 9.117 29739 Z= 0.288 Chirality : 0.046 0.196 3281 Planarity : 0.004 0.040 3827 Dihedral : 7.378 105.271 3048 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.57 % Allowed : 14.55 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.17), residues: 2691 helix: 0.32 (0.17), residues: 960 sheet: -0.09 (0.23), residues: 553 loop : 0.19 (0.20), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 372 TYR 0.015 0.001 TYR E 166 PHE 0.011 0.001 PHE D 90 TRP 0.014 0.002 TRP A 101 HIS 0.032 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00305 (21924) covalent geometry : angle 0.58832 (29739) hydrogen bonds : bond 0.03375 ( 921) hydrogen bonds : angle 5.01776 ( 2397) *********************** 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 282 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8685 (tp) cc_final: 0.8435 (tt) REVERT: A 320 THR cc_start: 0.8252 (m) cc_final: 0.7906 (t) REVERT: A 474 HIS cc_start: 0.5847 (p-80) cc_final: 0.5304 (p90) REVERT: B 44 MET cc_start: 0.8628 (mmm) cc_final: 0.8354 (mtt) REVERT: B 211 ASP cc_start: 0.8437 (t0) cc_final: 0.8065 (m-30) REVERT: B 325 MET cc_start: 0.8455 (mmm) cc_final: 0.7968 (mmt) REVERT: C 24 ASP cc_start: 0.7667 (m-30) cc_final: 0.7374 (m-30) REVERT: C 72 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: C 123 MET cc_start: 0.8425 (tpp) cc_final: 0.8031 (tpt) REVERT: C 325 MET cc_start: 0.7258 (ptt) cc_final: 0.6769 (ptm) REVERT: C 336 LYS cc_start: 0.8074 (tttt) cc_final: 0.7750 (tppt) REVERT: D 24 ASP cc_start: 0.6887 (m-30) cc_final: 0.6671 (m-30) REVERT: D 123 MET cc_start: 0.8150 (tpp) cc_final: 0.7751 (tpp) REVERT: E 45 VAL cc_start: 0.8660 (t) cc_final: 0.8295 (p) REVERT: E 113 LYS cc_start: 0.5838 (mptt) cc_final: 0.4612 (mttt) REVERT: E 179 ASP cc_start: 0.8545 (m-30) cc_final: 0.8299 (m-30) REVERT: E 362 TYR cc_start: 0.6637 (t80) cc_final: 0.6380 (t80) REVERT: E 369 ILE cc_start: 0.8645 (pt) cc_final: 0.8440 (tp) REVERT: F 107 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: F 196 ARG cc_start: 0.8062 (mtp85) cc_final: 0.7752 (ttm-80) REVERT: F 246 GLN cc_start: 0.7927 (mp10) cc_final: 0.7622 (mp10) REVERT: G 227 MET cc_start: 0.7774 (mmm) cc_final: 0.7531 (mmm) REVERT: G 372 ARG cc_start: 0.7746 (mtp180) cc_final: 0.7231 (ttp-170) outliers start: 36 outliers final: 31 residues processed: 272 average time/residue: 0.1502 time to fit residues: 65.9121 Evaluate side-chains 268 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 87 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 192 ILE 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 267 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 198 TYR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 267 ILE 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 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 128 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118781 restraints weight = 31277.452| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.73 r_work: 0.3284 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2588 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= 0.166 Angle : 0.613 11.000 29739 Z= 0.299 Chirality : 0.047 0.208 3281 Planarity : 0.004 0.041 3827 Dihedral : 7.402 105.360 3048 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.53 % Allowed : 14.77 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.17), residues: 2691 helix: 0.30 (0.17), residues: 960 sheet: -0.14 (0.23), residues: 562 loop : 0.18 (0.20), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 372 TYR 0.026 0.001 TYR E 306 PHE 0.009 0.001 PHE G 31 TRP 0.041 0.002 TRP A 171 HIS 0.011 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00408 (21924) covalent geometry : angle 0.61269 (29739) hydrogen bonds : bond 0.03621 ( 921) hydrogen bonds : angle 5.04284 ( 2397) ********************** 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 269 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8699 (tp) cc_final: 0.8435 (tt) REVERT: A 320 THR cc_start: 0.8303 (m) cc_final: 0.7959 (t) REVERT: B 12 ASN cc_start: 0.8091 (p0) cc_final: 0.7772 (p0) REVERT: B 44 MET cc_start: 0.8671 (mmm) cc_final: 0.8382 (mtt) REVERT: B 211 ASP cc_start: 0.8474 (t0) cc_final: 0.8076 (m-30) REVERT: B 325 MET cc_start: 0.8497 (mmm) cc_final: 0.7976 (mmt) REVERT: C 24 ASP cc_start: 0.7758 (m-30) cc_final: 0.7537 (m-30) REVERT: C 72 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: C 123 MET cc_start: 0.8399 (tpp) cc_final: 0.8036 (tpt) REVERT: C 325 MET cc_start: 0.7408 (ptt) cc_final: 0.6849 (ptm) REVERT: C 336 LYS cc_start: 0.8139 (tttt) cc_final: 0.7465 (mmtt) REVERT: D 123 MET cc_start: 0.8138 (tpp) cc_final: 0.7746 (tpp) REVERT: E 45 VAL cc_start: 0.8687 (t) cc_final: 0.8325 (p) REVERT: E 113 LYS cc_start: 0.5926 (mptt) cc_final: 0.4566 (mttt) REVERT: E 362 TYR cc_start: 0.6588 (t80) cc_final: 0.6338 (t80) REVERT: E 369 ILE cc_start: 0.8661 (pt) cc_final: 0.8458 (tp) REVERT: F 107 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7879 (tm-30) REVERT: F 246 GLN cc_start: 0.7942 (mp10) cc_final: 0.7599 (mp10) REVERT: G 372 ARG cc_start: 0.7740 (mtp180) cc_final: 0.7252 (ttp-170) outliers start: 35 outliers final: 30 residues processed: 262 average time/residue: 0.1423 time to fit residues: 60.1950 Evaluate side-chains 264 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 326 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 34 ILE 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 139 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR 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 198 TYR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 64 ILE 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 247 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 243 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 D 87 HIS D 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120492 restraints weight = 31123.378| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.71 r_work: 0.3350 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21924 Z= 0.129 Angle : 0.591 12.663 29739 Z= 0.287 Chirality : 0.046 0.209 3281 Planarity : 0.004 0.041 3827 Dihedral : 7.240 103.298 3048 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.66 % Allowed : 14.72 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2691 helix: 0.34 (0.17), residues: 960 sheet: -0.06 (0.23), residues: 552 loop : 0.22 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 372 TYR 0.024 0.001 TYR E 306 PHE 0.009 0.001 PHE E 124 TRP 0.013 0.002 TRP A 101 HIS 0.005 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00313 (21924) covalent geometry : angle 0.59149 (29739) hydrogen bonds : bond 0.03286 ( 921) hydrogen bonds : angle 4.94775 ( 2397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5872.36 seconds wall clock time: 101 minutes 20.42 seconds (6080.42 seconds total)