Starting phenix.real_space_refine on Wed May 21 03:39:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1n_39731/05_2025/8z1n_39731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1n_39731/05_2025/8z1n_39731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z1n_39731/05_2025/8z1n_39731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1n_39731/05_2025/8z1n_39731.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1n_39731/05_2025/8z1n_39731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1n_39731/05_2025/8z1n_39731.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 13119 2.51 5 N 3618 2.21 5 O 3974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20789 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3454 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 443} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "F" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "B" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "C" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "A" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Time building chain proxies: 11.89, per 1000 atoms: 0.57 Number of scatterers: 20789 At special positions: 0 Unit cell: (116.63, 120.91, 111.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3974 8.00 N 3618 7.00 C 13119 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.20 Conformation dependent library (CDL) restraints added in 2.8 seconds 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 14 sheets defined 53.0% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'D' and resid 7 through 24 removed outlier: 3.588A pdb=" N SER D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 32 through 41 removed outlier: 4.111A pdb=" N ALA D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 106 removed outlier: 3.822A pdb=" N PHE D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 141 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 158 through 174 Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'D' and resid 199 through 213 Processing helix chain 'D' and resid 231 through 243 removed outlier: 3.969A pdb=" N TYR D 235 " --> pdb=" O ASN D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 281 Processing helix chain 'D' and resid 285 through 291 removed outlier: 3.774A pdb=" N VAL D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP D 291 " --> pdb=" O GLU D 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 285 through 291' Processing helix chain 'D' and resid 291 through 296 removed outlier: 4.089A pdb=" N ASP D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 336 Processing helix chain 'D' and resid 350 through 364 Processing helix chain 'D' and resid 381 through 396 Processing helix chain 'D' and resid 400 through 426 Processing helix chain 'D' and resid 436 through 457 Processing helix chain 'E' and resid 7 through 24 Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 32 through 41 removed outlier: 4.195A pdb=" N ALA E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 107 removed outlier: 3.836A pdb=" N PHE E 101 " --> pdb=" O PHE E 97 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY E 107 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 141 Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 158 through 174 Processing helix chain 'E' and resid 192 through 213 removed outlier: 5.580A pdb=" N VAL E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL E 202 " --> pdb=" O GLY E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 243 Processing helix chain 'E' and resid 268 through 281 Processing helix chain 'E' and resid 285 through 291 removed outlier: 3.656A pdb=" N VAL E 289 " --> pdb=" O ILE E 285 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 296 removed outlier: 4.062A pdb=" N ASP E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 336 Processing helix chain 'E' and resid 350 through 364 Processing helix chain 'E' and resid 381 through 396 Processing helix chain 'E' and resid 400 through 426 removed outlier: 4.403A pdb=" N ASN E 418 " --> pdb=" O SER E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 457 Processing helix chain 'F' and resid 7 through 24 removed outlier: 3.516A pdb=" N SER F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 32 through 41 removed outlier: 4.259A pdb=" N ALA F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA F 38 " --> pdb=" O ARG F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 107 Processing helix chain 'F' and resid 125 through 141 Processing helix chain 'F' and resid 158 through 174 Processing helix chain 'F' and resid 192 through 211 Processing helix chain 'F' and resid 231 through 243 Processing helix chain 'F' and resid 268 through 281 Processing helix chain 'F' and resid 285 through 291 removed outlier: 3.683A pdb=" N VAL F 289 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR F 290 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 285 through 291' Processing helix chain 'F' and resid 291 through 297 Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.813A pdb=" N VAL F 308 " --> pdb=" O ARG F 305 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL F 310 " --> pdb=" O TRP F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 336 Processing helix chain 'F' and resid 350 through 364 Processing helix chain 'F' and resid 381 through 396 Processing helix chain 'F' and resid 400 through 426 Processing helix chain 'F' and resid 436 through 457 Processing helix chain 'B' and resid 7 through 24 removed outlier: 3.605A pdb=" N SER B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 33 through 41 removed outlier: 3.576A pdb=" N LEU B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 39 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 106 removed outlier: 3.831A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 141 Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 158 through 174 Processing helix chain 'B' and resid 192 through 213 removed outlier: 4.932A pdb=" N GLY B 198 " --> pdb=" O PRO B 194 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 243 Processing helix chain 'B' and resid 268 through 281 Processing helix chain 'B' and resid 285 through 291 removed outlier: 3.552A pdb=" N ASP B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.903A pdb=" N VAL B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 310 " --> pdb=" O TRP B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 336 Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 381 through 388 removed outlier: 3.657A pdb=" N VAL B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 400 through 426 removed outlier: 4.506A pdb=" N ASN B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 457 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.680A pdb=" N SER C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 31 through 34 Processing helix chain 'C' and resid 35 through 41 removed outlier: 3.734A pdb=" N VAL C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 106 removed outlier: 3.863A pdb=" N PHE C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 141 Processing helix chain 'C' and resid 158 through 174 Processing helix chain 'C' and resid 184 through 188 removed outlier: 3.973A pdb=" N GLY C 188 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 213 removed outlier: 4.598A pdb=" N VAL C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 243 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 284 through 290 removed outlier: 4.068A pdb=" N VAL C 289 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 290 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 296 Processing helix chain 'C' and resid 305 through 309 removed outlier: 3.986A pdb=" N VAL C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 336 Processing helix chain 'C' and resid 350 through 364 Processing helix chain 'C' and resid 381 through 396 Processing helix chain 'C' and resid 400 through 426 Processing helix chain 'C' and resid 436 through 457 Processing helix chain 'A' and resid 7 through 24 removed outlier: 3.686A pdb=" N SER A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 33 through 41 removed outlier: 3.849A pdb=" N ALA A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 106 removed outlier: 3.830A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 141 Processing helix chain 'A' and resid 158 through 174 Processing helix chain 'A' and resid 193 through 213 removed outlier: 4.308A pdb=" N GLY A 198 " --> pdb=" O PRO A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 removed outlier: 4.233A pdb=" N TYR A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.506A pdb=" N VAL A 289 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 290 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 326 through 336 Processing helix chain 'A' and resid 350 through 364 Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 400 through 427 Processing helix chain 'A' and resid 437 through 457 Processing sheet with id=AA1, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.533A pdb=" N GLY D 112 " --> pdb=" O PHE D 70 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY B 112 " --> pdb=" O PHE B 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 246 through 247 removed outlier: 3.506A pdb=" N VAL D 224 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG D 223 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU D 317 " --> pdb=" O ARG D 223 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA D 225 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 255 through 259 Processing sheet with id=AA4, first strand: chain 'E' and resid 81 through 83 removed outlier: 6.268A pdb=" N ARG E 82 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY E 112 " --> pdb=" O PHE E 70 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY A 112 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG A 82 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 246 through 250 removed outlier: 6.300A pdb=" N VAL E 224 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER E 249 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ARG E 223 " --> pdb=" O VAL E 315 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU E 317 " --> pdb=" O ARG E 223 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA E 225 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA E 316 " --> pdb=" O ALA E 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 255 through 259 removed outlier: 3.806A pdb=" N LEU E 301 " --> pdb=" O SER E 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 81 through 83 removed outlier: 6.296A pdb=" N ARG F 82 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY F 112 " --> pdb=" O PHE F 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE F 70 " --> pdb=" O GLY F 112 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY C 112 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG C 82 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 246 through 247 removed outlier: 6.134A pdb=" N ARG F 223 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU F 317 " --> pdb=" O ARG F 223 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA F 225 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE F 341 " --> pdb=" O ALA F 373 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 255 through 259 removed outlier: 3.580A pdb=" N LEU F 301 " --> pdb=" O SER F 256 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 246 through 247 removed outlier: 3.625A pdb=" N SER B 227 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA B 316 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 255 through 259 Processing sheet with id=AB3, first strand: chain 'C' and resid 246 through 250 removed outlier: 6.337A pdb=" N VAL C 224 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER C 249 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG C 223 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA C 316 " --> pdb=" O ALA C 342 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE C 341 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 255 through 259 Processing sheet with id=AB5, first strand: chain 'A' and resid 298 through 302 removed outlier: 7.988A pdb=" N VAL A 248 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 224 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 250 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE A 226 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG A 223 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA A 316 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 341 " --> pdb=" O ALA A 373 " (cutoff:3.500A) 1140 hydrogen bonds defined for protein. 3372 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: 6.42 Time building geometry restraints manager: 6.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4482 1.33 - 1.45: 6227 1.45 - 1.58: 10373 1.58 - 1.71: 0 1.71 - 1.83: 126 Bond restraints: 21208 Sorted by residual: bond pdb=" C VAL D 46 " pdb=" O VAL D 46 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.07e-02 8.73e+03 1.01e+01 bond pdb=" C PHE F 97 " pdb=" O PHE F 97 " ideal model delta sigma weight residual 1.236 1.265 -0.028 1.15e-02 7.56e+03 6.11e+00 bond pdb=" CA SER F 90 " pdb=" CB SER F 90 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.55e-02 4.16e+03 5.94e+00 bond pdb=" C ARG F 45 " pdb=" O ARG F 45 " ideal model delta sigma weight residual 1.235 1.205 0.029 1.25e-02 6.40e+03 5.51e+00 bond pdb=" C GLY A 115 " pdb=" O GLY A 115 " ideal model delta sigma weight residual 1.234 1.207 0.027 1.20e-02 6.94e+03 5.17e+00 ... (remaining 21203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 27826 1.90 - 3.80: 807 3.80 - 5.70: 45 5.70 - 7.60: 17 7.60 - 9.50: 2 Bond angle restraints: 28697 Sorted by residual: angle pdb=" N PRO C 269 " pdb=" CD PRO C 269 " pdb=" CG PRO C 269 " ideal model delta sigma weight residual 103.20 93.84 9.36 1.50e+00 4.44e-01 3.89e+01 angle pdb=" N GLU B 389 " pdb=" CA GLU B 389 " pdb=" C GLU B 389 " ideal model delta sigma weight residual 108.96 102.19 6.77 1.49e+00 4.50e-01 2.06e+01 angle pdb=" CB GLU D 98 " pdb=" CG GLU D 98 " pdb=" CD GLU D 98 " ideal model delta sigma weight residual 112.60 119.91 -7.31 1.70e+00 3.46e-01 1.85e+01 angle pdb=" CB GLU A 98 " pdb=" CG GLU A 98 " pdb=" CD GLU A 98 " ideal model delta sigma weight residual 112.60 119.89 -7.29 1.70e+00 3.46e-01 1.84e+01 angle pdb=" CB GLU B 98 " pdb=" CG GLU B 98 " pdb=" CD GLU B 98 " ideal model delta sigma weight residual 112.60 119.64 -7.04 1.70e+00 3.46e-01 1.71e+01 ... (remaining 28692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 10939 17.83 - 35.65: 1205 35.65 - 53.48: 258 53.48 - 71.30: 86 71.30 - 89.13: 33 Dihedral angle restraints: 12521 sinusoidal: 4776 harmonic: 7745 Sorted by residual: dihedral pdb=" CA CYS E 415 " pdb=" C CYS E 415 " pdb=" N PHE E 416 " pdb=" CA PHE E 416 " ideal model delta harmonic sigma weight residual -180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ASN C 109 " pdb=" C ASN C 109 " pdb=" N MET C 110 " pdb=" CA MET C 110 " ideal model delta harmonic sigma weight residual 180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA CYS F 415 " pdb=" C CYS F 415 " pdb=" N PHE F 416 " pdb=" CA PHE F 416 " ideal model delta harmonic sigma weight residual 180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 12518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1516 0.039 - 0.077: 1031 0.077 - 0.115: 449 0.115 - 0.154: 102 0.154 - 0.192: 21 Chirality restraints: 3119 Sorted by residual: chirality pdb=" CA GLU B 206 " pdb=" N GLU B 206 " pdb=" C GLU B 206 " pdb=" CB GLU B 206 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA THR B 428 " pdb=" N THR B 428 " pdb=" C THR B 428 " pdb=" CB THR B 428 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CA TYR B 426 " pdb=" N TYR B 426 " pdb=" C TYR B 426 " pdb=" CB TYR B 426 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 3116 not shown) Planarity restraints: 3784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 67 " 0.247 9.50e-02 1.11e+02 1.13e-01 1.42e+01 pdb=" NE ARG A 67 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 67 " 0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG A 67 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A 67 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 50 " -0.256 9.50e-02 1.11e+02 1.16e-01 1.08e+01 pdb=" NE ARG C 50 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG C 50 " -0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG C 50 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG C 50 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 76 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" C PRO F 76 " 0.053 2.00e-02 2.50e+03 pdb=" O PRO F 76 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR F 77 " -0.018 2.00e-02 2.50e+03 ... (remaining 3781 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 502 2.68 - 3.24: 21516 3.24 - 3.79: 34695 3.79 - 4.35: 47345 4.35 - 4.90: 76251 Nonbonded interactions: 180309 Sorted by model distance: nonbonded pdb=" OD2 ASP C 147 " pdb=" OG SER A 175 " model vdw 2.130 3.040 nonbonded pdb=" OE1 GLU D 44 " pdb=" OH TYR D 77 " model vdw 2.187 3.040 nonbonded pdb=" OE1 GLU C 44 " pdb=" OH TYR C 77 " model vdw 2.196 3.040 nonbonded pdb=" NH2 ARG D 170 " pdb=" OE1 GLN F 456 " model vdw 2.216 3.120 nonbonded pdb=" OG SER F 229 " pdb=" OD2 ASP F 252 " model vdw 2.217 3.040 ... (remaining 180304 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 'A' and (resid 1 through 194 or (resid 195 through 197 and (name N or nam \ e CA or name C or name O or name CB )) or resid 198 or (resid 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 460)) selection = (chain 'B' and (resid 1 through 194 or (resid 195 through 197 and (name N or nam \ e CA or name C or name O or name CB )) or resid 198 or (resid 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 460)) selection = (chain 'C' and (resid 1 through 194 or (resid 195 through 197 and (name N or nam \ e CA or name C or name O or name CB )) or resid 198 or (resid 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 460)) selection = chain 'D' selection = (chain 'E' and (resid 1 through 194 or (resid 195 through 197 and (name N or nam \ e CA or name C or name O or name CB )) or resid 198 or (resid 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 460)) selection = (chain 'F' and (resid 1 through 194 or (resid 195 through 197 and (name N or nam \ e CA or name C or name O or name CB )) or resid 198 or (resid 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 460)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 44.930 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.080 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 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 : 0.008 0.056 21208 Z= 0.480 Angle : 0.821 9.498 28697 Z= 0.512 Chirality : 0.057 0.192 3119 Planarity : 0.009 0.116 3784 Dihedral : 16.730 89.126 7601 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.39 % Favored : 94.25 % Rotamer: Outliers : 0.95 % Allowed : 21.87 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2748 helix: 0.93 (0.14), residues: 1368 sheet: -2.07 (0.26), residues: 396 loop : -1.09 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.006 TRP C 460 HIS 0.010 0.003 HIS A 360 PHE 0.027 0.006 PHE F 416 TYR 0.023 0.005 TYR B 199 ARG 0.045 0.004 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.14089 ( 1140) hydrogen bonds : angle 6.36982 ( 3372) covalent geometry : bond 0.00779 (21208) covalent geometry : angle 0.82055 (28697) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 455 ASP cc_start: 0.7247 (t70) cc_final: 0.6917 (t0) REVERT: F 78 LYS cc_start: 0.7307 (tmtt) cc_final: 0.7098 (tptp) REVERT: F 426 TYR cc_start: 0.5172 (t80) cc_final: 0.4936 (t80) REVERT: C 32 GLU cc_start: 0.6717 (tt0) cc_final: 0.6508 (mp0) outliers start: 20 outliers final: 10 residues processed: 183 average time/residue: 0.3188 time to fit residues: 94.6944 Evaluate side-chains 170 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain E residue 309 HIS Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain A residue 70 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 chunk 141 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 216 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS E 331 GLN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS C 143 HIS ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.203187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.155506 restraints weight = 27183.970| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.02 r_work: 0.3648 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21208 Z= 0.131 Angle : 0.530 7.480 28697 Z= 0.286 Chirality : 0.041 0.140 3119 Planarity : 0.004 0.040 3784 Dihedral : 4.894 56.985 2973 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.11 % Favored : 95.63 % Rotamer: Outliers : 3.52 % Allowed : 19.16 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2748 helix: 1.34 (0.14), residues: 1386 sheet: -1.58 (0.29), residues: 354 loop : -0.97 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 176 HIS 0.004 0.001 HIS C 360 PHE 0.016 0.002 PHE F 416 TYR 0.021 0.002 TYR E 426 ARG 0.004 0.001 ARG B 361 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 1140) hydrogen bonds : angle 5.01069 ( 3372) covalent geometry : bond 0.00278 (21208) covalent geometry : angle 0.53023 (28697) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 205 time to evaluate : 2.447 Fit side-chains revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: D 226 ILE cc_start: 0.6003 (OUTLIER) cc_final: 0.5724 (mt) REVERT: D 329 GLU cc_start: 0.8099 (mp0) cc_final: 0.7531 (mp0) REVERT: E 307 TRP cc_start: 0.6859 (m100) cc_final: 0.6596 (m100) REVERT: E 403 GLU cc_start: 0.6423 (mm-30) cc_final: 0.6028 (tp30) REVERT: E 417 GLN cc_start: 0.6043 (mt0) cc_final: 0.5730 (mm-40) REVERT: F 78 LYS cc_start: 0.7847 (tmtt) cc_final: 0.7505 (tptp) REVERT: B 301 LEU cc_start: 0.5400 (mm) cc_final: 0.5093 (mt) REVERT: B 309 HIS cc_start: 0.3819 (p90) cc_final: 0.3538 (p-80) REVERT: B 390 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.4530 (pmm) REVERT: B 403 GLU cc_start: 0.6217 (mm-30) cc_final: 0.5881 (tp30) REVERT: B 412 MET cc_start: 0.3157 (ppp) cc_final: 0.2810 (ppp) REVERT: C 149 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6964 (m-30) REVERT: C 206 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: C 208 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6271 (mmm) REVERT: C 219 PHE cc_start: 0.6257 (OUTLIER) cc_final: 0.5766 (m-80) REVERT: A 219 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.5474 (m-80) outliers start: 74 outliers final: 31 residues processed: 259 average time/residue: 0.2750 time to fit residues: 116.4640 Evaluate side-chains 212 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 234 GLN Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 219 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 127 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 253 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS D 379 ASN F 48 GLN F 71 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.199010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.150866 restraints weight = 27154.700| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.98 r_work: 0.3587 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 21208 Z= 0.238 Angle : 0.603 7.323 28697 Z= 0.326 Chirality : 0.043 0.261 3119 Planarity : 0.004 0.040 3784 Dihedral : 4.609 46.753 2959 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.68 % Favored : 94.07 % Rotamer: Outliers : 4.76 % Allowed : 18.78 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 2748 helix: 1.16 (0.14), residues: 1374 sheet: -1.63 (0.28), residues: 354 loop : -1.00 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 176 HIS 0.016 0.002 HIS F 207 PHE 0.018 0.003 PHE F 66 TYR 0.021 0.002 TYR F 77 ARG 0.004 0.001 ARG B 361 Details of bonding type rmsd hydrogen bonds : bond 0.05248 ( 1140) hydrogen bonds : angle 5.04725 ( 3372) covalent geometry : bond 0.00553 (21208) covalent geometry : angle 0.60318 (28697) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 188 time to evaluate : 2.107 Fit side-chains revert: symmetry clash REVERT: D 1 MET cc_start: 0.5111 (mtp) cc_final: 0.4847 (mmp) REVERT: D 226 ILE cc_start: 0.6119 (OUTLIER) cc_final: 0.5835 (mt) REVERT: D 329 GLU cc_start: 0.8120 (mp0) cc_final: 0.7593 (mp0) REVERT: E 238 LEU cc_start: 0.5450 (tt) cc_final: 0.4733 (mp) REVERT: E 307 TRP cc_start: 0.6981 (m100) cc_final: 0.6590 (m100) REVERT: E 403 GLU cc_start: 0.6412 (mm-30) cc_final: 0.6054 (tp30) REVERT: B 301 LEU cc_start: 0.5390 (mm) cc_final: 0.5140 (mt) REVERT: B 309 HIS cc_start: 0.3865 (p90) cc_final: 0.3620 (p-80) REVERT: B 389 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5864 (tp30) REVERT: B 390 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5247 (pmm) REVERT: B 403 GLU cc_start: 0.6244 (mm-30) cc_final: 0.5858 (tp30) REVERT: B 412 MET cc_start: 0.3087 (ppp) cc_final: 0.2643 (ppp) REVERT: C 56 ASP cc_start: 0.8329 (m-30) cc_final: 0.7972 (m-30) REVERT: C 206 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: C 219 PHE cc_start: 0.6313 (OUTLIER) cc_final: 0.5776 (m-80) REVERT: A 206 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6653 (mt-10) REVERT: A 219 PHE cc_start: 0.6213 (OUTLIER) cc_final: 0.5431 (m-80) REVERT: A 258 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6710 (mp) outliers start: 100 outliers final: 51 residues processed: 266 average time/residue: 0.2738 time to fit residues: 119.5395 Evaluate side-chains 229 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 416 PHE Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 234 GLN Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 347 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 198 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 229 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 110 optimal weight: 0.0000 chunk 121 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.202466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.152209 restraints weight = 27335.781| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.89 r_work: 0.3638 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21208 Z= 0.130 Angle : 0.517 7.757 28697 Z= 0.278 Chirality : 0.040 0.145 3119 Planarity : 0.003 0.042 3784 Dihedral : 4.373 46.738 2959 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.44 % Favored : 95.34 % Rotamer: Outliers : 3.71 % Allowed : 20.11 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2748 helix: 1.33 (0.14), residues: 1386 sheet: -1.52 (0.29), residues: 354 loop : -0.96 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 176 HIS 0.011 0.001 HIS F 207 PHE 0.017 0.002 PHE A 294 TYR 0.019 0.002 TYR F 235 ARG 0.003 0.000 ARG B 361 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 1140) hydrogen bonds : angle 4.82870 ( 3372) covalent geometry : bond 0.00287 (21208) covalent geometry : angle 0.51746 (28697) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 197 time to evaluate : 2.499 Fit side-chains revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: D 329 GLU cc_start: 0.8034 (mp0) cc_final: 0.7494 (mp0) REVERT: E 4 LEU cc_start: 0.8438 (tt) cc_final: 0.8015 (mp) REVERT: E 268 THR cc_start: 0.6323 (OUTLIER) cc_final: 0.6094 (t) REVERT: E 307 TRP cc_start: 0.6922 (m100) cc_final: 0.6631 (m100) REVERT: E 403 GLU cc_start: 0.6456 (mm-30) cc_final: 0.6111 (tp30) REVERT: E 426 TYR cc_start: 0.5134 (t80) cc_final: 0.4371 (t80) REVERT: F 206 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6373 (mt-10) REVERT: F 301 LEU cc_start: 0.5698 (mm) cc_final: 0.5412 (mt) REVERT: B 155 ILE cc_start: 0.8268 (mt) cc_final: 0.7963 (tp) REVERT: B 187 TRP cc_start: 0.7369 (p90) cc_final: 0.6942 (p90) REVERT: B 301 LEU cc_start: 0.5403 (mm) cc_final: 0.5034 (mt) REVERT: B 389 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.5689 (tp30) REVERT: B 390 MET cc_start: 0.5641 (OUTLIER) cc_final: 0.5340 (pmm) REVERT: B 403 GLU cc_start: 0.6270 (mm-30) cc_final: 0.5888 (tp30) REVERT: C 56 ASP cc_start: 0.8298 (m-30) cc_final: 0.7973 (m-30) REVERT: C 149 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6891 (m-30) REVERT: C 187 TRP cc_start: 0.6271 (p90) cc_final: 0.5866 (p90) REVERT: C 206 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: C 219 PHE cc_start: 0.6274 (OUTLIER) cc_final: 0.5565 (m-80) REVERT: A 206 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6640 (mt-10) REVERT: A 219 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.5366 (m-80) REVERT: A 258 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6741 (mp) outliers start: 78 outliers final: 41 residues processed: 256 average time/residue: 0.2765 time to fit residues: 116.0430 Evaluate side-chains 226 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 416 PHE Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 234 GLN Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 347 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 187 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 275 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 217 optimal weight: 20.0000 chunk 255 optimal weight: 0.0570 chunk 10 optimal weight: 0.9980 chunk 265 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.203776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.154875 restraints weight = 27245.101| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.12 r_work: 0.3662 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21208 Z= 0.120 Angle : 0.514 7.929 28697 Z= 0.275 Chirality : 0.040 0.138 3119 Planarity : 0.003 0.043 3784 Dihedral : 4.211 46.399 2959 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.80 % Favored : 94.98 % Rotamer: Outliers : 4.04 % Allowed : 20.35 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2748 helix: 1.44 (0.14), residues: 1386 sheet: -1.38 (0.29), residues: 342 loop : -0.88 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 176 HIS 0.009 0.001 HIS F 207 PHE 0.039 0.002 PHE F 340 TYR 0.024 0.001 TYR F 235 ARG 0.002 0.000 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 1140) hydrogen bonds : angle 4.70462 ( 3372) covalent geometry : bond 0.00261 (21208) covalent geometry : angle 0.51430 (28697) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 197 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: D 219 PHE cc_start: 0.6158 (OUTLIER) cc_final: 0.5651 (m-80) REVERT: D 226 ILE cc_start: 0.5911 (OUTLIER) cc_final: 0.5659 (mt) REVERT: D 329 GLU cc_start: 0.8055 (mp0) cc_final: 0.7509 (mp0) REVERT: E 4 LEU cc_start: 0.8395 (tt) cc_final: 0.7982 (mp) REVERT: E 187 TRP cc_start: 0.6950 (p90) cc_final: 0.6608 (p90) REVERT: E 268 THR cc_start: 0.6292 (OUTLIER) cc_final: 0.6059 (t) REVERT: E 301 LEU cc_start: 0.5839 (mm) cc_final: 0.5442 (mt) REVERT: E 307 TRP cc_start: 0.6878 (m100) cc_final: 0.6581 (m100) REVERT: E 329 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7821 (mt-10) REVERT: E 403 GLU cc_start: 0.6439 (mm-30) cc_final: 0.6098 (tp30) REVERT: E 426 TYR cc_start: 0.5397 (t80) cc_final: 0.5119 (t80) REVERT: F 199 TYR cc_start: 0.4206 (m-10) cc_final: 0.3999 (m-10) REVERT: F 206 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6394 (mt-10) REVERT: F 301 LEU cc_start: 0.5659 (mm) cc_final: 0.5372 (mt) REVERT: B 155 ILE cc_start: 0.8224 (mt) cc_final: 0.7927 (tp) REVERT: B 301 LEU cc_start: 0.5699 (mm) cc_final: 0.5309 (mt) REVERT: B 403 GLU cc_start: 0.6284 (mm-30) cc_final: 0.5923 (tp30) REVERT: B 412 MET cc_start: 0.2580 (ppp) cc_final: 0.2372 (ppp) REVERT: C 56 ASP cc_start: 0.8168 (m-30) cc_final: 0.7795 (m-30) REVERT: C 149 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6933 (m-30) REVERT: C 206 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: C 208 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.6237 (mmm) REVERT: C 219 PHE cc_start: 0.6269 (OUTLIER) cc_final: 0.5396 (m-80) REVERT: A 206 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: A 219 PHE cc_start: 0.6281 (OUTLIER) cc_final: 0.5378 (m-80) REVERT: A 258 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6774 (mp) outliers start: 85 outliers final: 48 residues processed: 263 average time/residue: 0.2880 time to fit residues: 123.8682 Evaluate side-chains 239 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 179 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 416 PHE Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 234 GLN Chi-restraints excluded: chain F residue 309 HIS Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 371 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 252 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 242 optimal weight: 0.0060 chunk 111 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 231 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS B 211 HIS B 309 HIS ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.200098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.149815 restraints weight = 27209.775| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.91 r_work: 0.3601 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21208 Z= 0.217 Angle : 0.586 7.051 28697 Z= 0.315 Chirality : 0.043 0.337 3119 Planarity : 0.004 0.042 3784 Dihedral : 4.444 41.765 2959 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.71 % Favored : 94.07 % Rotamer: Outliers : 4.56 % Allowed : 20.78 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2748 helix: 1.30 (0.14), residues: 1386 sheet: -1.49 (0.27), residues: 414 loop : -0.93 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 187 HIS 0.011 0.002 HIS F 207 PHE 0.025 0.002 PHE F 340 TYR 0.023 0.002 TYR D 235 ARG 0.005 0.000 ARG F 142 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 1140) hydrogen bonds : angle 4.83847 ( 3372) covalent geometry : bond 0.00507 (21208) covalent geometry : angle 0.58565 (28697) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 177 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: D 226 ILE cc_start: 0.6081 (OUTLIER) cc_final: 0.5809 (mt) REVERT: D 329 GLU cc_start: 0.8119 (mp0) cc_final: 0.7545 (mp0) REVERT: E 4 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8000 (mp) REVERT: E 307 TRP cc_start: 0.6993 (m100) cc_final: 0.6689 (m100) REVERT: E 403 GLU cc_start: 0.6345 (mm-30) cc_final: 0.6003 (tp30) REVERT: F 206 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6503 (mt-10) REVERT: F 298 PHE cc_start: 0.4749 (OUTLIER) cc_final: 0.2945 (m-80) REVERT: B 301 LEU cc_start: 0.6005 (mm) cc_final: 0.5538 (mt) REVERT: B 307 TRP cc_start: 0.6664 (m100) cc_final: 0.6414 (m100) REVERT: B 389 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5987 (tp30) REVERT: B 403 GLU cc_start: 0.6163 (mm-30) cc_final: 0.5814 (tp30) REVERT: C 56 ASP cc_start: 0.8320 (m-30) cc_final: 0.7893 (m-30) REVERT: C 149 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.6966 (m-30) REVERT: C 206 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: C 219 PHE cc_start: 0.6439 (OUTLIER) cc_final: 0.5438 (m-10) REVERT: A 187 TRP cc_start: 0.7109 (p90) cc_final: 0.6766 (p90) REVERT: A 206 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6698 (mt-10) REVERT: A 219 PHE cc_start: 0.6274 (OUTLIER) cc_final: 0.5405 (m-80) REVERT: A 258 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6786 (mp) outliers start: 96 outliers final: 60 residues processed: 252 average time/residue: 0.2778 time to fit residues: 114.7409 Evaluate side-chains 244 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 172 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 234 GLN Chi-restraints excluded: chain F residue 298 PHE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 309 HIS Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 371 TRP Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 347 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 150 optimal weight: 0.9980 chunk 263 optimal weight: 0.7980 chunk 207 optimal weight: 8.9990 chunk 205 optimal weight: 0.0030 chunk 38 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 120 optimal weight: 0.4980 chunk 109 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN D 360 HIS E 360 HIS ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.203656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.152549 restraints weight = 27034.723| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.17 r_work: 0.3635 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21208 Z= 0.120 Angle : 0.518 7.286 28697 Z= 0.276 Chirality : 0.040 0.207 3119 Planarity : 0.003 0.043 3784 Dihedral : 4.067 35.715 2955 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.66 % Favored : 95.16 % Rotamer: Outliers : 3.71 % Allowed : 21.45 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.16), residues: 2748 helix: 1.46 (0.14), residues: 1386 sheet: -1.41 (0.29), residues: 342 loop : -0.86 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 187 HIS 0.008 0.001 HIS F 207 PHE 0.021 0.002 PHE F 340 TYR 0.045 0.002 TYR B 235 ARG 0.005 0.000 ARG F 142 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 1140) hydrogen bonds : angle 4.67859 ( 3372) covalent geometry : bond 0.00264 (21208) covalent geometry : angle 0.51789 (28697) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 190 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: D 226 ILE cc_start: 0.5895 (OUTLIER) cc_final: 0.5650 (mt) REVERT: D 329 GLU cc_start: 0.8131 (mp0) cc_final: 0.7555 (mp0) REVERT: E 4 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7997 (mp) REVERT: E 187 TRP cc_start: 0.7372 (p90) cc_final: 0.6816 (p90) REVERT: E 268 THR cc_start: 0.6264 (OUTLIER) cc_final: 0.6052 (t) REVERT: E 301 LEU cc_start: 0.5768 (mm) cc_final: 0.5370 (mt) REVERT: E 307 TRP cc_start: 0.6839 (m100) cc_final: 0.6533 (m100) REVERT: E 403 GLU cc_start: 0.6393 (mm-30) cc_final: 0.6084 (tp30) REVERT: F 206 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6364 (mt-10) REVERT: F 298 PHE cc_start: 0.4730 (OUTLIER) cc_final: 0.2935 (m-80) REVERT: F 301 LEU cc_start: 0.5671 (mm) cc_final: 0.5331 (mt) REVERT: F 354 ILE cc_start: 0.6655 (OUTLIER) cc_final: 0.6441 (mp) REVERT: B 154 ASP cc_start: 0.5874 (OUTLIER) cc_final: 0.5638 (t0) REVERT: B 155 ILE cc_start: 0.8103 (mt) cc_final: 0.7805 (tp) REVERT: B 301 LEU cc_start: 0.6113 (mm) cc_final: 0.5702 (mt) REVERT: B 309 HIS cc_start: 0.3927 (p90) cc_final: 0.3555 (p-80) REVERT: B 389 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5733 (tp30) REVERT: B 403 GLU cc_start: 0.6169 (mm-30) cc_final: 0.5856 (tp30) REVERT: B 412 MET cc_start: 0.2221 (ppp) cc_final: 0.1971 (ppp) REVERT: C 56 ASP cc_start: 0.8022 (m-30) cc_final: 0.7657 (m-30) REVERT: C 149 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6847 (m-30) REVERT: C 208 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6604 (mmm) REVERT: C 219 PHE cc_start: 0.6302 (OUTLIER) cc_final: 0.5285 (m-10) REVERT: A 206 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6607 (mt-10) REVERT: A 219 PHE cc_start: 0.6238 (OUTLIER) cc_final: 0.5341 (m-80) REVERT: A 258 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6746 (mp) outliers start: 78 outliers final: 49 residues processed: 250 average time/residue: 0.2744 time to fit residues: 112.8781 Evaluate side-chains 242 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 178 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 298 PHE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 371 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 55 optimal weight: 0.7980 chunk 247 optimal weight: 0.0570 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 232 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS B 109 ASN ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.202369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.152177 restraints weight = 27215.618| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.75 r_work: 0.3649 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21208 Z= 0.153 Angle : 0.544 7.316 28697 Z= 0.290 Chirality : 0.041 0.178 3119 Planarity : 0.004 0.042 3784 Dihedral : 4.095 36.170 2955 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.09 % Favored : 94.72 % Rotamer: Outliers : 4.04 % Allowed : 21.78 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.16), residues: 2748 helix: 1.44 (0.14), residues: 1386 sheet: -1.35 (0.29), residues: 360 loop : -0.83 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 187 HIS 0.008 0.001 HIS F 207 PHE 0.017 0.002 PHE F 340 TYR 0.044 0.002 TYR B 235 ARG 0.004 0.000 ARG F 142 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 1140) hydrogen bonds : angle 4.68300 ( 3372) covalent geometry : bond 0.00350 (21208) covalent geometry : angle 0.54363 (28697) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 183 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: D 187 TRP cc_start: 0.7205 (p90) cc_final: 0.6893 (p90) REVERT: D 226 ILE cc_start: 0.6086 (OUTLIER) cc_final: 0.5802 (mt) REVERT: D 329 GLU cc_start: 0.8119 (mp0) cc_final: 0.7544 (mp0) REVERT: E 4 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7988 (mp) REVERT: E 268 THR cc_start: 0.6318 (OUTLIER) cc_final: 0.6101 (t) REVERT: E 301 LEU cc_start: 0.5910 (mm) cc_final: 0.5452 (mt) REVERT: E 307 TRP cc_start: 0.6941 (m100) cc_final: 0.6620 (m100) REVERT: E 309 HIS cc_start: 0.4338 (m90) cc_final: 0.3958 (m90) REVERT: E 403 GLU cc_start: 0.6423 (mm-30) cc_final: 0.6022 (tp30) REVERT: F 206 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6508 (mt-10) REVERT: F 298 PHE cc_start: 0.4753 (OUTLIER) cc_final: 0.2914 (m-80) REVERT: F 301 LEU cc_start: 0.5802 (mm) cc_final: 0.5442 (mt) REVERT: F 331 GLN cc_start: 0.6712 (mm-40) cc_final: 0.6497 (mp10) REVERT: B 154 ASP cc_start: 0.6023 (OUTLIER) cc_final: 0.5759 (t0) REVERT: B 155 ILE cc_start: 0.8239 (mt) cc_final: 0.7920 (tp) REVERT: B 301 LEU cc_start: 0.6052 (mm) cc_final: 0.5641 (mt) REVERT: B 307 TRP cc_start: 0.6601 (m100) cc_final: 0.6350 (m100) REVERT: B 389 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5888 (tp30) REVERT: B 403 GLU cc_start: 0.6209 (mm-30) cc_final: 0.5878 (tp30) REVERT: B 412 MET cc_start: 0.2511 (ppp) cc_final: 0.2206 (ppp) REVERT: B 417 GLN cc_start: 0.6393 (OUTLIER) cc_final: 0.6117 (tm-30) REVERT: C 56 ASP cc_start: 0.8197 (m-30) cc_final: 0.7771 (m-30) REVERT: C 64 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8323 (mtm-85) REVERT: C 149 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6973 (m-30) REVERT: C 219 PHE cc_start: 0.6332 (OUTLIER) cc_final: 0.5322 (m-10) REVERT: A 206 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6789 (mt-10) REVERT: A 219 PHE cc_start: 0.6275 (OUTLIER) cc_final: 0.5300 (m-80) REVERT: A 258 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6793 (mp) outliers start: 85 outliers final: 59 residues processed: 249 average time/residue: 0.2820 time to fit residues: 114.7181 Evaluate side-chains 249 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 175 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 298 PHE Chi-restraints excluded: chain F residue 309 HIS Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 371 TRP Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 347 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 118 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS F 109 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.200568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152306 restraints weight = 27241.137| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.96 r_work: 0.3607 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 : 0.005 0.069 21208 Z= 0.209 Angle : 0.591 7.405 28697 Z= 0.316 Chirality : 0.043 0.180 3119 Planarity : 0.004 0.041 3784 Dihedral : 4.273 37.293 2955 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.46 % Favored : 94.32 % Rotamer: Outliers : 3.99 % Allowed : 22.02 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2748 helix: 1.14 (0.14), residues: 1428 sheet: -1.49 (0.26), residues: 414 loop : -1.03 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 187 HIS 0.018 0.002 HIS F 309 PHE 0.016 0.002 PHE F 94 TYR 0.034 0.002 TYR B 199 ARG 0.004 0.000 ARG F 142 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 1140) hydrogen bonds : angle 4.77435 ( 3372) covalent geometry : bond 0.00489 (21208) covalent geometry : angle 0.59103 (28697) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 177 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: D 226 ILE cc_start: 0.6133 (OUTLIER) cc_final: 0.5865 (mt) REVERT: D 329 GLU cc_start: 0.8149 (mp0) cc_final: 0.7519 (mp0) REVERT: E 4 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7988 (mp) REVERT: E 307 TRP cc_start: 0.7062 (m100) cc_final: 0.6708 (m100) REVERT: E 309 HIS cc_start: 0.4590 (m90) cc_final: 0.4326 (m90) REVERT: E 403 GLU cc_start: 0.6573 (mm-30) cc_final: 0.6148 (tp30) REVERT: F 206 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6782 (mt-10) REVERT: F 298 PHE cc_start: 0.4840 (OUTLIER) cc_final: 0.2794 (m-80) REVERT: F 301 LEU cc_start: 0.5773 (mm) cc_final: 0.5464 (mt) REVERT: F 329 GLU cc_start: 0.8141 (mp0) cc_final: 0.7623 (mp0) REVERT: F 390 MET cc_start: 0.5361 (mtp) cc_final: 0.5144 (mtp) REVERT: F 420 LEU cc_start: 0.5645 (mm) cc_final: 0.5406 (mt) REVERT: B 128 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: B 154 ASP cc_start: 0.6074 (OUTLIER) cc_final: 0.5795 (t0) REVERT: B 155 ILE cc_start: 0.8313 (mt) cc_final: 0.7973 (tp) REVERT: B 301 LEU cc_start: 0.5935 (mm) cc_final: 0.5481 (mt) REVERT: B 307 TRP cc_start: 0.6632 (m100) cc_final: 0.6396 (m100) REVERT: B 389 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6032 (tp30) REVERT: B 403 GLU cc_start: 0.6275 (mm-30) cc_final: 0.6022 (tp30) REVERT: B 412 MET cc_start: 0.2674 (ppp) cc_final: 0.2362 (ppp) REVERT: C 56 ASP cc_start: 0.8290 (m-30) cc_final: 0.7864 (m-30) REVERT: C 64 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8398 (mtm-85) REVERT: C 149 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6995 (m-30) REVERT: C 219 PHE cc_start: 0.6438 (OUTLIER) cc_final: 0.5446 (m-10) REVERT: C 376 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7580 (ptpp) REVERT: A 206 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6811 (mt-10) REVERT: A 219 PHE cc_start: 0.6248 (OUTLIER) cc_final: 0.5313 (m-80) REVERT: A 258 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6807 (mp) outliers start: 84 outliers final: 62 residues processed: 241 average time/residue: 0.2777 time to fit residues: 109.8815 Evaluate side-chains 249 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 172 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 298 PHE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 309 HIS Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 371 TRP Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 376 LYS Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 347 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 216 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 259 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS F 109 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.202050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152621 restraints weight = 27057.370| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.10 r_work: 0.3632 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21208 Z= 0.153 Angle : 0.557 8.117 28697 Z= 0.297 Chirality : 0.041 0.169 3119 Planarity : 0.004 0.042 3784 Dihedral : 4.188 37.873 2955 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.09 % Favored : 94.72 % Rotamer: Outliers : 3.66 % Allowed : 22.06 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2748 helix: 1.20 (0.14), residues: 1428 sheet: -1.46 (0.26), residues: 414 loop : -1.00 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 187 HIS 0.011 0.001 HIS F 309 PHE 0.016 0.002 PHE F 340 TYR 0.039 0.002 TYR B 235 ARG 0.004 0.000 ARG F 142 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 1140) hydrogen bonds : angle 4.71463 ( 3372) covalent geometry : bond 0.00347 (21208) covalent geometry : angle 0.55676 (28697) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 177 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: D 226 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5738 (mt) REVERT: D 329 GLU cc_start: 0.8123 (mp0) cc_final: 0.7489 (mp0) REVERT: E 4 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7950 (mp) REVERT: E 301 LEU cc_start: 0.5861 (mm) cc_final: 0.5407 (mt) REVERT: E 307 TRP cc_start: 0.6974 (m100) cc_final: 0.6614 (m100) REVERT: E 309 HIS cc_start: 0.4518 (m90) cc_final: 0.4205 (m90) REVERT: E 403 GLU cc_start: 0.6444 (mm-30) cc_final: 0.6125 (tp30) REVERT: F 206 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: F 298 PHE cc_start: 0.4821 (OUTLIER) cc_final: 0.2762 (m-80) REVERT: F 301 LEU cc_start: 0.5785 (mm) cc_final: 0.5508 (mt) REVERT: F 329 GLU cc_start: 0.8136 (mp0) cc_final: 0.7715 (mp0) REVERT: F 390 MET cc_start: 0.5139 (mtp) cc_final: 0.4913 (mtp) REVERT: B 128 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: B 154 ASP cc_start: 0.6030 (OUTLIER) cc_final: 0.5725 (t0) REVERT: B 155 ILE cc_start: 0.8293 (mt) cc_final: 0.7955 (tp) REVERT: B 301 LEU cc_start: 0.5982 (mm) cc_final: 0.5551 (mt) REVERT: B 389 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5955 (tp30) REVERT: B 403 GLU cc_start: 0.6261 (mm-30) cc_final: 0.5918 (tp30) REVERT: B 412 MET cc_start: 0.2470 (ppp) cc_final: 0.2184 (ppp) REVERT: C 56 ASP cc_start: 0.8294 (m-30) cc_final: 0.7871 (m-30) REVERT: C 149 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7007 (m-30) REVERT: C 208 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6318 (mmm) REVERT: C 219 PHE cc_start: 0.6433 (OUTLIER) cc_final: 0.5340 (m-10) REVERT: A 206 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6710 (mt-10) REVERT: A 219 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.5305 (m-80) REVERT: A 258 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6740 (mp) outliers start: 77 outliers final: 57 residues processed: 240 average time/residue: 0.2773 time to fit residues: 110.0148 Evaluate side-chains 243 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 172 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 298 PHE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 371 TRP Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 347 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 100 optimal weight: 0.3980 chunk 253 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 12 optimal weight: 0.0020 chunk 189 optimal weight: 1.9990 chunk 171 optimal weight: 0.4980 chunk 230 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.204059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.157731 restraints weight = 27080.987| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.94 r_work: 0.3663 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21208 Z= 0.120 Angle : 0.531 10.072 28697 Z= 0.282 Chirality : 0.040 0.167 3119 Planarity : 0.003 0.043 3784 Dihedral : 4.038 37.596 2955 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.73 % Favored : 95.09 % Rotamer: Outliers : 3.66 % Allowed : 21.92 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2748 helix: 1.31 (0.14), residues: 1428 sheet: -1.23 (0.29), residues: 348 loop : -0.97 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 187 HIS 0.011 0.001 HIS F 309 PHE 0.016 0.002 PHE F 340 TYR 0.032 0.002 TYR D 235 ARG 0.004 0.000 ARG F 142 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 1140) hydrogen bonds : angle 4.61090 ( 3372) covalent geometry : bond 0.00262 (21208) covalent geometry : angle 0.53147 (28697) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12414.19 seconds wall clock time: 214 minutes 54.18 seconds (12894.18 seconds total)