Starting phenix.real_space_refine on Sat Aug 23 02:53:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yiy_33866/08_2025/7yiy_33866.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yiy_33866/08_2025/7yiy_33866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yiy_33866/08_2025/7yiy_33866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yiy_33866/08_2025/7yiy_33866.map" model { file = "/net/cci-nas-00/data/ceres_data/7yiy_33866/08_2025/7yiy_33866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yiy_33866/08_2025/7yiy_33866.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 52 5.16 5 C 5971 2.51 5 N 1559 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9257 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 3940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3940 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 481} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 324 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1236 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "C" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 411 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "A" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3285 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'Z1T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.64, per 1000 atoms: 0.18 Number of scatterers: 9257 At special positions: 0 Unit cell: (91.8, 85.32, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 1 15.00 O 1674 8.00 N 1559 7.00 C 5971 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 237.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 53.9% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 67 through 92 removed outlier: 3.855A pdb=" N TYR B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 76 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.530A pdb=" N GLN B 108 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 109' Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.942A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP B 134 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 4.281A pdb=" N PHE B 181 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.513A pdb=" N GLU B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.614A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.781A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 263 through 274 removed outlier: 4.033A pdb=" N GLY B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 299 removed outlier: 3.692A pdb=" N ILE B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 337 removed outlier: 3.803A pdb=" N LYS B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 363 removed outlier: 4.133A pdb=" N GLU B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 391 through 402 removed outlier: 3.749A pdb=" N THR B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 removed outlier: 3.507A pdb=" N VAL B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 removed outlier: 3.522A pdb=" N GLN B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 455 removed outlier: 3.713A pdb=" N GLU B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.942A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'E' and resid 10 through 19 Processing helix chain 'E' and resid 21 through 40 removed outlier: 3.527A pdb=" N LEU E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU E 27 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 19 removed outlier: 3.766A pdb=" N ARG D 15 " --> pdb=" O PRO D 12 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL D 16 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N MET D 17 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 removed outlier: 3.599A pdb=" N ILE D 30 " --> pdb=" O TYR D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 66 Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 96 through 116 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 120 through 133 removed outlier: 3.789A pdb=" N VAL D 125 " --> pdb=" O GLN D 121 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 Proline residue: D 137 - end of helix Proline residue: D 140 - end of helix removed outlier: 3.531A pdb=" N HIS D 143 " --> pdb=" O PRO D 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 143' Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 25 through 29 removed outlier: 3.614A pdb=" N MET C 28 " --> pdb=" O ALA C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 55 removed outlier: 3.614A pdb=" N VAL C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE C 44 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 51 " --> pdb=" O MET C 47 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.527A pdb=" N LYS A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.676A pdb=" N LYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.756A pdb=" N ALA A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 230 removed outlier: 3.789A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.641A pdb=" N LYS A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.545A pdb=" N ILE A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.537A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 removed outlier: 3.942A pdb=" N GLN A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS A 374 " --> pdb=" O CYS A 370 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.695A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 removed outlier: 4.138A pdb=" N GLU A 436 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA3, first strand: chain 'B' and resid 137 through 138 Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 152 removed outlier: 5.156A pdb=" N ILE B 148 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LYS B 168 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU B 150 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B 166 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 11.136A pdb=" N GLN B 152 " --> pdb=" O GLY B 164 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N GLY B 164 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 234 removed outlier: 8.201A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 317 through 318 removed outlier: 3.575A pdb=" N SER B 323 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.833A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.433A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 160 through 164 removed outlier: 8.558A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N ASN A 306 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG A 240 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N PHE A 272 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLU A 274 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 244 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 383 through 386 Processing sheet with id=AB2, first strand: chain 'A' and resid 427 through 428 removed outlier: 4.507A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1173 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: 1.24 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2604 1.33 - 1.45: 1510 1.45 - 1.57: 5255 1.57 - 1.69: 1 1.69 - 1.81: 87 Bond restraints: 9457 Sorted by residual: bond pdb=" C14 Z1T D 201 " pdb=" C15 Z1T D 201 " ideal model delta sigma weight residual 1.329 1.523 -0.194 2.00e-02 2.50e+03 9.45e+01 bond pdb=" C2 PLP B 601 " pdb=" C3 PLP B 601 " ideal model delta sigma weight residual 1.390 1.485 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C4 PLP B 601 " pdb=" C5 PLP B 601 " ideal model delta sigma weight residual 1.390 1.483 -0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C3 PLP B 601 " pdb=" C4 PLP B 601 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C PHE B 498 " pdb=" O PHE B 498 " ideal model delta sigma weight residual 1.241 1.212 0.029 9.80e-03 1.04e+04 8.78e+00 ... (remaining 9452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 12423 2.43 - 4.85: 301 4.85 - 7.28: 50 7.28 - 9.70: 8 9.70 - 12.13: 5 Bond angle restraints: 12787 Sorted by residual: angle pdb=" N ILE B 503 " pdb=" CA ILE B 503 " pdb=" C ILE B 503 " ideal model delta sigma weight residual 110.62 118.43 -7.81 1.02e+00 9.61e-01 5.86e+01 angle pdb=" N GLN B 116 " pdb=" CA GLN B 116 " pdb=" C GLN B 116 " ideal model delta sigma weight residual 109.76 99.56 10.20 1.59e+00 3.96e-01 4.12e+01 angle pdb=" N PRO A 78 " pdb=" CA PRO A 78 " pdb=" CB PRO A 78 " ideal model delta sigma weight residual 103.44 109.98 -6.54 1.12e+00 7.97e-01 3.41e+01 angle pdb=" N GLY B 497 " pdb=" CA GLY B 497 " pdb=" C GLY B 497 " ideal model delta sigma weight residual 112.81 120.13 -7.32 1.38e+00 5.25e-01 2.82e+01 angle pdb=" N ASN B 60 " pdb=" CA ASN B 60 " pdb=" C ASN B 60 " ideal model delta sigma weight residual 108.34 116.90 -8.56 1.64e+00 3.72e-01 2.72e+01 ... (remaining 12782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 4933 16.31 - 32.63: 482 32.63 - 48.94: 174 48.94 - 65.26: 66 65.26 - 81.57: 12 Dihedral angle restraints: 5667 sinusoidal: 2298 harmonic: 3369 Sorted by residual: dihedral pdb=" CA ASN B 120 " pdb=" C ASN B 120 " pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta harmonic sigma weight residual 180.00 155.33 24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA ILE B 96 " pdb=" C ILE B 96 " pdb=" N GLU B 97 " pdb=" CA GLU B 97 " ideal model delta harmonic sigma weight residual -180.00 -158.19 -21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C TYR E 44 " pdb=" N TYR E 44 " pdb=" CA TYR E 44 " pdb=" CB TYR E 44 " ideal model delta harmonic sigma weight residual -122.60 -132.97 10.37 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 5664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1247 0.087 - 0.174: 157 0.174 - 0.261: 19 0.261 - 0.347: 2 0.347 - 0.434: 3 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CA LYS B 168 " pdb=" N LYS B 168 " pdb=" C LYS B 168 " pdb=" CB LYS B 168 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA TYR E 44 " pdb=" N TYR E 44 " pdb=" C TYR E 44 " pdb=" CB TYR E 44 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CA PHE B 498 " pdb=" N PHE B 498 " pdb=" C PHE B 498 " pdb=" CB PHE B 498 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.41 2.00e-01 2.50e+01 4.10e+00 ... (remaining 1425 not shown) Planarity restraints: 1619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO B 502 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 166 " 0.022 2.00e-02 2.50e+03 1.68e-02 5.62e+00 pdb=" CG TYR A 166 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 166 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 166 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 166 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 166 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 166 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 166 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 501 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C THR B 501 " 0.039 2.00e-02 2.50e+03 pdb=" O THR B 501 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO B 502 " -0.013 2.00e-02 2.50e+03 ... (remaining 1616 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1023 2.74 - 3.28: 8357 3.28 - 3.82: 14320 3.82 - 4.36: 18141 4.36 - 4.90: 31287 Nonbonded interactions: 73128 Sorted by model distance: nonbonded pdb=" O ALA B 201 " pdb=" OG SER B 412 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR B 407 " pdb=" OE2 GLU A 436 " model vdw 2.218 3.040 nonbonded pdb=" O THR B 66 " pdb=" NH1 ARG D 20 " model vdw 2.240 3.120 nonbonded pdb=" OG1 THR B 432 " pdb=" CD2 LEU B 434 " model vdw 2.261 3.460 nonbonded pdb=" NZ LYS B 338 " pdb=" O TRP A 64 " model vdw 2.296 3.120 ... (remaining 73123 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.80 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 0.282 9458 Z= 0.456 Angle : 0.981 12.129 12787 Z= 0.587 Chirality : 0.063 0.434 1428 Planarity : 0.006 0.086 1619 Dihedral : 16.225 81.572 3511 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.20 % Favored : 94.19 % Rotamer: Outliers : 4.77 % Allowed : 2.44 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.24), residues: 1154 helix: -0.40 (0.22), residues: 505 sheet: -0.01 (0.50), residues: 118 loop : -1.77 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 81 TYR 0.039 0.003 TYR A 166 PHE 0.032 0.003 PHE A 138 TRP 0.017 0.002 TRP B 134 HIS 0.005 0.001 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00764 ( 9457) covalent geometry : angle 0.98084 (12787) hydrogen bonds : bond 0.25212 ( 419) hydrogen bonds : angle 7.08114 ( 1173) Misc. bond : bond 0.28211 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 0.229 Fit side-chains REVERT: B 93 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6711 (m-10) REVERT: B 152 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: B 183 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.8112 (ptm160) REVERT: B 281 LYS cc_start: 0.8394 (mttp) cc_final: 0.8153 (mttt) REVERT: B 344 ASP cc_start: 0.8647 (t0) cc_final: 0.8445 (t70) REVERT: B 427 MET cc_start: 0.9006 (mtm) cc_final: 0.8589 (mtm) REVERT: B 434 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6958 (tp) REVERT: B 436 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7592 (mtpp) REVERT: B 518 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8162 (tppt) REVERT: E 42 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6616 (mmtm) REVERT: C 11 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7289 (tmtt) REVERT: C 13 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7928 (mmp) REVERT: A 56 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: A 375 LYS cc_start: 0.8657 (tttm) cc_final: 0.8448 (tttp) REVERT: A 434 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8239 (mmpt) REVERT: A 435 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: A 459 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7018 (tmm-80) outliers start: 47 outliers final: 22 residues processed: 149 average time/residue: 0.6983 time to fit residues: 108.9672 Evaluate side-chains 145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 459 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN B 189 GLN A 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.116071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.095725 restraints weight = 11400.658| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.64 r_work: 0.2881 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9458 Z= 0.132 Angle : 0.592 6.800 12787 Z= 0.320 Chirality : 0.045 0.179 1428 Planarity : 0.005 0.048 1619 Dihedral : 11.293 73.360 1423 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.84 % Allowed : 8.93 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.24), residues: 1154 helix: 0.74 (0.23), residues: 527 sheet: 0.24 (0.49), residues: 117 loop : -1.74 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 20 TYR 0.015 0.001 TYR B 235 PHE 0.014 0.001 PHE A 209 TRP 0.017 0.001 TRP B 134 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9457) covalent geometry : angle 0.59209 (12787) hydrogen bonds : bond 0.05428 ( 419) hydrogen bonds : angle 4.81617 ( 1173) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.350 Fit side-chains REVERT: B 93 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.6729 (m-10) REVERT: B 150 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: B 152 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: B 189 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6923 (mm-40) REVERT: B 197 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8168 (tp30) REVERT: B 260 GLU cc_start: 0.8443 (tt0) cc_final: 0.8199 (tt0) REVERT: B 427 MET cc_start: 0.8728 (mtm) cc_final: 0.8386 (mtm) REVERT: B 434 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.6641 (tp) REVERT: B 518 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7787 (tppt) REVERT: B 530 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: D 19 SER cc_start: 0.8949 (m) cc_final: 0.8647 (m) REVERT: C 11 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7155 (mptt) REVERT: A 56 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: A 107 ASN cc_start: 0.8671 (p0) cc_final: 0.8386 (p0) REVERT: A 205 ASP cc_start: 0.8557 (m-30) cc_final: 0.8276 (m-30) REVERT: A 434 LYS cc_start: 0.8757 (mmtm) cc_final: 0.8267 (mmpt) REVERT: A 435 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7129 (mm-30) outliers start: 28 outliers final: 9 residues processed: 140 average time/residue: 0.7115 time to fit residues: 104.6008 Evaluate side-chains 127 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 34 optimal weight: 0.0980 chunk 95 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 GLN A 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.113804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.093165 restraints weight = 11450.108| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.65 r_work: 0.2824 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9458 Z= 0.157 Angle : 0.612 8.068 12787 Z= 0.326 Chirality : 0.047 0.197 1428 Planarity : 0.005 0.051 1619 Dihedral : 10.128 71.149 1365 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.93 % Allowed : 12.18 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.25), residues: 1154 helix: 1.16 (0.23), residues: 530 sheet: 0.25 (0.49), residues: 117 loop : -1.63 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 81 TYR 0.017 0.002 TYR A 166 PHE 0.017 0.002 PHE A 138 TRP 0.013 0.001 TRP B 134 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9457) covalent geometry : angle 0.61193 (12787) hydrogen bonds : bond 0.05841 ( 419) hydrogen bonds : angle 4.61028 ( 1173) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.309 Fit side-chains REVERT: B 93 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.6745 (m-10) REVERT: B 150 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: B 152 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8488 (pm20) REVERT: B 197 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8242 (tp30) REVERT: B 427 MET cc_start: 0.8794 (mtm) cc_final: 0.8443 (mtm) REVERT: B 518 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7954 (tppt) REVERT: B 530 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: E 9 VAL cc_start: 0.5583 (OUTLIER) cc_final: 0.4948 (t) REVERT: D 19 SER cc_start: 0.9035 (m) cc_final: 0.8727 (m) REVERT: A 56 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: A 107 ASN cc_start: 0.8660 (p0) cc_final: 0.8445 (p0) REVERT: A 205 ASP cc_start: 0.8531 (m-30) cc_final: 0.8257 (m-30) REVERT: A 422 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8355 (mmm-85) REVERT: A 434 LYS cc_start: 0.8810 (mmtm) cc_final: 0.8280 (mmpt) REVERT: A 435 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7430 (mm-30) outliers start: 19 outliers final: 8 residues processed: 121 average time/residue: 0.7603 time to fit residues: 96.3243 Evaluate side-chains 124 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN B 440 GLN B 463 ASN A 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.110953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.090155 restraints weight = 11538.195| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.67 r_work: 0.2785 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9458 Z= 0.221 Angle : 0.688 8.682 12787 Z= 0.364 Chirality : 0.050 0.207 1428 Planarity : 0.005 0.056 1619 Dihedral : 9.764 69.312 1357 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.05 % Allowed : 12.39 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.25), residues: 1154 helix: 1.18 (0.23), residues: 526 sheet: 0.19 (0.48), residues: 122 loop : -1.68 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 136 TYR 0.018 0.002 TYR B 235 PHE 0.023 0.002 PHE A 138 TRP 0.012 0.002 TRP B 134 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 9457) covalent geometry : angle 0.68798 (12787) hydrogen bonds : bond 0.06805 ( 419) hydrogen bonds : angle 4.67604 ( 1173) Misc. bond : bond 0.00076 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.333 Fit side-chains REVERT: B 93 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.6566 (m-10) REVERT: B 150 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: B 152 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8476 (pm20) REVERT: B 197 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8231 (tp30) REVERT: B 315 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8904 (mt-10) REVERT: B 427 MET cc_start: 0.8795 (mtm) cc_final: 0.8524 (mtm) REVERT: B 436 LYS cc_start: 0.8439 (mtmm) cc_final: 0.7744 (mtpt) REVERT: B 518 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8000 (tppt) REVERT: B 530 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: A 144 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 205 ASP cc_start: 0.8562 (m-30) cc_final: 0.8298 (m-30) REVERT: A 434 LYS cc_start: 0.8885 (mmtm) cc_final: 0.8372 (mmpt) outliers start: 30 outliers final: 14 residues processed: 127 average time/residue: 0.7110 time to fit residues: 94.8726 Evaluate side-chains 129 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 70 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: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.114056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.093453 restraints weight = 11399.167| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.65 r_work: 0.2810 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9458 Z= 0.154 Angle : 0.604 7.740 12787 Z= 0.322 Chirality : 0.046 0.200 1428 Planarity : 0.005 0.053 1619 Dihedral : 8.894 68.915 1348 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.25 % Allowed : 13.10 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.25), residues: 1154 helix: 1.43 (0.23), residues: 526 sheet: 0.03 (0.47), residues: 124 loop : -1.66 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 271 TYR 0.018 0.002 TYR B 235 PHE 0.016 0.002 PHE A 209 TRP 0.014 0.002 TRP B 134 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9457) covalent geometry : angle 0.60404 (12787) hydrogen bonds : bond 0.05597 ( 419) hydrogen bonds : angle 4.51261 ( 1173) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.364 Fit side-chains REVERT: B 93 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6557 (m-10) REVERT: B 150 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: B 152 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8510 (pm20) REVERT: B 190 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8337 (mt-10) REVERT: B 197 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8238 (tp30) REVERT: B 427 MET cc_start: 0.8744 (mtm) cc_final: 0.8467 (mtm) REVERT: B 436 LYS cc_start: 0.8439 (mtmm) cc_final: 0.7743 (mtpt) REVERT: B 518 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7965 (tppt) REVERT: B 530 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: D 19 SER cc_start: 0.9122 (m) cc_final: 0.8830 (m) REVERT: A 58 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7444 (mp0) REVERT: A 107 ASN cc_start: 0.8658 (p0) cc_final: 0.8437 (p0) REVERT: A 205 ASP cc_start: 0.8545 (m-30) cc_final: 0.8333 (m-30) REVERT: A 422 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7707 (mtm-85) REVERT: A 434 LYS cc_start: 0.8896 (mmtm) cc_final: 0.8431 (mmpt) outliers start: 32 outliers final: 19 residues processed: 131 average time/residue: 0.7152 time to fit residues: 98.4842 Evaluate side-chains 136 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 12 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN B 262 ASN B 440 GLN A 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.112789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.092039 restraints weight = 11488.499| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.67 r_work: 0.2808 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9458 Z= 0.160 Angle : 0.609 7.691 12787 Z= 0.323 Chirality : 0.046 0.198 1428 Planarity : 0.005 0.053 1619 Dihedral : 8.693 68.387 1348 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.55 % Allowed : 13.20 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.25), residues: 1154 helix: 1.52 (0.23), residues: 526 sheet: -0.12 (0.46), residues: 126 loop : -1.61 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 271 TYR 0.018 0.002 TYR B 235 PHE 0.016 0.002 PHE A 209 TRP 0.013 0.002 TRP B 134 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9457) covalent geometry : angle 0.60888 (12787) hydrogen bonds : bond 0.05586 ( 419) hydrogen bonds : angle 4.47250 ( 1173) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.296 Fit side-chains REVERT: B 93 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.6477 (m-10) REVERT: B 150 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: B 152 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8549 (pm20) REVERT: B 190 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8320 (mt-10) REVERT: B 197 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8217 (tp30) REVERT: B 427 MET cc_start: 0.8757 (mtm) cc_final: 0.8481 (mtm) REVERT: B 434 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6610 (tp) REVERT: B 475 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.7857 (mtp) REVERT: B 530 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: D 19 SER cc_start: 0.9054 (m) cc_final: 0.8762 (m) REVERT: C 11 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7119 (mptt) REVERT: A 58 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7463 (mp0) REVERT: A 107 ASN cc_start: 0.8638 (p0) cc_final: 0.8430 (p0) REVERT: A 144 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8355 (p) REVERT: A 205 ASP cc_start: 0.8557 (m-30) cc_final: 0.8298 (m-30) REVERT: A 422 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7563 (mtm-85) REVERT: A 423 SER cc_start: 0.8737 (m) cc_final: 0.8145 (p) REVERT: A 434 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8426 (mmpt) REVERT: A 435 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8015 (mm-30) outliers start: 35 outliers final: 17 residues processed: 138 average time/residue: 0.6673 time to fit residues: 96.7404 Evaluate side-chains 139 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.0010 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.117759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.097563 restraints weight = 11475.295| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.62 r_work: 0.2859 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9458 Z= 0.112 Angle : 0.538 8.124 12787 Z= 0.287 Chirality : 0.043 0.193 1428 Planarity : 0.005 0.067 1619 Dihedral : 8.241 68.018 1344 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.05 % Allowed : 14.01 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.25), residues: 1154 helix: 1.82 (0.24), residues: 528 sheet: -0.02 (0.45), residues: 124 loop : -1.52 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 271 TYR 0.012 0.001 TYR B 235 PHE 0.013 0.001 PHE B 121 TRP 0.014 0.001 TRP B 134 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9457) covalent geometry : angle 0.53843 (12787) hydrogen bonds : bond 0.04411 ( 419) hydrogen bonds : angle 4.30606 ( 1173) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.275 Fit side-chains REVERT: B 93 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6549 (m-10) REVERT: B 109 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8217 (mmtt) REVERT: B 150 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8070 (mt-10) REVERT: B 152 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8566 (pm20) REVERT: B 197 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8229 (tp30) REVERT: B 427 MET cc_start: 0.8698 (mtm) cc_final: 0.8428 (mtm) REVERT: B 434 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.6728 (tp) REVERT: B 475 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.7575 (mtp) REVERT: B 530 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: D 19 SER cc_start: 0.9010 (m) cc_final: 0.8691 (m) REVERT: C 11 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.6664 (pptt) REVERT: A 205 ASP cc_start: 0.8526 (m-30) cc_final: 0.8282 (m-30) REVERT: A 423 SER cc_start: 0.8741 (m) cc_final: 0.8182 (p) REVERT: A 434 LYS cc_start: 0.8885 (mmtm) cc_final: 0.8484 (mmpt) REVERT: A 435 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8046 (mm-30) outliers start: 30 outliers final: 13 residues processed: 137 average time/residue: 0.6544 time to fit residues: 94.4043 Evaluate side-chains 135 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 488 LYS Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 41 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 45 optimal weight: 0.0010 chunk 102 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.117761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.097298 restraints weight = 11399.309| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.65 r_work: 0.2873 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9458 Z= 0.111 Angle : 0.537 8.122 12787 Z= 0.285 Chirality : 0.043 0.192 1428 Planarity : 0.004 0.056 1619 Dihedral : 7.845 66.898 1341 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.44 % Allowed : 14.52 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.26), residues: 1154 helix: 1.98 (0.24), residues: 528 sheet: 0.09 (0.46), residues: 124 loop : -1.41 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 271 TYR 0.012 0.001 TYR B 235 PHE 0.016 0.001 PHE B 121 TRP 0.012 0.001 TRP B 134 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9457) covalent geometry : angle 0.53690 (12787) hydrogen bonds : bond 0.04184 ( 419) hydrogen bonds : angle 4.22310 ( 1173) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.254 Fit side-chains REVERT: B 93 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6494 (m-10) REVERT: B 109 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8105 (mmtt) REVERT: B 150 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8077 (mt-10) REVERT: B 152 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8574 (pm20) REVERT: B 427 MET cc_start: 0.8674 (mtm) cc_final: 0.8395 (mtm) REVERT: B 434 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.6755 (tp) REVERT: B 475 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.7525 (mtp) REVERT: B 530 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: D 19 SER cc_start: 0.8962 (m) cc_final: 0.8625 (m) REVERT: D 39 SER cc_start: 0.8378 (m) cc_final: 0.8091 (t) REVERT: D 118 LYS cc_start: 0.8915 (mttp) cc_final: 0.8640 (mttp) REVERT: C 11 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6656 (pptt) REVERT: A 205 ASP cc_start: 0.8561 (m-30) cc_final: 0.8321 (m-30) REVERT: A 407 GLN cc_start: 0.7790 (mt0) cc_final: 0.7515 (mt0) REVERT: A 423 SER cc_start: 0.8750 (m) cc_final: 0.8191 (p) REVERT: A 434 LYS cc_start: 0.8875 (mmtm) cc_final: 0.8466 (mmpt) REVERT: A 435 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8050 (mm-30) outliers start: 24 outliers final: 8 residues processed: 128 average time/residue: 0.6811 time to fit residues: 91.8042 Evaluate side-chains 129 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.095761 restraints weight = 11445.377| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.66 r_work: 0.2865 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9458 Z= 0.114 Angle : 0.544 8.674 12787 Z= 0.289 Chirality : 0.044 0.187 1428 Planarity : 0.004 0.050 1619 Dihedral : 7.520 65.862 1338 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.13 % Allowed : 15.03 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.26), residues: 1154 helix: 2.02 (0.24), residues: 528 sheet: -0.01 (0.46), residues: 126 loop : -1.35 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 271 TYR 0.013 0.001 TYR B 235 PHE 0.015 0.001 PHE B 121 TRP 0.012 0.001 TRP B 134 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9457) covalent geometry : angle 0.54403 (12787) hydrogen bonds : bond 0.04237 ( 419) hydrogen bonds : angle 4.20772 ( 1173) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.355 Fit side-chains REVERT: B 93 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6515 (m-10) REVERT: B 109 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8133 (mmtt) REVERT: B 116 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8544 (mt0) REVERT: B 150 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8060 (mt-10) REVERT: B 152 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: B 427 MET cc_start: 0.8674 (mtm) cc_final: 0.8396 (mtm) REVERT: B 434 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.6759 (tp) REVERT: B 475 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.7585 (mtp) REVERT: B 530 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: D 19 SER cc_start: 0.8945 (m) cc_final: 0.8597 (m) REVERT: D 39 SER cc_start: 0.8377 (m) cc_final: 0.8063 (t) REVERT: C 11 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7095 (mptt) REVERT: A 144 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8330 (p) REVERT: A 205 ASP cc_start: 0.8578 (m-30) cc_final: 0.8325 (m-30) REVERT: A 407 GLN cc_start: 0.7818 (mt0) cc_final: 0.7486 (mt0) REVERT: A 423 SER cc_start: 0.8746 (m) cc_final: 0.8173 (p) REVERT: A 434 LYS cc_start: 0.8865 (mmtm) cc_final: 0.8417 (mmpt) REVERT: A 435 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8054 (mm-30) outliers start: 21 outliers final: 8 residues processed: 126 average time/residue: 0.6805 time to fit residues: 90.3353 Evaluate side-chains 131 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN A 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.095688 restraints weight = 11426.601| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.66 r_work: 0.2870 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9458 Z= 0.114 Angle : 0.544 7.826 12787 Z= 0.289 Chirality : 0.044 0.195 1428 Planarity : 0.004 0.049 1619 Dihedral : 7.376 64.397 1338 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.83 % Allowed : 15.84 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.26), residues: 1154 helix: 2.05 (0.24), residues: 528 sheet: -0.01 (0.46), residues: 126 loop : -1.32 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 271 TYR 0.012 0.001 TYR B 235 PHE 0.015 0.001 PHE B 121 TRP 0.012 0.001 TRP B 134 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9457) covalent geometry : angle 0.54362 (12787) hydrogen bonds : bond 0.04231 ( 419) hydrogen bonds : angle 4.19809 ( 1173) Misc. bond : bond 0.00033 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.224 Fit side-chains REVERT: B 93 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.6497 (m-10) REVERT: B 109 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8122 (mmtt) REVERT: B 150 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8066 (mt-10) REVERT: B 152 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8493 (pm20) REVERT: B 427 MET cc_start: 0.8678 (mtm) cc_final: 0.8404 (mtm) REVERT: B 434 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.6698 (tp) REVERT: B 475 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.7603 (mtp) REVERT: B 530 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: D 1 MET cc_start: 0.8246 (mpp) cc_final: 0.7753 (mpp) REVERT: D 19 SER cc_start: 0.8970 (m) cc_final: 0.8631 (m) REVERT: D 39 SER cc_start: 0.8376 (m) cc_final: 0.8039 (t) REVERT: C 11 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7150 (mptt) REVERT: A 144 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8323 (p) REVERT: A 205 ASP cc_start: 0.8587 (m-30) cc_final: 0.8331 (m-30) REVERT: A 407 GLN cc_start: 0.7830 (mt0) cc_final: 0.7443 (mt0) REVERT: A 423 SER cc_start: 0.8749 (m) cc_final: 0.8178 (p) REVERT: A 434 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8394 (mmpt) REVERT: A 435 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8090 (mm-30) outliers start: 18 outliers final: 9 residues processed: 127 average time/residue: 0.6694 time to fit residues: 89.5919 Evaluate side-chains 131 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN A 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.114044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.093311 restraints weight = 11357.291| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.65 r_work: 0.2830 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9458 Z= 0.147 Angle : 0.593 8.017 12787 Z= 0.315 Chirality : 0.046 0.201 1428 Planarity : 0.005 0.050 1619 Dihedral : 7.535 63.693 1338 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.44 % Allowed : 15.43 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.25), residues: 1154 helix: 1.82 (0.23), residues: 534 sheet: 0.06 (0.46), residues: 124 loop : -1.37 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 271 TYR 0.017 0.002 TYR B 235 PHE 0.016 0.001 PHE B 121 TRP 0.011 0.001 TRP B 134 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9457) covalent geometry : angle 0.59347 (12787) hydrogen bonds : bond 0.05122 ( 419) hydrogen bonds : angle 4.32045 ( 1173) Misc. bond : bond 0.00049 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2996.56 seconds wall clock time: 51 minutes 39.60 seconds (3099.60 seconds total)