Starting phenix.real_space_refine on Fri Feb 6 08:03:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hiq_52198/02_2026/9hiq_52198_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hiq_52198/02_2026/9hiq_52198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hiq_52198/02_2026/9hiq_52198_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hiq_52198/02_2026/9hiq_52198_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hiq_52198/02_2026/9hiq_52198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hiq_52198/02_2026/9hiq_52198.map" } resolution = 4.02 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= 1.000 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 16 5.49 5 S 74 5.16 5 C 14511 2.51 5 N 4156 2.21 5 O 4491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23248 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3283 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 424} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 2, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3381 Classifications: {'peptide': 451} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4824 Classifications: {'peptide': 622} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 34, 'TRANS': 587} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4834 Classifications: {'peptide': 622} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 34, 'TRANS': 587} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3387 Classifications: {'peptide': 451} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3305 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 4, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.69, per 1000 atoms: 0.29 Number of scatterers: 23248 At special positions: 0 Unit cell: (224.842, 199.015, 123.055, 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 74 16.00 P 16 15.00 O 4491 8.00 N 4156 7.00 C 14511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.4 seconds 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5542 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 20 sheets defined 47.4% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 86 through 100 removed outlier: 3.747A pdb=" N ILE A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 118 removed outlier: 3.636A pdb=" N ALA A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.588A pdb=" N ALA A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 150 Processing helix chain 'A' and resid 150 through 171 removed outlier: 3.899A pdb=" N ARG A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 210 Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.977A pdb=" N GLU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 Processing helix chain 'A' and resid 279 through 296 removed outlier: 4.269A pdb=" N GLU A 294 " --> pdb=" O TRP A 290 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN A 295 " --> pdb=" O GLN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.517A pdb=" N ILE A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 removed outlier: 3.857A pdb=" N ILE A 321 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 322 " --> pdb=" O PRO A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.791A pdb=" N THR A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 removed outlier: 3.791A pdb=" N MET A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 413 Processing helix chain 'A' and resid 415 through 433 removed outlier: 4.281A pdb=" N ILE A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 449 removed outlier: 3.576A pdb=" N LEU A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 38 Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.719A pdb=" N GLU B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 143 removed outlier: 3.574A pdb=" N ASP B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 176 removed outlier: 3.759A pdb=" N ARG B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALA B 173 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 207 removed outlier: 4.007A pdb=" N ALA B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 196 " --> pdb=" O GLN B 192 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 238 Processing helix chain 'B' and resid 279 through 296 removed outlier: 3.550A pdb=" N GLU B 294 " --> pdb=" O TRP B 290 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 317 through 324 removed outlier: 3.607A pdb=" N ILE B 321 " --> pdb=" O TRP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 364 through 376 removed outlier: 4.107A pdb=" N MET B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 396 removed outlier: 3.652A pdb=" N HIS B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 411 removed outlier: 3.920A pdb=" N ALA B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N HIS B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 removed outlier: 3.758A pdb=" N LEU B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 56 through 66 Processing helix chain 'C' and resid 69 through 75 removed outlier: 3.985A pdb=" N ASP C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.641A pdb=" N ASN C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 190 removed outlier: 3.967A pdb=" N SER C 184 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG C 185 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.689A pdb=" N VAL C 214 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.766A pdb=" N GLN C 235 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS C 236 " --> pdb=" O ALA C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 236' Processing helix chain 'C' and resid 248 through 258 removed outlier: 3.516A pdb=" N HIS C 252 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 287 removed outlier: 3.561A pdb=" N LYS C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 377 through 396 removed outlier: 4.036A pdb=" N ALA C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 419 removed outlier: 3.513A pdb=" N VAL C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 433 Processing helix chain 'C' and resid 443 through 455 removed outlier: 5.754A pdb=" N GLU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE C 451 " --> pdb=" O ARG C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 482 Processing helix chain 'C' and resid 491 through 498 removed outlier: 3.733A pdb=" N VAL C 495 " --> pdb=" O ALA C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 513 Processing helix chain 'C' and resid 519 through 525 removed outlier: 3.821A pdb=" N LEU C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 560 removed outlier: 4.202A pdb=" N GLN C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLY C 550 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR C 551 " --> pdb=" O LYS C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 Processing helix chain 'C' and resid 575 through 579 Processing helix chain 'C' and resid 583 through 594 Processing helix chain 'C' and resid 597 through 603 Processing helix chain 'C' and resid 608 through 623 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 56 through 66 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 100 through 114 removed outlier: 3.628A pdb=" N ASN D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 190 removed outlier: 3.968A pdb=" N SER D 184 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 185 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 190 " --> pdb=" O ARG D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 211 through 215 removed outlier: 3.682A pdb=" N VAL D 214 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 236 removed outlier: 3.745A pdb=" N GLN D 235 " --> pdb=" O ASN D 232 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS D 236 " --> pdb=" O ALA D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 232 through 236' Processing helix chain 'D' and resid 248 through 258 removed outlier: 3.516A pdb=" N HIS D 252 " --> pdb=" O ASN D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 287 removed outlier: 3.573A pdb=" N LYS D 283 " --> pdb=" O SER D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 327 Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 377 through 396 removed outlier: 4.033A pdb=" N ALA D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 419 removed outlier: 3.512A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 433 Processing helix chain 'D' and resid 443 through 455 removed outlier: 5.734A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE D 451 " --> pdb=" O ARG D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 482 Processing helix chain 'D' and resid 491 through 498 removed outlier: 3.693A pdb=" N VAL D 495 " --> pdb=" O ALA D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 513 Processing helix chain 'D' and resid 519 through 525 removed outlier: 3.804A pdb=" N LEU D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 560 removed outlier: 4.202A pdb=" N GLN D 541 " --> pdb=" O GLN D 537 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL D 542 " --> pdb=" O ALA D 538 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLY D 550 " --> pdb=" O VAL D 546 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR D 551 " --> pdb=" O LYS D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 Processing helix chain 'D' and resid 575 through 579 Processing helix chain 'D' and resid 583 through 594 Processing helix chain 'D' and resid 597 through 603 Processing helix chain 'D' and resid 608 through 623 Processing helix chain 'E' and resid 28 through 38 Processing helix chain 'E' and resid 86 through 99 Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.718A pdb=" N GLU E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 143 removed outlier: 3.585A pdb=" N ASP E 134 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER E 136 " --> pdb=" O LEU E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 176 removed outlier: 3.764A pdb=" N ARG E 155 " --> pdb=" O ALA E 151 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL E 156 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ASN E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA E 172 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALA E 173 " --> pdb=" O TYR E 169 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 207 removed outlier: 3.823A pdb=" N ALA E 191 " --> pdb=" O GLY E 187 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL E 196 " --> pdb=" O GLN E 192 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA E 202 " --> pdb=" O ALA E 198 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA E 207 " --> pdb=" O VAL E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 238 Processing helix chain 'E' and resid 279 through 296 removed outlier: 3.567A pdb=" N GLU E 294 " --> pdb=" O TRP E 290 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 317 Processing helix chain 'E' and resid 317 through 324 removed outlier: 3.610A pdb=" N ILE E 321 " --> pdb=" O TRP E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 341 Processing helix chain 'E' and resid 364 through 376 removed outlier: 4.110A pdb=" N MET E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 396 removed outlier: 3.715A pdb=" N HIS E 392 " --> pdb=" O ALA E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 411 removed outlier: 3.952A pdb=" N ALA E 400 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N HIS E 402 " --> pdb=" O GLN E 398 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU E 410 " --> pdb=" O GLY E 406 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU E 411 " --> pdb=" O LYS E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 431 removed outlier: 3.764A pdb=" N LEU E 419 " --> pdb=" O ALA E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 450 Processing helix chain 'F' and resid 28 through 38 Processing helix chain 'F' and resid 86 through 100 removed outlier: 3.753A pdb=" N ILE F 100 " --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 118 removed outlier: 3.633A pdb=" N ALA F 115 " --> pdb=" O PHE F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 130 removed outlier: 3.580A pdb=" N ALA F 126 " --> pdb=" O ASP F 122 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 150 removed outlier: 3.637A pdb=" N GLY F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 173 removed outlier: 3.507A pdb=" N ALA F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 210 removed outlier: 3.545A pdb=" N ILE F 197 " --> pdb=" O LEU F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 238 Processing helix chain 'F' and resid 279 through 296 removed outlier: 4.264A pdb=" N GLU F 294 " --> pdb=" O TRP F 290 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN F 295 " --> pdb=" O GLN F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 317 removed outlier: 3.521A pdb=" N ILE F 316 " --> pdb=" O ASP F 312 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP F 317 " --> pdb=" O PRO F 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 312 through 317' Processing helix chain 'F' and resid 317 through 324 removed outlier: 3.866A pdb=" N ILE F 321 " --> pdb=" O TRP F 317 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 341 removed outlier: 3.798A pdb=" N THR F 340 " --> pdb=" O LYS F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 376 removed outlier: 3.702A pdb=" N MET F 376 " --> pdb=" O LEU F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 414 Processing helix chain 'F' and resid 415 through 433 removed outlier: 4.280A pdb=" N ILE F 433 " --> pdb=" O ASN F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 449 removed outlier: 3.585A pdb=" N LEU F 443 " --> pdb=" O SER F 439 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER F 449 " --> pdb=" O ARG F 445 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.736A pdb=" N ASP A 47 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 49 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY A 62 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP A 60 " --> pdb=" O PHE A 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 259 removed outlier: 3.706A pdb=" N LEU A 255 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 219 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 299 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A 333 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE A 301 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASN A 335 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL A 303 " --> pdb=" O ASN A 335 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 353 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.656A pdb=" N ASP B 47 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 62 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP B 60 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 261 removed outlier: 3.734A pdb=" N MET B 217 " --> pdb=" O PRO B 265 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS B 218 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LEU B 300 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 220 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N MET B 302 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA B 222 " --> pdb=" O MET B 302 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N ASP B 304 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 353 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 345 " --> pdb=" O ARG B 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 122 removed outlier: 6.413A pdb=" N THR C 32 " --> pdb=" O MET C 119 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE C 121 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU C 34 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL C 9 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU C 35 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE C 11 " --> pdb=" O LEU C 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 50 through 52 removed outlier: 6.353A pdb=" N ALA C 94 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE C 83 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG C 96 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE C 81 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN C 98 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 130 removed outlier: 6.947A pdb=" N VAL C 139 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU C 128 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLY C 137 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 130 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL C 135 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 168 through 171 Processing sheet with id=AA9, first strand: chain 'C' and resid 216 through 218 removed outlier: 3.670A pdb=" N ALA C 216 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS C 242 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG C 204 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 353 through 354 removed outlier: 3.702A pdb=" N GLU C 358 " --> pdb=" O LYS C 354 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 118 through 122 removed outlier: 6.412A pdb=" N THR D 32 " --> pdb=" O MET D 119 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE D 121 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU D 34 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL D 9 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU D 35 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE D 11 " --> pdb=" O LEU D 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 50 through 52 removed outlier: 6.266A pdb=" N ALA D 94 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE D 83 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG D 96 " --> pdb=" O PHE D 81 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE D 81 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN D 98 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 125 through 130 removed outlier: 6.949A pdb=" N VAL D 139 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU D 128 " --> pdb=" O GLY D 137 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLY D 137 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL D 130 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL D 135 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 168 through 171 Processing sheet with id=AB6, first strand: chain 'D' and resid 216 through 218 removed outlier: 3.677A pdb=" N ALA D 216 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG D 338 " --> pdb=" O ARG D 204 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP D 206 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE D 336 " --> pdb=" O ASP D 206 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 353 through 354 removed outlier: 3.703A pdb=" N GLU D 358 " --> pdb=" O LYS D 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 47 through 52 removed outlier: 3.650A pdb=" N ASP E 47 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 49 " --> pdb=" O GLY E 62 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 62 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP E 60 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E 8 " --> pdb=" O ARG E 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 255 through 261 removed outlier: 3.737A pdb=" N MET E 217 " --> pdb=" O PRO E 265 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS E 218 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LEU E 300 " --> pdb=" O LYS E 218 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL E 220 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N MET E 302 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA E 222 " --> pdb=" O MET E 302 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASP E 304 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE E 330 " --> pdb=" O ALA E 353 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N ILE E 355 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL E 332 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG E 356 " --> pdb=" O GLY E 345 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY E 345 " --> pdb=" O ARG E 356 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 47 through 52 removed outlier: 3.742A pdb=" N ASP F 47 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU F 49 " --> pdb=" O GLY F 62 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY F 62 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP F 60 " --> pdb=" O PHE F 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 255 through 259 removed outlier: 3.701A pdb=" N LEU F 255 " --> pdb=" O ASP F 270 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL F 219 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL F 299 " --> pdb=" O THR F 331 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL F 333 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE F 301 " --> pdb=" O VAL F 333 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN F 335 " --> pdb=" O PHE F 301 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL F 303 " --> pdb=" O ASN F 335 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA F 353 " --> pdb=" O ILE F 330 " (cutoff:3.500A) 1078 hydrogen bonds defined for protein. 3114 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.59 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8031 1.34 - 1.46: 2500 1.46 - 1.57: 12947 1.57 - 1.69: 28 1.69 - 1.81: 136 Bond restraints: 23642 Sorted by residual: bond pdb=" N3B GNP F 501 " pdb=" PG GNP F 501 " ideal model delta sigma weight residual 1.801 1.608 0.193 2.00e-02 2.50e+03 9.27e+01 bond pdb=" N3B GNP E 501 " pdb=" PG GNP E 501 " ideal model delta sigma weight residual 1.801 1.629 0.172 2.00e-02 2.50e+03 7.42e+01 bond pdb=" N3B GNP A 501 " pdb=" PG GNP A 501 " ideal model delta sigma weight residual 1.801 1.630 0.171 2.00e-02 2.50e+03 7.34e+01 bond pdb=" N3B GNP B 501 " pdb=" PG GNP B 501 " ideal model delta sigma weight residual 1.801 1.634 0.167 2.00e-02 2.50e+03 6.93e+01 bond pdb=" O3A GNP F 501 " pdb=" PB GNP F 501 " ideal model delta sigma weight residual 1.687 1.576 0.111 2.00e-02 2.50e+03 3.06e+01 ... (remaining 23637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 31960 3.01 - 6.01: 116 6.01 - 9.02: 14 9.02 - 12.02: 5 12.02 - 15.03: 2 Bond angle restraints: 32097 Sorted by residual: angle pdb=" PB GNP F 501 " pdb=" N3B GNP F 501 " pdb=" PG GNP F 501 " ideal model delta sigma weight residual 123.35 108.32 15.03 3.00e+00 1.11e-01 2.51e+01 angle pdb=" N3B GNP F 501 " pdb=" PG GNP F 501 " pdb=" O1G GNP F 501 " ideal model delta sigma weight residual 101.20 113.73 -12.53 3.00e+00 1.11e-01 1.74e+01 angle pdb=" N3B GNP E 501 " pdb=" PG GNP E 501 " pdb=" O1G GNP E 501 " ideal model delta sigma weight residual 101.20 111.85 -10.65 3.00e+00 1.11e-01 1.26e+01 angle pdb=" N3B GNP B 501 " pdb=" PG GNP B 501 " pdb=" O1G GNP B 501 " ideal model delta sigma weight residual 101.20 111.78 -10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O1G GNP F 501 " pdb=" PG GNP F 501 " pdb=" O3G GNP F 501 " ideal model delta sigma weight residual 114.34 104.08 10.26 3.00e+00 1.11e-01 1.17e+01 ... (remaining 32092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 13477 17.69 - 35.38: 758 35.38 - 53.07: 130 53.07 - 70.75: 46 70.75 - 88.44: 16 Dihedral angle restraints: 14427 sinusoidal: 5822 harmonic: 8605 Sorted by residual: dihedral pdb=" CA THR D 527 " pdb=" C THR D 527 " pdb=" N PRO D 528 " pdb=" CA PRO D 528 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ALA A 191 " pdb=" C ALA A 191 " pdb=" N GLN A 192 " pdb=" CA GLN A 192 " ideal model delta harmonic sigma weight residual 180.00 162.76 17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ALA C 97 " pdb=" C ALA C 97 " pdb=" N GLN C 98 " pdb=" CA GLN C 98 " ideal model delta harmonic sigma weight residual 180.00 164.18 15.82 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 14424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2523 0.031 - 0.062: 751 0.062 - 0.093: 220 0.093 - 0.124: 142 0.124 - 0.155: 14 Chirality restraints: 3650 Sorted by residual: chirality pdb=" CA LEU D 192 " pdb=" N LEU D 192 " pdb=" C LEU D 192 " pdb=" CB LEU D 192 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.15 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" C1B FAD C 701 " pdb=" C2B FAD C 701 " pdb=" N9A FAD C 701 " pdb=" O4B FAD C 701 " both_signs ideal model delta sigma weight residual False 2.35 2.49 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ARG C 193 " pdb=" N ARG C 193 " pdb=" C ARG C 193 " pdb=" CB ARG C 193 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 3647 not shown) Planarity restraints: 4231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 160 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.81e+00 pdb=" C VAL E 160 " -0.023 2.00e-02 2.50e+03 pdb=" O VAL E 160 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU E 161 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 160 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C VAL B 160 " -0.023 2.00e-02 2.50e+03 pdb=" O VAL B 160 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU B 161 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 152 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" C PHE A 152 " 0.022 2.00e-02 2.50e+03 pdb=" O PHE A 152 " -0.008 2.00e-02 2.50e+03 pdb=" N SER A 153 " -0.007 2.00e-02 2.50e+03 ... (remaining 4228 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 380 2.62 - 3.19: 22884 3.19 - 3.76: 35768 3.76 - 4.33: 48818 4.33 - 4.90: 79639 Nonbonded interactions: 187489 Sorted by model distance: nonbonded pdb=" NH2 ARG D 275 " pdb=" OD1 ASP E 440 " model vdw 2.053 3.120 nonbonded pdb=" OH TYR E 48 " pdb=" OE1 GLN E 61 " model vdw 2.054 3.040 nonbonded pdb=" OD1 ASP B 440 " pdb=" NH2 ARG C 275 " model vdw 2.056 3.120 nonbonded pdb=" OH TYR B 48 " pdb=" OE1 GLN B 61 " model vdw 2.061 3.040 nonbonded pdb=" NH2 ARG C 208 " pdb=" O LEU D 118 " model vdw 2.080 3.120 ... (remaining 187484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 9 or (resid 10 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 15 or (resid 16 and (name \ N or name CA or name C or name O or name CB )) or resid 17 through 38 or (resid \ 39 and (name N or name CA or name C or name O or name CB )) or resid 40 through \ 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or res \ id 45 through 142 or (resid 143 through 144 and (name N or name CA or name C or \ name O or name CB )) or resid 145 through 188 or (resid 189 through 192 and (nam \ e N or name CA or name C or name O or name CB )) or resid 193 or (resid 194 and \ (name N or name CA or name C or name O or name CB )) or resid 195 through 203 or \ (resid 204 through 207 and (name N or name CA or name C or name O or name CB )) \ or resid 208 through 212 or (resid 213 through 214 and (name N or name CA or na \ me C or name O or name CB )) or resid 215 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 263 or (resid \ 264 and (name N or name CA or name C or name O or name CB )) or resid 265 throug \ h 287 or (resid 288 through 289 and (name N or name CA or name C or name O or na \ me CB )) or resid 290 through 355 or (resid 356 through 357 and (name N or name \ CA or name C or name O or name CB )) or resid 358 through 359 or (resid 360 and \ (name N or name CA or name C or name O or name CB )) or resid 361 through 376 or \ resid 380 through 382 or (resid 383 and (name N or name CA or name C or name O \ or name CB )) or resid 384 through 386 or (resid 387 through 388 and (name N or \ name CA or name C or name O or name CB )) or resid 389 through 402 or (resid 403 \ and (name N or name CA or name C or name O or name CB )) or resid 404 or (resid \ 405 and (name N or name CA or name C or name O or name CB )) or resid 406 throu \ gh 408 or (resid 409 and (name N or name CA or name C or name O or name CB )) or \ resid 410 through 501)) selection = (chain 'B' and (resid 1 through 7 or (resid 8 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 15 or (resid 16 and (name \ N or name CA or name C or name O or name CB )) or resid 17 through 41 or (resid \ 42 and (name N or name CA or name C or name O or name CB )) or resid 43 or (resi \ d 44 and (name N or name CA or name C or name O or name CB )) or resid 45 throug \ h 113 or (resid 114 through 115 and (name N or name CA or name C or name O or na \ me CB )) or resid 116 through 154 or (resid 155 and (name N or name CA or name C \ or name O or name CB )) or resid 156 through 162 or (resid 163 and (name N or n \ ame CA or name C or name O or name CB )) or resid 164 through 166 or (resid 167 \ and (name N or name CA or name C or name O or name CB )) or resid 168 through 17 \ 3 or (resid 187 through 192 and (name N or name CA or name C or name O or name C \ B )) or resid 193 or (resid 194 and (name N or name CA or name C or name O or na \ me CB )) or resid 195 through 203 or (resid 204 through 207 and (name N or name \ CA or name C or name O or name CB )) or resid 208 through 223 or (resid 224 and \ (name N or name CA or name C or name O or name CB )) or resid 225 through 232 or \ (resid 233 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 4 through 238 or (resid 239 through 242 and (name N or name CA or name C or name \ O or name CB )) or resid 243 through 287 or (resid 288 through 289 and (name N \ or name CA or name C or name O or name CB )) or resid 290 through 294 or (resid \ 295 through 296 and (name N or name CA or name C or name O or name CB )) or resi \ d 297 through 386 or (resid 387 through 388 and (name N or name CA or name C or \ name O or name CB )) or resid 389 through 393 or (resid 394 through 395 and (nam \ e N or name CA or name C or name O or name CB )) or resid 396 through 402 or (re \ sid 403 and (name N or name CA or name C or name O or name CB )) or resid 404 th \ rough 440 or (resid 441 and (name N or name CA or name C or name O or name CB )) \ or resid 442 through 444 or (resid 445 and (name N or name CA or name C or name \ O or name CB )) or resid 446 through 501)) selection = (chain 'E' and (resid 1 through 7 or (resid 8 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 41 or (resid 42 and (name \ N or name CA or name C or name O or name CB )) or resid 43 or (resid 44 and (nam \ e N or name CA or name C or name O or name CB )) or resid 45 through 113 or (res \ id 114 through 115 and (name N or name CA or name C or name O or name CB )) or r \ esid 116 through 154 or (resid 155 and (name N or name CA or name C or name O or \ name CB )) or resid 156 through 162 or (resid 163 and (name N or name CA or nam \ e C or name O or name CB )) or resid 164 through 166 or (resid 167 and (name N o \ r name CA or name C or name O or name CB )) or resid 168 through 173 or (resid 1 \ 87 through 192 and (name N or name CA or name C or name O or name CB )) or resid \ 193 or (resid 194 and (name N or name CA or name C or name O or name CB )) or r \ esid 195 through 203 or (resid 204 through 207 and (name N or name CA or name C \ or name O or name CB )) or resid 208 through 223 or (resid 224 and (name N or na \ me CA or name C or name O or name CB )) or resid 225 through 232 or (resid 233 a \ nd (name N or name CA or name C or name O or name CB )) or resid 234 through 238 \ or (resid 239 through 242 and (name N or name CA or name C or name O or name CB \ )) or resid 243 through 294 or (resid 295 through 296 and (name N or name CA or \ name C or name O or name CB )) or resid 297 through 355 or (resid 356 through 3 \ 57 and (name N or name CA or name C or name O or name CB )) or resid 358 through \ 359 or (resid 360 and (name N or name CA or name C or name O or name CB )) or r \ esid 361 through 386 or (resid 387 through 388 and (name N or name CA or name C \ or name O or name CB )) or resid 389 through 393 or (resid 394 through 395 and ( \ name N or name CA or name C or name O or name CB )) or resid 396 through 402 or \ (resid 403 and (name N or name CA or name C or name O or name CB )) or resid 404 \ through 440 or (resid 441 and (name N or name CA or name C or name O or name CB \ )) or resid 442 through 444 or (resid 445 and (name N or name CA or name C or n \ ame O or name CB )) or resid 446 through 501)) selection = (chain 'F' and (resid 1 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 38 or (resid 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 41 or (resid 42 and (n \ ame N or name CA or name C or name O or name CB )) or resid 43 through 142 or (r \ esid 143 through 144 and (name N or name CA or name C or name O or name CB )) or \ resid 145 through 154 or (resid 155 and (name N or name CA or name C or name O \ or name CB )) or resid 156 through 162 or (resid 163 and (name N or name CA or n \ ame C or name O or name CB )) or resid 164 through 166 or (resid 167 and (name N \ or name CA or name C or name O or name CB )) or resid 168 through 170 or (resid \ 171 through 173 and (name N or name CA or name C or name O or name CB )) or (re \ sid 187 through 192 and (name N or name CA or name C or name O or name CB )) or \ resid 193 through 205 or (resid 206 through 207 and (name N or name CA or name C \ or name O or name CB )) or resid 208 through 212 or (resid 213 through 214 and \ (name N or name CA or name C or name O or name CB )) or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 238 or (resid 239 through 242 and (name N or name CA or name C or name \ O or name CB )) or resid 243 through 263 or (resid 264 and (name N or name CA o \ r name C or name O or name CB )) or resid 265 through 287 or (resid 288 through \ 289 and (name N or name CA or name C or name O or name CB )) or resid 290 throug \ h 355 or (resid 356 through 357 and (name N or name CA or name C or name O or na \ me CB )) or resid 358 through 359 or (resid 360 and (name N or name CA or name C \ or name O or name CB )) or resid 361 through 376 or resid 380 through 382 or (r \ esid 383 and (name N or name CA or name C or name O or name CB )) or resid 384 t \ hrough 404 or (resid 405 and (name N or name CA or name C or name O or name CB ) \ ) or resid 406 through 408 or (resid 409 and (name N or name CA or name C or nam \ e O or name CB )) or resid 410 through 440 or (resid 441 and (name N or name CA \ or name C or name O or name CB )) or resid 442 through 444 or (resid 445 and (na \ me N or name CA or name C or name O or name CB )) or resid 446 through 501)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 1 through 188 or (resid 189 and (name N or name CA or name \ C or name O or name CB )) or resid 190 through 191 or (resid 192 and (name N or \ name CA or name C or name O or name CB )) or resid 193 through 221 or (resid 22 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 223 through \ 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.470 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.870 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 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 : 0.004 0.193 23642 Z= 0.200 Angle : 0.532 15.030 32097 Z= 0.260 Chirality : 0.038 0.155 3650 Planarity : 0.003 0.036 4231 Dihedral : 12.106 88.443 8885 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 34.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.16), residues: 3005 helix: 1.37 (0.15), residues: 1278 sheet: 0.54 (0.24), residues: 478 loop : -0.76 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 369 TYR 0.012 0.001 TYR C 265 PHE 0.010 0.001 PHE B 320 TRP 0.014 0.001 TRP E 66 HIS 0.005 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00386 (23642) covalent geometry : angle 0.53192 (32097) hydrogen bonds : bond 0.14325 ( 1078) hydrogen bonds : angle 6.36865 ( 3114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1072 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.7280 (t80) cc_final: 0.6985 (t80) REVERT: A 51 PHE cc_start: 0.8147 (m-10) cc_final: 0.7828 (m-10) REVERT: A 52 LYS cc_start: 0.7372 (mmtm) cc_final: 0.6475 (mmmt) REVERT: A 61 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7276 (mp-120) REVERT: A 67 PHE cc_start: 0.7181 (m-80) cc_final: 0.5729 (m-80) REVERT: A 166 LEU cc_start: 0.8125 (tp) cc_final: 0.7623 (mt) REVERT: A 211 SER cc_start: 0.7412 (p) cc_final: 0.6416 (p) REVERT: A 215 GLU cc_start: 0.6686 (mp0) cc_final: 0.5243 (tm-30) REVERT: A 343 THR cc_start: 0.8942 (p) cc_final: 0.8718 (p) REVERT: A 376 MET cc_start: 0.6455 (ppp) cc_final: 0.6016 (ppp) REVERT: A 393 LEU cc_start: 0.9398 (mp) cc_final: 0.9163 (mp) REVERT: A 397 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8368 (mp0) REVERT: A 398 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8504 (tm-30) REVERT: B 27 PHE cc_start: 0.7036 (m-80) cc_final: 0.6226 (m-10) REVERT: B 84 HIS cc_start: 0.7334 (m90) cc_final: 0.6743 (m90) REVERT: B 95 LYS cc_start: 0.8784 (tttt) cc_final: 0.8408 (mtpt) REVERT: B 127 GLU cc_start: 0.8650 (pm20) cc_final: 0.8427 (tp30) REVERT: B 139 GLN cc_start: 0.8494 (tt0) cc_final: 0.8199 (pp30) REVERT: B 179 GLU cc_start: 0.5654 (mm-30) cc_final: 0.5311 (mm-30) REVERT: B 279 ASP cc_start: 0.7693 (t0) cc_final: 0.7259 (t70) REVERT: B 317 TRP cc_start: 0.6453 (t-100) cc_final: 0.6210 (t-100) REVERT: B 394 GLN cc_start: 0.7683 (tp40) cc_final: 0.7262 (tm-30) REVERT: C 140 THR cc_start: 0.7084 (p) cc_final: 0.6768 (p) REVERT: C 206 ASP cc_start: 0.6844 (t0) cc_final: 0.6049 (t0) REVERT: C 306 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7458 (mt-10) REVERT: C 397 ASP cc_start: 0.7151 (t0) cc_final: 0.6861 (t0) REVERT: C 409 TYR cc_start: 0.8492 (m-80) cc_final: 0.8222 (m-80) REVERT: C 419 THR cc_start: 0.7260 (t) cc_final: 0.7049 (p) REVERT: C 429 PHE cc_start: 0.9125 (m-80) cc_final: 0.8570 (m-10) REVERT: C 459 ASP cc_start: 0.6815 (p0) cc_final: 0.6452 (p0) REVERT: C 481 LYS cc_start: 0.9003 (mtmt) cc_final: 0.8602 (mtmm) REVERT: C 562 GLN cc_start: 0.7516 (mp10) cc_final: 0.5514 (mp10) REVERT: C 566 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8251 (mm-30) REVERT: D 197 LEU cc_start: 0.8223 (mt) cc_final: 0.7945 (mt) REVERT: D 259 LEU cc_start: 0.7617 (tt) cc_final: 0.7275 (tp) REVERT: D 347 PHE cc_start: 0.6698 (p90) cc_final: 0.6386 (p90) REVERT: D 353 LEU cc_start: 0.8617 (pt) cc_final: 0.8341 (pt) REVERT: D 397 ASP cc_start: 0.7373 (t0) cc_final: 0.6995 (t0) REVERT: D 419 THR cc_start: 0.7336 (t) cc_final: 0.7094 (p) REVERT: D 429 PHE cc_start: 0.9097 (m-80) cc_final: 0.8576 (m-10) REVERT: D 562 GLN cc_start: 0.7189 (mp10) cc_final: 0.4762 (mp10) REVERT: D 566 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8116 (mm-30) REVERT: D 576 TYR cc_start: 0.8333 (m-80) cc_final: 0.7961 (m-80) REVERT: E 40 LEU cc_start: 0.6993 (tp) cc_final: 0.6585 (tp) REVERT: E 77 ASP cc_start: 0.7377 (m-30) cc_final: 0.6910 (t0) REVERT: E 84 HIS cc_start: 0.7426 (m90) cc_final: 0.6946 (m90) REVERT: E 95 LYS cc_start: 0.8930 (tttt) cc_final: 0.8654 (mtpt) REVERT: E 139 GLN cc_start: 0.8510 (tt0) cc_final: 0.8220 (pp30) REVERT: E 161 GLU cc_start: 0.7384 (tp30) cc_final: 0.7031 (tp30) REVERT: E 179 GLU cc_start: 0.5160 (mm-30) cc_final: 0.4734 (mm-30) REVERT: E 212 LEU cc_start: 0.7688 (tp) cc_final: 0.7451 (tp) REVERT: E 317 TRP cc_start: 0.6508 (t-100) cc_final: 0.6083 (t-100) REVERT: E 319 GLU cc_start: 0.7219 (mp0) cc_final: 0.6920 (mm-30) REVERT: E 382 MET cc_start: 0.6407 (mtt) cc_final: 0.6170 (mtp) REVERT: E 394 GLN cc_start: 0.7701 (tp40) cc_final: 0.7035 (tm-30) REVERT: E 397 GLU cc_start: 0.6673 (tm-30) cc_final: 0.6211 (tm-30) REVERT: E 443 LEU cc_start: 0.8681 (mt) cc_final: 0.8291 (mt) REVERT: F 1 MET cc_start: 0.7100 (mtp) cc_final: 0.6570 (mtp) REVERT: F 19 VAL cc_start: 0.8421 (t) cc_final: 0.7745 (t) REVERT: F 36 VAL cc_start: 0.8421 (t) cc_final: 0.8023 (p) REVERT: F 37 LEU cc_start: 0.8615 (mt) cc_final: 0.8155 (tp) REVERT: F 52 LYS cc_start: 0.6837 (mmtm) cc_final: 0.5759 (mmmt) REVERT: F 60 ASP cc_start: 0.7273 (t0) cc_final: 0.6654 (t0) REVERT: F 71 ASN cc_start: 0.8122 (m110) cc_final: 0.7737 (p0) REVERT: F 82 GLN cc_start: 0.7913 (mt0) cc_final: 0.7632 (mt0) REVERT: F 95 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8851 (ptpt) REVERT: F 229 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7919 (mtmm) REVERT: F 260 HIS cc_start: 0.5860 (p-80) cc_final: 0.5613 (p90) REVERT: F 335 ASN cc_start: 0.8157 (t0) cc_final: 0.7348 (p0) REVERT: F 336 LYS cc_start: 0.6793 (mttt) cc_final: 0.6495 (mtmm) REVERT: F 343 THR cc_start: 0.9092 (p) cc_final: 0.8742 (p) REVERT: F 355 ILE cc_start: 0.6003 (mm) cc_final: 0.5782 (mm) REVERT: F 393 LEU cc_start: 0.9338 (mp) cc_final: 0.9058 (mp) REVERT: F 398 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8336 (tm-30) REVERT: F 427 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7599 (tt0) outliers start: 0 outliers final: 0 residues processed: 1072 average time/residue: 0.1945 time to fit residues: 308.5740 Evaluate side-chains 738 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 738 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 20.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN B 267 HIS C 58 HIS C 123 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN C 537 GLN C 541 GLN D 58 HIS D 123 GLN D 258 ASN D 390 ASN D 467 ASN D 537 GLN D 541 GLN E 82 GLN E 267 HIS F 82 GLN ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 GLN F 429 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.222197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.164176 restraints weight = 46256.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.167196 restraints weight = 25093.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.170117 restraints weight = 16042.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.171332 restraints weight = 11684.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.171796 restraints weight = 10244.773| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23642 Z= 0.187 Angle : 0.728 12.839 32097 Z= 0.366 Chirality : 0.045 0.179 3650 Planarity : 0.006 0.066 4231 Dihedral : 7.604 75.533 3495 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.13 % Allowed : 4.32 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 3005 helix: 1.04 (0.15), residues: 1282 sheet: 0.61 (0.24), residues: 474 loop : -0.74 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 477 TYR 0.039 0.002 TYR A 169 PHE 0.032 0.003 PHE F 447 TRP 0.021 0.002 TRP F 290 HIS 0.009 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00408 (23642) covalent geometry : angle 0.72815 (32097) hydrogen bonds : bond 0.03895 ( 1078) hydrogen bonds : angle 5.47024 ( 3114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 887 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.6324 (mttp) cc_final: 0.5434 (ttpt) REVERT: A 51 PHE cc_start: 0.8075 (m-10) cc_final: 0.7480 (m-10) REVERT: A 52 LYS cc_start: 0.7375 (mmtm) cc_final: 0.6616 (mmmt) REVERT: A 60 ASP cc_start: 0.5993 (t0) cc_final: 0.5361 (t0) REVERT: A 92 LEU cc_start: 0.8779 (mt) cc_final: 0.8511 (mt) REVERT: A 95 LYS cc_start: 0.9349 (ptpt) cc_final: 0.8925 (pttp) REVERT: A 103 LEU cc_start: 0.6265 (tt) cc_final: 0.5793 (tp) REVERT: A 166 LEU cc_start: 0.8127 (tp) cc_final: 0.7751 (mt) REVERT: A 211 SER cc_start: 0.7880 (p) cc_final: 0.6941 (p) REVERT: A 215 GLU cc_start: 0.6617 (mp0) cc_final: 0.5658 (tm-30) REVERT: A 264 MET cc_start: 0.6156 (mtm) cc_final: 0.5654 (pmm) REVERT: A 355 ILE cc_start: 0.7088 (mp) cc_final: 0.6784 (mt) REVERT: A 398 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8371 (pt0) REVERT: A 443 LEU cc_start: 0.9331 (mt) cc_final: 0.9109 (mt) REVERT: B 27 PHE cc_start: 0.6951 (m-80) cc_final: 0.6461 (m-80) REVERT: B 51 PHE cc_start: 0.8628 (m-80) cc_final: 0.8346 (m-80) REVERT: B 77 ASP cc_start: 0.5797 (t0) cc_final: 0.5417 (t0) REVERT: B 84 HIS cc_start: 0.7788 (m90) cc_final: 0.6977 (m90) REVERT: B 95 LYS cc_start: 0.8599 (tttt) cc_final: 0.8188 (ttmm) REVERT: B 110 GLU cc_start: 0.8137 (tt0) cc_final: 0.7921 (tt0) REVERT: B 125 GLN cc_start: 0.8397 (pm20) cc_final: 0.8017 (pm20) REVERT: B 134 ASP cc_start: 0.8621 (t0) cc_final: 0.7578 (t0) REVERT: B 138 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8045 (mm-30) REVERT: B 139 GLN cc_start: 0.8893 (tt0) cc_final: 0.8364 (pt0) REVERT: B 175 ASP cc_start: 0.8273 (t0) cc_final: 0.7984 (t0) REVERT: B 266 LEU cc_start: 0.9264 (mt) cc_final: 0.9039 (mt) REVERT: B 374 GLN cc_start: 0.8867 (pt0) cc_final: 0.8556 (mm-40) REVERT: B 381 ASN cc_start: 0.7086 (t0) cc_final: 0.6685 (m-40) REVERT: B 394 GLN cc_start: 0.8191 (tp40) cc_final: 0.7608 (tm-30) REVERT: B 446 ILE cc_start: 0.8818 (mt) cc_final: 0.8262 (tp) REVERT: C 1 MET cc_start: 0.7897 (mmm) cc_final: 0.7686 (mmm) REVERT: C 11 ILE cc_start: 0.9532 (mp) cc_final: 0.9224 (tt) REVERT: C 197 LEU cc_start: 0.8280 (mt) cc_final: 0.7734 (mt) REVERT: C 333 ASN cc_start: 0.7978 (p0) cc_final: 0.7636 (p0) REVERT: C 347 PHE cc_start: 0.7462 (p90) cc_final: 0.7161 (p90) REVERT: C 378 GLU cc_start: 0.8293 (mp0) cc_final: 0.8052 (mp0) REVERT: C 397 ASP cc_start: 0.7533 (t0) cc_final: 0.7000 (t0) REVERT: C 419 THR cc_start: 0.7464 (t) cc_final: 0.7263 (p) REVERT: C 481 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8672 (mtmm) REVERT: C 554 ARG cc_start: 0.8681 (mtm180) cc_final: 0.8463 (mtm-85) REVERT: C 562 GLN cc_start: 0.8361 (mp10) cc_final: 0.7239 (mp10) REVERT: C 564 ARG cc_start: 0.6790 (tpt170) cc_final: 0.6317 (tpt170) REVERT: C 566 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8525 (mm-30) REVERT: D 206 ASP cc_start: 0.7628 (t0) cc_final: 0.5971 (t0) REVERT: D 208 ARG cc_start: 0.7911 (ptt-90) cc_final: 0.7401 (ptp90) REVERT: D 258 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8154 (p0) REVERT: D 259 LEU cc_start: 0.7328 (tt) cc_final: 0.6671 (mt) REVERT: D 333 ASN cc_start: 0.7185 (m-40) cc_final: 0.6033 (m110) REVERT: D 345 TYR cc_start: 0.8423 (p90) cc_final: 0.8015 (p90) REVERT: D 397 ASP cc_start: 0.7846 (t0) cc_final: 0.7451 (t0) REVERT: D 562 GLN cc_start: 0.8109 (mp10) cc_final: 0.7389 (mp10) REVERT: D 564 ARG cc_start: 0.6654 (tpt170) cc_final: 0.6239 (tpt170) REVERT: D 566 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8380 (mm-30) REVERT: D 594 LYS cc_start: 0.7834 (mmtt) cc_final: 0.7601 (mmtt) REVERT: E 30 ARG cc_start: 0.8208 (tpt90) cc_final: 0.7960 (mmm160) REVERT: E 31 GLU cc_start: 0.8240 (mp0) cc_final: 0.7855 (mp0) REVERT: E 34 GLU cc_start: 0.7883 (pp20) cc_final: 0.7545 (pp20) REVERT: E 40 LEU cc_start: 0.7128 (tp) cc_final: 0.6771 (tp) REVERT: E 77 ASP cc_start: 0.7799 (m-30) cc_final: 0.7529 (m-30) REVERT: E 84 HIS cc_start: 0.7803 (m90) cc_final: 0.7109 (m90) REVERT: E 95 LYS cc_start: 0.8688 (tttt) cc_final: 0.8196 (ttmm) REVERT: E 110 GLU cc_start: 0.8015 (tt0) cc_final: 0.7753 (tt0) REVERT: E 116 PHE cc_start: 0.8807 (t80) cc_final: 0.8599 (t80) REVERT: E 138 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8530 (tp30) REVERT: E 139 GLN cc_start: 0.8941 (tt0) cc_final: 0.8520 (pt0) REVERT: E 142 ARG cc_start: 0.8985 (ttt-90) cc_final: 0.8700 (ttt90) REVERT: E 371 HIS cc_start: 0.9083 (t-90) cc_final: 0.8651 (t-90) REVERT: E 381 ASN cc_start: 0.7312 (t0) cc_final: 0.6785 (m-40) REVERT: E 394 GLN cc_start: 0.8368 (tp40) cc_final: 0.8051 (tp40) REVERT: E 421 GLU cc_start: 0.8884 (tt0) cc_final: 0.8458 (tt0) REVERT: E 428 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7696 (pp30) REVERT: E 443 LEU cc_start: 0.8626 (mt) cc_final: 0.8242 (mt) REVERT: E 447 PHE cc_start: 0.8288 (m-80) cc_final: 0.7847 (m-80) REVERT: F 28 LYS cc_start: 0.6739 (mttp) cc_final: 0.5995 (ptmt) REVERT: F 60 ASP cc_start: 0.7057 (t0) cc_final: 0.6497 (t0) REVERT: F 65 LEU cc_start: 0.7452 (tt) cc_final: 0.6467 (tp) REVERT: F 71 ASN cc_start: 0.8175 (m110) cc_final: 0.7738 (p0) REVERT: F 92 LEU cc_start: 0.8718 (mt) cc_final: 0.8436 (mt) REVERT: F 95 LYS cc_start: 0.9363 (mtpt) cc_final: 0.9092 (ptpt) REVERT: F 111 PHE cc_start: 0.8287 (m-80) cc_final: 0.7114 (m-80) REVERT: F 125 GLN cc_start: 0.7674 (tt0) cc_final: 0.7436 (mm-40) REVERT: F 217 MET cc_start: 0.6613 (mtm) cc_final: 0.6367 (mtp) REVERT: F 262 ASP cc_start: 0.7377 (t0) cc_final: 0.7080 (t0) REVERT: F 288 ARG cc_start: 0.8651 (tpp-160) cc_final: 0.8367 (tpp-160) REVERT: F 335 ASN cc_start: 0.7771 (t0) cc_final: 0.6676 (p0) REVERT: F 397 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: F 398 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8105 (tm-30) REVERT: F 429 ASN cc_start: 0.7788 (m110) cc_final: 0.7045 (m110) REVERT: F 447 PHE cc_start: 0.9194 (m-80) cc_final: 0.8923 (m-80) outliers start: 3 outliers final: 0 residues processed: 887 average time/residue: 0.1667 time to fit residues: 224.2687 Evaluate side-chains 678 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 676 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 135 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 158 HIS A 165 HIS A 209 GLN ** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS B 267 HIS C 37 HIS C 80 GLN C 219 HIS D 37 HIS D 106 GLN ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN D 390 ASN D 600 GLN E 82 GLN E 84 HIS E 258 HIS E 267 HIS E 429 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 374 GLN F 392 HIS F 402 HIS F 404 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.216030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.159833 restraints weight = 45716.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157385 restraints weight = 33164.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.160060 restraints weight = 20467.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.161554 restraints weight = 14541.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.162364 restraints weight = 12349.169| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23642 Z= 0.178 Angle : 0.662 9.976 32097 Z= 0.334 Chirality : 0.044 0.171 3650 Planarity : 0.005 0.103 4231 Dihedral : 7.383 69.622 3495 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.21 % Allowed : 3.64 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.16), residues: 3005 helix: 0.95 (0.15), residues: 1298 sheet: 0.63 (0.24), residues: 452 loop : -0.84 (0.18), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 356 TYR 0.025 0.002 TYR A 169 PHE 0.033 0.002 PHE A 320 TRP 0.027 0.002 TRP A 317 HIS 0.009 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00394 (23642) covalent geometry : angle 0.66247 (32097) hydrogen bonds : bond 0.03654 ( 1078) hydrogen bonds : angle 5.20251 ( 3114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 818 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.6692 (mttp) cc_final: 0.5804 (pttt) REVERT: A 60 ASP cc_start: 0.6090 (t0) cc_final: 0.5881 (t0) REVERT: A 63 ILE cc_start: 0.7715 (mm) cc_final: 0.7475 (mm) REVERT: A 65 LEU cc_start: 0.8607 (mt) cc_final: 0.8332 (tp) REVERT: A 91 ASP cc_start: 0.8827 (t0) cc_final: 0.8575 (t0) REVERT: A 92 LEU cc_start: 0.8786 (mt) cc_final: 0.8467 (mt) REVERT: A 95 LYS cc_start: 0.9417 (ptpt) cc_final: 0.8870 (pttp) REVERT: A 166 LEU cc_start: 0.8044 (tp) cc_final: 0.7716 (mt) REVERT: A 201 ASP cc_start: 0.8636 (t0) cc_final: 0.8413 (m-30) REVERT: A 211 SER cc_start: 0.7044 (p) cc_final: 0.6259 (p) REVERT: A 215 GLU cc_start: 0.6417 (mp0) cc_final: 0.5741 (tm-30) REVERT: A 324 LEU cc_start: 0.8491 (mt) cc_final: 0.8203 (mt) REVERT: A 397 GLU cc_start: 0.8398 (pt0) cc_final: 0.8176 (pp20) REVERT: B 5 ASP cc_start: 0.7691 (p0) cc_final: 0.7284 (p0) REVERT: B 7 ILE cc_start: 0.6766 (tp) cc_final: 0.6431 (tp) REVERT: B 21 ILE cc_start: 0.8203 (mm) cc_final: 0.7966 (mm) REVERT: B 27 PHE cc_start: 0.6374 (m-80) cc_final: 0.6009 (m-80) REVERT: B 34 GLU cc_start: 0.7820 (pp20) cc_final: 0.7349 (pp20) REVERT: B 95 LYS cc_start: 0.8665 (tttt) cc_final: 0.8364 (tttp) REVERT: B 97 ILE cc_start: 0.8810 (mm) cc_final: 0.8572 (mm) REVERT: B 110 GLU cc_start: 0.7870 (tt0) cc_final: 0.7553 (tt0) REVERT: B 125 GLN cc_start: 0.8468 (pm20) cc_final: 0.8124 (pm20) REVERT: B 138 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8555 (tp30) REVERT: B 139 GLN cc_start: 0.8827 (tt0) cc_final: 0.8519 (pt0) REVERT: B 175 ASP cc_start: 0.7951 (t0) cc_final: 0.7719 (t0) REVERT: B 266 LEU cc_start: 0.9061 (mt) cc_final: 0.8801 (mt) REVERT: B 373 LYS cc_start: 0.8377 (tppt) cc_final: 0.7964 (ptpp) REVERT: B 381 ASN cc_start: 0.6915 (t0) cc_final: 0.6468 (m-40) REVERT: B 390 ARG cc_start: 0.7309 (tpp80) cc_final: 0.6129 (tpp80) REVERT: B 394 GLN cc_start: 0.8127 (tp40) cc_final: 0.7696 (tm-30) REVERT: B 421 GLU cc_start: 0.8486 (tt0) cc_final: 0.8240 (tt0) REVERT: B 425 LEU cc_start: 0.8446 (tp) cc_final: 0.8073 (tp) REVERT: C 39 ILE cc_start: 0.8928 (mt) cc_final: 0.8669 (mm) REVERT: C 265 TYR cc_start: 0.4439 (m-10) cc_final: 0.3838 (m-80) REVERT: C 327 SER cc_start: 0.8660 (m) cc_final: 0.8435 (t) REVERT: C 328 MET cc_start: 0.4971 (ttm) cc_final: 0.4531 (ttm) REVERT: C 331 MET cc_start: 0.7420 (mpp) cc_final: 0.7170 (mpp) REVERT: C 375 THR cc_start: 0.8030 (t) cc_final: 0.7731 (p) REVERT: C 397 ASP cc_start: 0.7399 (t0) cc_final: 0.6858 (t0) REVERT: C 438 MET cc_start: 0.6429 (mtp) cc_final: 0.6177 (mmm) REVERT: C 450 GLU cc_start: 0.7688 (pp20) cc_final: 0.7215 (tp30) REVERT: C 481 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8573 (mtmm) REVERT: C 551 TYR cc_start: 0.8816 (m-80) cc_final: 0.8594 (m-80) REVERT: C 558 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7904 (tm-30) REVERT: C 562 GLN cc_start: 0.8177 (mp10) cc_final: 0.7520 (mp10) REVERT: C 566 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8590 (mm-30) REVERT: D 197 LEU cc_start: 0.8383 (mt) cc_final: 0.8089 (mt) REVERT: D 206 ASP cc_start: 0.7554 (t0) cc_final: 0.7105 (t0) REVERT: D 208 ARG cc_start: 0.7962 (ptt-90) cc_final: 0.7565 (ptp90) REVERT: D 224 MET cc_start: 0.7808 (mtp) cc_final: 0.7308 (mtt) REVERT: D 285 MET cc_start: 0.6420 (mtp) cc_final: 0.6203 (mtp) REVERT: D 347 PHE cc_start: 0.7360 (p90) cc_final: 0.7037 (p90) REVERT: D 397 ASP cc_start: 0.7927 (t0) cc_final: 0.7543 (t0) REVERT: D 438 MET cc_start: 0.6691 (mtp) cc_final: 0.6342 (mmm) REVERT: D 450 GLU cc_start: 0.7564 (pm20) cc_final: 0.7284 (tp30) REVERT: D 562 GLN cc_start: 0.8091 (mp10) cc_final: 0.7573 (mp10) REVERT: D 564 ARG cc_start: 0.6489 (tpt170) cc_final: 0.6253 (tpt170) REVERT: D 566 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8480 (mm-30) REVERT: D 577 ARG cc_start: 0.8405 (ptp-110) cc_final: 0.8070 (ptp-110) REVERT: E 28 LYS cc_start: 0.8975 (mttt) cc_final: 0.8742 (tttt) REVERT: E 30 ARG cc_start: 0.8111 (tpt90) cc_final: 0.7869 (tpt90) REVERT: E 31 GLU cc_start: 0.8207 (mp0) cc_final: 0.7580 (mp0) REVERT: E 34 GLU cc_start: 0.7823 (pp20) cc_final: 0.7379 (pp20) REVERT: E 77 ASP cc_start: 0.7951 (m-30) cc_final: 0.7722 (m-30) REVERT: E 84 HIS cc_start: 0.7662 (m-70) cc_final: 0.7036 (m-70) REVERT: E 95 LYS cc_start: 0.8759 (tttt) cc_final: 0.8442 (ttmm) REVERT: E 118 ASN cc_start: 0.8378 (m-40) cc_final: 0.8137 (m-40) REVERT: E 139 GLN cc_start: 0.8772 (tt0) cc_final: 0.8068 (pp30) REVERT: E 266 LEU cc_start: 0.9236 (mt) cc_final: 0.9002 (mt) REVERT: E 286 ILE cc_start: 0.7923 (tt) cc_final: 0.7662 (pt) REVERT: E 370 ASN cc_start: 0.8925 (m110) cc_final: 0.8724 (m110) REVERT: E 371 HIS cc_start: 0.8779 (t-90) cc_final: 0.8247 (t-90) REVERT: E 382 MET cc_start: 0.7199 (mtp) cc_final: 0.6925 (mtt) REVERT: E 390 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7897 (tpp80) REVERT: E 410 LEU cc_start: 0.8103 (tp) cc_final: 0.7861 (tp) REVERT: E 421 GLU cc_start: 0.8493 (tt0) cc_final: 0.8175 (tt0) REVERT: F 28 LYS cc_start: 0.7011 (mttp) cc_final: 0.6101 (ptmt) REVERT: F 60 ASP cc_start: 0.6613 (t0) cc_final: 0.6127 (t0) REVERT: F 71 ASN cc_start: 0.8222 (m110) cc_final: 0.7780 (p0) REVERT: F 90 LEU cc_start: 0.9088 (mt) cc_final: 0.8843 (mt) REVERT: F 92 LEU cc_start: 0.8767 (mt) cc_final: 0.8395 (mt) REVERT: F 94 LEU cc_start: 0.9521 (mm) cc_final: 0.9033 (mm) REVERT: F 95 LYS cc_start: 0.9312 (mtpt) cc_final: 0.8970 (ptpt) REVERT: F 111 PHE cc_start: 0.8076 (m-80) cc_final: 0.6808 (m-80) REVERT: F 125 GLN cc_start: 0.7769 (tt0) cc_final: 0.7518 (mm-40) REVERT: F 335 ASN cc_start: 0.7205 (t0) cc_final: 0.6308 (p0) REVERT: F 393 LEU cc_start: 0.9520 (mp) cc_final: 0.9191 (pp) REVERT: F 443 LEU cc_start: 0.8788 (mt) cc_final: 0.8440 (mt) REVERT: F 447 PHE cc_start: 0.8980 (m-80) cc_final: 0.8596 (m-80) outliers start: 5 outliers final: 2 residues processed: 821 average time/residue: 0.1616 time to fit residues: 202.3777 Evaluate side-chains 651 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 649 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 123 optimal weight: 0.0020 chunk 285 optimal weight: 5.9990 chunk 273 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 chunk 225 optimal weight: 0.9980 chunk 187 optimal weight: 0.5980 chunk 272 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 301 optimal weight: 7.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 149 GLN A 209 GLN A 226 ASN ** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 HIS ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN C 141 GLN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 GLN D 252 HIS ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 ASN D 390 ASN D 537 GLN E 267 HIS ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 234 ASN F 374 GLN F 428 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.214495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.155533 restraints weight = 45398.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.156790 restraints weight = 34223.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.158511 restraints weight = 17865.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.160560 restraints weight = 14093.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.160793 restraints weight = 11890.495| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23642 Z= 0.148 Angle : 0.645 10.819 32097 Z= 0.320 Chirality : 0.043 0.164 3650 Planarity : 0.005 0.055 4231 Dihedral : 7.235 65.075 3495 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 3005 helix: 0.92 (0.14), residues: 1298 sheet: 0.54 (0.23), residues: 461 loop : -0.86 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 107 TYR 0.021 0.002 TYR D 276 PHE 0.027 0.002 PHE A 386 TRP 0.023 0.002 TRP A 317 HIS 0.010 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00338 (23642) covalent geometry : angle 0.64461 (32097) hydrogen bonds : bond 0.03367 ( 1078) hydrogen bonds : angle 5.04515 ( 3114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 787 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.6775 (mttp) cc_final: 0.5965 (ptmt) REVERT: A 51 PHE cc_start: 0.7464 (m-10) cc_final: 0.7262 (m-10) REVERT: A 52 LYS cc_start: 0.6115 (mppt) cc_final: 0.5045 (mmmt) REVERT: A 63 ILE cc_start: 0.7609 (mm) cc_final: 0.7409 (mm) REVERT: A 67 PHE cc_start: 0.6623 (m-80) cc_final: 0.6273 (m-80) REVERT: A 91 ASP cc_start: 0.8801 (t0) cc_final: 0.8530 (t0) REVERT: A 92 LEU cc_start: 0.8764 (mt) cc_final: 0.8499 (mt) REVERT: A 95 LYS cc_start: 0.9372 (ptpt) cc_final: 0.8828 (pttp) REVERT: A 105 ILE cc_start: 0.8210 (pt) cc_final: 0.7682 (pt) REVERT: A 116 PHE cc_start: 0.8046 (t80) cc_final: 0.7686 (t80) REVERT: A 138 GLU cc_start: 0.8272 (mp0) cc_final: 0.8037 (mp0) REVERT: A 142 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.7555 (mtm-85) REVERT: A 166 LEU cc_start: 0.8287 (tp) cc_final: 0.7951 (mt) REVERT: A 262 ASP cc_start: 0.7619 (t0) cc_final: 0.7200 (p0) REVERT: A 324 LEU cc_start: 0.8211 (mt) cc_final: 0.7926 (mt) REVERT: A 393 LEU cc_start: 0.9423 (mp) cc_final: 0.9127 (mp) REVERT: B 5 ASP cc_start: 0.7754 (p0) cc_final: 0.7299 (p0) REVERT: B 28 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8385 (ttpt) REVERT: B 30 ARG cc_start: 0.8189 (tpt90) cc_final: 0.7979 (tpt90) REVERT: B 34 GLU cc_start: 0.7765 (pp20) cc_final: 0.7313 (pp20) REVERT: B 77 ASP cc_start: 0.7001 (p0) cc_final: 0.6466 (p0) REVERT: B 95 LYS cc_start: 0.8693 (tttt) cc_final: 0.8295 (ttmm) REVERT: B 110 GLU cc_start: 0.7867 (tt0) cc_final: 0.7604 (tt0) REVERT: B 116 PHE cc_start: 0.8441 (t80) cc_final: 0.8034 (t80) REVERT: B 125 GLN cc_start: 0.8494 (pm20) cc_final: 0.8100 (pm20) REVERT: B 138 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8480 (tp30) REVERT: B 139 GLN cc_start: 0.8702 (tt0) cc_final: 0.8464 (pt0) REVERT: B 266 LEU cc_start: 0.9111 (mt) cc_final: 0.8887 (mt) REVERT: B 373 LYS cc_start: 0.8381 (tppt) cc_final: 0.7974 (ptpp) REVERT: B 389 ARG cc_start: 0.8124 (ttt90) cc_final: 0.7698 (mtp85) REVERT: B 390 ARG cc_start: 0.7335 (tpp80) cc_final: 0.6570 (tpp80) REVERT: B 394 GLN cc_start: 0.8166 (tp40) cc_final: 0.7734 (tm-30) REVERT: B 425 LEU cc_start: 0.8363 (tp) cc_final: 0.8033 (tp) REVERT: C 1 MET cc_start: 0.8075 (mmm) cc_final: 0.7784 (mmm) REVERT: C 39 ILE cc_start: 0.9030 (mt) cc_final: 0.8794 (mm) REVERT: C 205 ILE cc_start: 0.8829 (mm) cc_final: 0.8436 (mm) REVERT: C 327 SER cc_start: 0.8674 (m) cc_final: 0.8342 (t) REVERT: C 333 ASN cc_start: 0.8254 (p0) cc_final: 0.7995 (p0) REVERT: C 397 ASP cc_start: 0.7709 (t0) cc_final: 0.7196 (t0) REVERT: C 419 THR cc_start: 0.7800 (t) cc_final: 0.7326 (p) REVERT: C 427 ARG cc_start: 0.7697 (mtm110) cc_final: 0.7462 (ptm160) REVERT: C 429 PHE cc_start: 0.8581 (m-80) cc_final: 0.8154 (m-10) REVERT: C 438 MET cc_start: 0.6940 (mtp) cc_final: 0.6554 (mmm) REVERT: C 450 GLU cc_start: 0.7774 (pp20) cc_final: 0.7511 (tp30) REVERT: C 481 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8511 (mtmm) REVERT: C 554 ARG cc_start: 0.8477 (mtm180) cc_final: 0.7872 (mtm-85) REVERT: C 558 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7739 (tm-30) REVERT: C 562 GLN cc_start: 0.8087 (mp10) cc_final: 0.7852 (mp10) REVERT: C 564 ARG cc_start: 0.6188 (tpt170) cc_final: 0.5815 (ttt180) REVERT: C 594 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7858 (mmtt) REVERT: D 106 GLN cc_start: 0.8075 (mt0) cc_final: 0.7740 (mm110) REVERT: D 208 ARG cc_start: 0.7912 (ptt-90) cc_final: 0.7662 (ptp90) REVERT: D 224 MET cc_start: 0.7845 (mtp) cc_final: 0.7436 (mtt) REVERT: D 243 TYR cc_start: 0.8014 (m-80) cc_final: 0.7809 (m-10) REVERT: D 347 PHE cc_start: 0.7367 (p90) cc_final: 0.7126 (p90) REVERT: D 397 ASP cc_start: 0.7980 (t0) cc_final: 0.7510 (t0) REVERT: D 438 MET cc_start: 0.6964 (mtp) cc_final: 0.6588 (mmm) REVERT: D 564 ARG cc_start: 0.7241 (mmm160) cc_final: 0.7025 (tpt170) REVERT: D 577 ARG cc_start: 0.8409 (ptp-110) cc_final: 0.8064 (ptp-110) REVERT: E 28 LYS cc_start: 0.8731 (mttt) cc_final: 0.8310 (mtpt) REVERT: E 31 GLU cc_start: 0.8192 (mp0) cc_final: 0.7746 (mp0) REVERT: E 34 GLU cc_start: 0.7817 (pp20) cc_final: 0.7308 (pp20) REVERT: E 77 ASP cc_start: 0.8017 (m-30) cc_final: 0.7775 (m-30) REVERT: E 84 HIS cc_start: 0.7641 (m-70) cc_final: 0.7116 (m-70) REVERT: E 95 LYS cc_start: 0.8724 (tttt) cc_final: 0.8463 (ttmm) REVERT: E 110 GLU cc_start: 0.7893 (tt0) cc_final: 0.7665 (tt0) REVERT: E 138 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8604 (tp30) REVERT: E 139 GLN cc_start: 0.8620 (tt0) cc_final: 0.8237 (pt0) REVERT: E 175 ASP cc_start: 0.7814 (t0) cc_final: 0.7541 (t0) REVERT: E 266 LEU cc_start: 0.9175 (mt) cc_final: 0.8956 (mt) REVERT: E 274 LEU cc_start: 0.5290 (tp) cc_final: 0.4891 (tt) REVERT: E 286 ILE cc_start: 0.7908 (tt) cc_final: 0.7628 (pt) REVERT: E 316 ILE cc_start: 0.8731 (tp) cc_final: 0.8338 (tt) REVERT: E 381 ASN cc_start: 0.7105 (t0) cc_final: 0.6613 (m-40) REVERT: E 389 ARG cc_start: 0.8294 (ttt90) cc_final: 0.7752 (mtp85) REVERT: E 390 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.7900 (tpp80) REVERT: E 410 LEU cc_start: 0.7923 (tp) cc_final: 0.7696 (tt) REVERT: E 421 GLU cc_start: 0.8789 (tt0) cc_final: 0.8259 (tt0) REVERT: F 12 THR cc_start: 0.6056 (p) cc_final: 0.5797 (p) REVERT: F 28 LYS cc_start: 0.7315 (mttp) cc_final: 0.6411 (ptmt) REVERT: F 60 ASP cc_start: 0.6745 (t0) cc_final: 0.6241 (t0) REVERT: F 71 ASN cc_start: 0.8114 (m110) cc_final: 0.7689 (p0) REVERT: F 91 ASP cc_start: 0.8840 (t0) cc_final: 0.8631 (t0) REVERT: F 92 LEU cc_start: 0.8715 (mt) cc_final: 0.8238 (mt) REVERT: F 94 LEU cc_start: 0.9466 (mm) cc_final: 0.9256 (mm) REVERT: F 95 LYS cc_start: 0.9304 (mtpt) cc_final: 0.8945 (ptpt) REVERT: F 111 PHE cc_start: 0.8108 (m-80) cc_final: 0.6853 (m-80) REVERT: F 234 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8620 (t0) REVERT: F 262 ASP cc_start: 0.6933 (t0) cc_final: 0.6559 (t0) REVERT: F 288 ARG cc_start: 0.7735 (tpm170) cc_final: 0.7529 (tpp-160) REVERT: F 335 ASN cc_start: 0.7318 (t0) cc_final: 0.6325 (p0) REVERT: F 381 ASN cc_start: 0.8845 (t0) cc_final: 0.8392 (m-40) REVERT: F 397 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8586 (pt0) REVERT: F 443 LEU cc_start: 0.8810 (mt) cc_final: 0.8360 (mt) REVERT: F 447 PHE cc_start: 0.8984 (m-80) cc_final: 0.8685 (m-80) outliers start: 3 outliers final: 0 residues processed: 788 average time/residue: 0.1550 time to fit residues: 187.5045 Evaluate side-chains 637 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 636 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 116 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 265 optimal weight: 0.0040 chunk 226 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 chunk 293 optimal weight: 0.7980 chunk 288 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 168 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 258 HIS A 267 HIS ** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 ASN B 139 GLN B 267 HIS C 58 HIS ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS D 333 ASN D 390 ASN D 600 GLN E 165 HIS E 267 HIS E 429 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.213181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.155696 restraints weight = 45024.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.152869 restraints weight = 36094.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155895 restraints weight = 19149.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.157624 restraints weight = 14001.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.158411 restraints weight = 12088.515| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23642 Z= 0.148 Angle : 0.629 10.686 32097 Z= 0.315 Chirality : 0.042 0.180 3650 Planarity : 0.004 0.055 4231 Dihedral : 7.150 62.793 3495 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.08 % Allowed : 2.79 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.16), residues: 3005 helix: 0.92 (0.15), residues: 1295 sheet: 0.49 (0.24), residues: 461 loop : -0.78 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 393 TYR 0.015 0.002 TYR A 169 PHE 0.033 0.002 PHE B 447 TRP 0.020 0.001 TRP A 317 HIS 0.008 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00331 (23642) covalent geometry : angle 0.62949 (32097) hydrogen bonds : bond 0.03292 ( 1078) hydrogen bonds : angle 5.00719 ( 3114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 785 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.6765 (mttp) cc_final: 0.5937 (ptmt) REVERT: A 63 ILE cc_start: 0.7409 (mm) cc_final: 0.7145 (mm) REVERT: A 91 ASP cc_start: 0.8858 (t0) cc_final: 0.8578 (t0) REVERT: A 92 LEU cc_start: 0.8730 (mt) cc_final: 0.8471 (mt) REVERT: A 95 LYS cc_start: 0.9369 (ptpt) cc_final: 0.8827 (pttp) REVERT: A 105 ILE cc_start: 0.8153 (pt) cc_final: 0.7667 (pt) REVERT: A 116 PHE cc_start: 0.8086 (t80) cc_final: 0.7670 (t80) REVERT: A 122 ASP cc_start: 0.6382 (t0) cc_final: 0.5854 (t70) REVERT: A 138 GLU cc_start: 0.8246 (mp0) cc_final: 0.8043 (mp0) REVERT: A 142 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7573 (mtm-85) REVERT: A 166 LEU cc_start: 0.8242 (tp) cc_final: 0.7888 (mt) REVERT: A 262 ASP cc_start: 0.7865 (t0) cc_final: 0.7360 (p0) REVERT: A 264 MET cc_start: 0.6798 (mtp) cc_final: 0.6304 (mtp) REVERT: A 346 MET cc_start: 0.5956 (tpt) cc_final: 0.5753 (tpt) REVERT: B 5 ASP cc_start: 0.7941 (p0) cc_final: 0.7424 (p0) REVERT: B 30 ARG cc_start: 0.8225 (tpt90) cc_final: 0.7950 (tpt90) REVERT: B 34 GLU cc_start: 0.7787 (pp20) cc_final: 0.7300 (pp20) REVERT: B 77 ASP cc_start: 0.7078 (p0) cc_final: 0.6522 (p0) REVERT: B 95 LYS cc_start: 0.8704 (tttt) cc_final: 0.8294 (ttmm) REVERT: B 110 GLU cc_start: 0.7848 (tt0) cc_final: 0.7620 (tt0) REVERT: B 116 PHE cc_start: 0.8546 (t80) cc_final: 0.8056 (t80) REVERT: B 125 GLN cc_start: 0.8431 (pm20) cc_final: 0.8046 (pm20) REVERT: B 145 LEU cc_start: 0.8112 (mm) cc_final: 0.7892 (mp) REVERT: B 197 ILE cc_start: 0.8485 (mp) cc_final: 0.8284 (mp) REVERT: B 266 LEU cc_start: 0.9126 (mt) cc_final: 0.8905 (mt) REVERT: B 373 LYS cc_start: 0.8435 (tppt) cc_final: 0.7967 (ptpp) REVERT: B 390 ARG cc_start: 0.7418 (tpp80) cc_final: 0.6841 (tpp80) REVERT: B 425 LEU cc_start: 0.8416 (tp) cc_final: 0.8026 (tp) REVERT: C 1 MET cc_start: 0.8105 (mmm) cc_final: 0.7834 (mmm) REVERT: C 39 ILE cc_start: 0.9241 (mt) cc_final: 0.8853 (mm) REVERT: C 238 GLN cc_start: 0.8343 (pp30) cc_final: 0.7970 (pp30) REVERT: C 283 LYS cc_start: 0.8856 (mttp) cc_final: 0.8464 (mttm) REVERT: C 327 SER cc_start: 0.8727 (m) cc_final: 0.8455 (t) REVERT: C 328 MET cc_start: 0.5510 (ttm) cc_final: 0.4902 (ttm) REVERT: C 331 MET cc_start: 0.7621 (mpp) cc_final: 0.7366 (mpp) REVERT: C 397 ASP cc_start: 0.7837 (t0) cc_final: 0.7267 (t0) REVERT: C 427 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7470 (ptm-80) REVERT: C 438 MET cc_start: 0.7041 (mtp) cc_final: 0.6644 (mmm) REVERT: C 481 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8532 (mtmm) REVERT: C 554 ARG cc_start: 0.8557 (mtm180) cc_final: 0.8295 (mtm180) REVERT: C 558 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7738 (tm-30) REVERT: C 564 ARG cc_start: 0.6190 (tpt170) cc_final: 0.5736 (ttt180) REVERT: C 585 GLU cc_start: 0.8026 (mp0) cc_final: 0.7791 (mp0) REVERT: C 594 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7850 (mmtt) REVERT: D 106 GLN cc_start: 0.8235 (mt0) cc_final: 0.7939 (mm-40) REVERT: D 305 ASN cc_start: 0.7210 (p0) cc_final: 0.7000 (p0) REVERT: D 315 SER cc_start: 0.8472 (p) cc_final: 0.8264 (t) REVERT: D 345 TYR cc_start: 0.8225 (p90) cc_final: 0.8018 (p90) REVERT: D 347 PHE cc_start: 0.7520 (p90) cc_final: 0.7207 (p90) REVERT: D 397 ASP cc_start: 0.7968 (t0) cc_final: 0.7514 (t0) REVERT: D 438 MET cc_start: 0.7291 (mtp) cc_final: 0.6915 (mmm) REVERT: D 510 GLU cc_start: 0.7607 (pm20) cc_final: 0.7120 (mm-30) REVERT: D 577 ARG cc_start: 0.8441 (ptp-110) cc_final: 0.8086 (ptp-110) REVERT: E 5 ASP cc_start: 0.7803 (p0) cc_final: 0.7444 (p0) REVERT: E 7 ILE cc_start: 0.6941 (tp) cc_final: 0.6679 (tp) REVERT: E 34 GLU cc_start: 0.7640 (pp20) cc_final: 0.7184 (pp20) REVERT: E 77 ASP cc_start: 0.7927 (m-30) cc_final: 0.7673 (m-30) REVERT: E 84 HIS cc_start: 0.7710 (m-70) cc_final: 0.7197 (m-70) REVERT: E 95 LYS cc_start: 0.8751 (tttt) cc_final: 0.8445 (ttmm) REVERT: E 98 LEU cc_start: 0.8809 (mt) cc_final: 0.8466 (mt) REVERT: E 110 GLU cc_start: 0.7938 (tt0) cc_final: 0.7714 (tt0) REVERT: E 138 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8647 (tp30) REVERT: E 139 GLN cc_start: 0.8678 (tt0) cc_final: 0.8277 (pt0) REVERT: E 145 LEU cc_start: 0.8301 (mm) cc_final: 0.8085 (mp) REVERT: E 266 LEU cc_start: 0.9134 (mt) cc_final: 0.8912 (mt) REVERT: E 274 LEU cc_start: 0.5312 (tp) cc_final: 0.5014 (tp) REVERT: E 286 ILE cc_start: 0.7896 (tt) cc_final: 0.7644 (pt) REVERT: E 302 MET cc_start: 0.3667 (mtt) cc_final: 0.3017 (mtt) REVERT: E 316 ILE cc_start: 0.8732 (tp) cc_final: 0.8295 (tt) REVERT: E 371 HIS cc_start: 0.8838 (t-90) cc_final: 0.8587 (t-90) REVERT: E 381 ASN cc_start: 0.7077 (t0) cc_final: 0.6704 (m-40) REVERT: E 389 ARG cc_start: 0.8336 (ttt90) cc_final: 0.7815 (tpp80) REVERT: E 390 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.7935 (tpp80) REVERT: E 410 LEU cc_start: 0.8007 (tp) cc_final: 0.7802 (tp) REVERT: E 421 GLU cc_start: 0.8818 (tt0) cc_final: 0.8300 (tt0) REVERT: F 12 THR cc_start: 0.6136 (p) cc_final: 0.5898 (p) REVERT: F 60 ASP cc_start: 0.6821 (t0) cc_final: 0.6195 (t0) REVERT: F 71 ASN cc_start: 0.8162 (m110) cc_final: 0.7804 (p0) REVERT: F 94 LEU cc_start: 0.9542 (mm) cc_final: 0.9329 (mm) REVERT: F 95 LYS cc_start: 0.9297 (mtpt) cc_final: 0.9000 (mtmt) REVERT: F 111 PHE cc_start: 0.8181 (m-80) cc_final: 0.6792 (m-80) REVERT: F 157 ASN cc_start: 0.7546 (t0) cc_final: 0.7238 (m-40) REVERT: F 215 GLU cc_start: 0.7107 (pm20) cc_final: 0.5776 (tm-30) REVERT: F 262 ASP cc_start: 0.7248 (t0) cc_final: 0.6961 (t0) REVERT: F 335 ASN cc_start: 0.7555 (t0) cc_final: 0.7206 (t0) REVERT: F 381 ASN cc_start: 0.8812 (t0) cc_final: 0.8357 (m-40) REVERT: F 393 LEU cc_start: 0.9492 (mp) cc_final: 0.9128 (pp) REVERT: F 397 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8465 (pt0) REVERT: F 398 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8023 (tm-30) REVERT: F 424 ARG cc_start: 0.8983 (tpt90) cc_final: 0.8537 (mmm160) REVERT: F 443 LEU cc_start: 0.8886 (mt) cc_final: 0.8459 (mt) REVERT: F 447 PHE cc_start: 0.9061 (m-80) cc_final: 0.8852 (m-80) outliers start: 2 outliers final: 0 residues processed: 785 average time/residue: 0.1560 time to fit residues: 187.6429 Evaluate side-chains 620 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 60 optimal weight: 0.9980 chunk 288 optimal weight: 0.8980 chunk 173 optimal weight: 0.0370 chunk 35 optimal weight: 0.6980 chunk 235 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 246 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 267 HIS ** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN A 429 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS B 267 HIS ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 141 GLN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN D 252 HIS D 333 ASN D 390 ASN D 565 ASN E 267 HIS ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 234 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.211304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.157727 restraints weight = 45642.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.153334 restraints weight = 22191.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155559 restraints weight = 17348.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.155902 restraints weight = 13077.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.156233 restraints weight = 11630.213| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23642 Z= 0.158 Angle : 0.632 10.921 32097 Z= 0.317 Chirality : 0.043 0.194 3650 Planarity : 0.004 0.045 4231 Dihedral : 7.041 62.087 3495 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.13 % Allowed : 2.03 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 3005 helix: 0.98 (0.15), residues: 1283 sheet: 0.43 (0.24), residues: 461 loop : -0.76 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 155 TYR 0.019 0.002 TYR D 276 PHE 0.031 0.002 PHE E 447 TRP 0.019 0.002 TRP F 290 HIS 0.010 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00349 (23642) covalent geometry : angle 0.63214 (32097) hydrogen bonds : bond 0.03284 ( 1078) hydrogen bonds : angle 4.96538 ( 3114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 769 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3840 (mpp) cc_final: 0.2957 (pmm) REVERT: A 28 LYS cc_start: 0.6940 (mttp) cc_final: 0.6683 (mtpp) REVERT: A 39 LYS cc_start: 0.8652 (pttm) cc_final: 0.8333 (mmtm) REVERT: A 63 ILE cc_start: 0.7370 (mm) cc_final: 0.7089 (mm) REVERT: A 91 ASP cc_start: 0.8851 (t0) cc_final: 0.8541 (t0) REVERT: A 92 LEU cc_start: 0.8725 (mt) cc_final: 0.8461 (mt) REVERT: A 95 LYS cc_start: 0.9371 (ptpt) cc_final: 0.8843 (pttp) REVERT: A 105 ILE cc_start: 0.8323 (pt) cc_final: 0.7736 (pt) REVERT: A 116 PHE cc_start: 0.8246 (t80) cc_final: 0.7836 (t80) REVERT: A 166 LEU cc_start: 0.8228 (tp) cc_final: 0.7887 (mt) REVERT: A 262 ASP cc_start: 0.7370 (t0) cc_final: 0.6829 (p0) REVERT: A 264 MET cc_start: 0.7291 (mtp) cc_final: 0.6665 (mtt) REVERT: A 324 LEU cc_start: 0.8661 (mt) cc_final: 0.8431 (mt) REVERT: A 346 MET cc_start: 0.5889 (tpt) cc_final: 0.5671 (tpt) REVERT: B 5 ASP cc_start: 0.8014 (p0) cc_final: 0.7548 (p0) REVERT: B 27 PHE cc_start: 0.6171 (m-80) cc_final: 0.5801 (m-80) REVERT: B 34 GLU cc_start: 0.7685 (pp20) cc_final: 0.7094 (pp20) REVERT: B 77 ASP cc_start: 0.7126 (p0) cc_final: 0.6562 (p0) REVERT: B 80 GLU cc_start: 0.7678 (tp30) cc_final: 0.7305 (tp30) REVERT: B 95 LYS cc_start: 0.8753 (tttt) cc_final: 0.8353 (ttmm) REVERT: B 110 GLU cc_start: 0.7841 (tt0) cc_final: 0.7558 (tt0) REVERT: B 113 GLU cc_start: 0.9055 (tp30) cc_final: 0.8799 (tm-30) REVERT: B 116 PHE cc_start: 0.8557 (t80) cc_final: 0.8025 (t80) REVERT: B 125 GLN cc_start: 0.8431 (pm20) cc_final: 0.8062 (pm20) REVERT: B 134 ASP cc_start: 0.8583 (t0) cc_final: 0.8125 (t0) REVERT: B 138 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8505 (mm-30) REVERT: B 139 GLN cc_start: 0.8347 (pt0) cc_final: 0.6681 (pp30) REVERT: B 266 LEU cc_start: 0.9117 (mt) cc_final: 0.8883 (mt) REVERT: B 373 LYS cc_start: 0.8439 (tppt) cc_final: 0.7706 (ptpp) REVERT: B 374 GLN cc_start: 0.8854 (pt0) cc_final: 0.8486 (mm-40) REVERT: B 390 ARG cc_start: 0.7477 (tpp80) cc_final: 0.6802 (tpp80) REVERT: B 394 GLN cc_start: 0.8130 (tp40) cc_final: 0.7744 (tp40) REVERT: B 397 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7593 (tm-30) REVERT: C 1 MET cc_start: 0.8127 (mmm) cc_final: 0.7867 (mmm) REVERT: C 39 ILE cc_start: 0.9274 (mt) cc_final: 0.8840 (mm) REVERT: C 238 GLN cc_start: 0.8443 (pp30) cc_final: 0.8002 (pp30) REVERT: C 283 LYS cc_start: 0.8977 (mttp) cc_final: 0.8766 (mttm) REVERT: C 327 SER cc_start: 0.8718 (m) cc_final: 0.8386 (t) REVERT: C 331 MET cc_start: 0.7841 (mpp) cc_final: 0.7514 (mpp) REVERT: C 333 ASN cc_start: 0.8168 (p0) cc_final: 0.7956 (p0) REVERT: C 397 ASP cc_start: 0.7986 (t0) cc_final: 0.7463 (t0) REVERT: C 438 MET cc_start: 0.7171 (mtp) cc_final: 0.6872 (mmm) REVERT: C 481 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8410 (mtmm) REVERT: C 554 ARG cc_start: 0.8472 (mtm180) cc_final: 0.8133 (mtm180) REVERT: C 558 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7822 (tm-30) REVERT: C 585 GLU cc_start: 0.8099 (mp0) cc_final: 0.7821 (mp0) REVERT: C 594 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7866 (mmtt) REVERT: D 39 ILE cc_start: 0.9191 (mt) cc_final: 0.8730 (mm) REVERT: D 347 PHE cc_start: 0.7636 (p90) cc_final: 0.7230 (p90) REVERT: D 370 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8672 (tp-100) REVERT: D 397 ASP cc_start: 0.8086 (t0) cc_final: 0.7615 (t0) REVERT: E 7 ILE cc_start: 0.7089 (tp) cc_final: 0.6789 (tp) REVERT: E 28 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8070 (ttpt) REVERT: E 31 GLU cc_start: 0.8158 (mp0) cc_final: 0.7677 (mp0) REVERT: E 34 GLU cc_start: 0.7591 (pp20) cc_final: 0.7137 (pp20) REVERT: E 95 LYS cc_start: 0.8743 (tttt) cc_final: 0.8408 (ttmm) REVERT: E 98 LEU cc_start: 0.8819 (mt) cc_final: 0.8403 (mt) REVERT: E 110 GLU cc_start: 0.7906 (tt0) cc_final: 0.7675 (tt0) REVERT: E 118 ASN cc_start: 0.8493 (m-40) cc_final: 0.8242 (m-40) REVERT: E 138 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8728 (tp30) REVERT: E 139 GLN cc_start: 0.8657 (tt0) cc_final: 0.8250 (pt0) REVERT: E 266 LEU cc_start: 0.9119 (mt) cc_final: 0.8894 (mt) REVERT: E 274 LEU cc_start: 0.5235 (tp) cc_final: 0.4961 (tp) REVERT: E 286 ILE cc_start: 0.7969 (tt) cc_final: 0.7701 (pt) REVERT: E 302 MET cc_start: 0.3720 (mtt) cc_final: 0.3220 (mtt) REVERT: E 316 ILE cc_start: 0.8785 (tp) cc_final: 0.8329 (tt) REVERT: E 370 ASN cc_start: 0.8960 (m110) cc_final: 0.8626 (m110) REVERT: E 373 LYS cc_start: 0.8328 (ptpp) cc_final: 0.7850 (ptpp) REVERT: E 381 ASN cc_start: 0.7065 (t0) cc_final: 0.6668 (t0) REVERT: E 390 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.7955 (tpp80) REVERT: E 394 GLN cc_start: 0.8681 (tp40) cc_final: 0.7613 (tp40) REVERT: E 397 GLU cc_start: 0.7084 (pp20) cc_final: 0.6410 (pp20) REVERT: E 410 LEU cc_start: 0.8144 (tp) cc_final: 0.7936 (tp) REVERT: E 421 GLU cc_start: 0.8865 (tt0) cc_final: 0.8268 (tt0) REVERT: F 12 THR cc_start: 0.6232 (p) cc_final: 0.6009 (p) REVERT: F 60 ASP cc_start: 0.6925 (t0) cc_final: 0.6251 (t0) REVERT: F 71 ASN cc_start: 0.8312 (m110) cc_final: 0.7605 (p0) REVERT: F 91 ASP cc_start: 0.8891 (t0) cc_final: 0.8663 (t0) REVERT: F 95 LYS cc_start: 0.9309 (mtpt) cc_final: 0.8990 (ptpt) REVERT: F 111 PHE cc_start: 0.7780 (m-80) cc_final: 0.6549 (m-80) REVERT: F 157 ASN cc_start: 0.7624 (t0) cc_final: 0.7326 (m-40) REVERT: F 262 ASP cc_start: 0.7322 (t0) cc_final: 0.7095 (t0) REVERT: F 335 ASN cc_start: 0.7579 (t0) cc_final: 0.6637 (p0) REVERT: F 381 ASN cc_start: 0.8707 (t0) cc_final: 0.8396 (m-40) REVERT: F 393 LEU cc_start: 0.9473 (mp) cc_final: 0.9256 (mp) REVERT: F 398 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8118 (tm-30) REVERT: F 443 LEU cc_start: 0.8915 (mt) cc_final: 0.8451 (mt) outliers start: 3 outliers final: 0 residues processed: 770 average time/residue: 0.1538 time to fit residues: 183.3415 Evaluate side-chains 624 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 33 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 254 optimal weight: 0.9980 chunk 267 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 93 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 165 HIS A 209 GLN A 335 ASN ** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS B 267 HIS B 429 ASN ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS D 333 ASN D 390 ASN E 267 HIS E 370 ASN ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 ASN F 429 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.210566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.158439 restraints weight = 45868.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.152698 restraints weight = 23474.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155059 restraints weight = 18125.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155355 restraints weight = 13386.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.155687 restraints weight = 12452.492| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.6818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23642 Z= 0.151 Angle : 0.641 10.999 32097 Z= 0.324 Chirality : 0.043 0.211 3650 Planarity : 0.005 0.051 4231 Dihedral : 7.153 61.618 3495 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.08 % Allowed : 1.48 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.16), residues: 3005 helix: 0.82 (0.15), residues: 1299 sheet: 0.56 (0.24), residues: 425 loop : -0.70 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 603 TYR 0.020 0.002 TYR C 265 PHE 0.025 0.002 PHE E 447 TRP 0.020 0.002 TRP F 290 HIS 0.014 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00340 (23642) covalent geometry : angle 0.64077 (32097) hydrogen bonds : bond 0.03342 ( 1078) hydrogen bonds : angle 4.94177 ( 3114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 764 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3348 (mpp) cc_final: 0.2306 (pmm) REVERT: A 28 LYS cc_start: 0.6933 (mttp) cc_final: 0.6688 (mtpp) REVERT: A 39 LYS cc_start: 0.8663 (pttm) cc_final: 0.8340 (mmtm) REVERT: A 63 ILE cc_start: 0.7420 (mm) cc_final: 0.7137 (mm) REVERT: A 95 LYS cc_start: 0.9359 (ptpt) cc_final: 0.8886 (pttp) REVERT: A 105 ILE cc_start: 0.8341 (pt) cc_final: 0.7744 (pt) REVERT: A 116 PHE cc_start: 0.8236 (t80) cc_final: 0.7819 (t80) REVERT: A 125 GLN cc_start: 0.7908 (tt0) cc_final: 0.7543 (mm-40) REVERT: A 166 LEU cc_start: 0.8230 (tp) cc_final: 0.7896 (mt) REVERT: A 229 LYS cc_start: 0.6767 (mmtt) cc_final: 0.5775 (mmtp) REVERT: A 262 ASP cc_start: 0.7309 (t0) cc_final: 0.7082 (p0) REVERT: A 302 MET cc_start: 0.7356 (mtp) cc_final: 0.7156 (pmm) REVERT: A 324 LEU cc_start: 0.8500 (mt) cc_final: 0.8232 (mt) REVERT: A 397 GLU cc_start: 0.8752 (pt0) cc_final: 0.8240 (pp20) REVERT: B 5 ASP cc_start: 0.8018 (p0) cc_final: 0.7514 (p0) REVERT: B 27 PHE cc_start: 0.6192 (m-80) cc_final: 0.5836 (m-80) REVERT: B 28 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8282 (ttpt) REVERT: B 34 GLU cc_start: 0.7636 (pp20) cc_final: 0.7054 (pp20) REVERT: B 53 ASP cc_start: 0.7854 (t0) cc_final: 0.7148 (t70) REVERT: B 77 ASP cc_start: 0.7140 (p0) cc_final: 0.6553 (p0) REVERT: B 80 GLU cc_start: 0.7136 (tp30) cc_final: 0.6876 (tp30) REVERT: B 95 LYS cc_start: 0.8776 (tttt) cc_final: 0.8430 (ttmm) REVERT: B 110 GLU cc_start: 0.7474 (tt0) cc_final: 0.7128 (tt0) REVERT: B 113 GLU cc_start: 0.9013 (tp30) cc_final: 0.8681 (tm-30) REVERT: B 116 PHE cc_start: 0.8563 (t80) cc_final: 0.7997 (t80) REVERT: B 125 GLN cc_start: 0.8420 (pm20) cc_final: 0.8100 (pm20) REVERT: B 138 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8464 (mt-10) REVERT: B 139 GLN cc_start: 0.8111 (pt0) cc_final: 0.7756 (pp30) REVERT: B 255 LEU cc_start: 0.8376 (mt) cc_final: 0.8164 (mt) REVERT: B 266 LEU cc_start: 0.9181 (mt) cc_final: 0.8916 (mt) REVERT: B 286 ILE cc_start: 0.8123 (tt) cc_final: 0.7796 (pt) REVERT: B 373 LYS cc_start: 0.8186 (tppt) cc_final: 0.7650 (ptpp) REVERT: B 374 GLN cc_start: 0.8840 (pt0) cc_final: 0.8461 (mm-40) REVERT: B 381 ASN cc_start: 0.6916 (p0) cc_final: 0.5458 (t0) REVERT: B 390 ARG cc_start: 0.7797 (tpp80) cc_final: 0.6974 (tpp80) REVERT: B 394 GLN cc_start: 0.8154 (tp40) cc_final: 0.7801 (tp40) REVERT: B 427 GLN cc_start: 0.8772 (tt0) cc_final: 0.8284 (tt0) REVERT: C 1 MET cc_start: 0.8154 (mmm) cc_final: 0.7896 (mmm) REVERT: C 39 ILE cc_start: 0.9231 (mt) cc_final: 0.8773 (mm) REVERT: C 80 GLN cc_start: 0.9194 (pp30) cc_final: 0.8791 (pp30) REVERT: C 276 TYR cc_start: 0.7808 (p90) cc_final: 0.7604 (p90) REVERT: C 283 LYS cc_start: 0.8963 (mttp) cc_final: 0.8377 (mtpt) REVERT: C 327 SER cc_start: 0.8849 (m) cc_final: 0.8463 (t) REVERT: C 331 MET cc_start: 0.7919 (mpp) cc_final: 0.7555 (mpp) REVERT: C 344 GLU cc_start: 0.7599 (tt0) cc_final: 0.7393 (tt0) REVERT: C 345 TYR cc_start: 0.8330 (p90) cc_final: 0.7941 (p90) REVERT: C 397 ASP cc_start: 0.8114 (t0) cc_final: 0.7611 (t0) REVERT: C 427 ARG cc_start: 0.7989 (mtm110) cc_final: 0.7668 (ptm160) REVERT: C 429 PHE cc_start: 0.8530 (m-80) cc_final: 0.8155 (m-10) REVERT: C 438 MET cc_start: 0.7230 (mtp) cc_final: 0.7011 (mmm) REVERT: C 481 LYS cc_start: 0.8638 (mtmt) cc_final: 0.8358 (mtmm) REVERT: C 554 ARG cc_start: 0.8322 (mtm180) cc_final: 0.7983 (mtm180) REVERT: C 558 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7857 (tm-30) REVERT: C 562 GLN cc_start: 0.8123 (mp10) cc_final: 0.7919 (mp10) REVERT: C 564 ARG cc_start: 0.6230 (tpt170) cc_final: 0.5949 (tpt170) REVERT: C 585 GLU cc_start: 0.8112 (mp0) cc_final: 0.7862 (mp0) REVERT: C 594 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7888 (mmtt) REVERT: D 39 ILE cc_start: 0.8984 (mt) cc_final: 0.8440 (mm) REVERT: D 283 LYS cc_start: 0.9041 (mttp) cc_final: 0.8100 (mtpp) REVERT: D 347 PHE cc_start: 0.7624 (p90) cc_final: 0.7268 (p90) REVERT: D 397 ASP cc_start: 0.8165 (t0) cc_final: 0.7714 (t0) REVERT: D 434 GLU cc_start: 0.8591 (pt0) cc_final: 0.8370 (pt0) REVERT: D 438 MET cc_start: 0.8061 (mmm) cc_final: 0.7792 (mmm) REVERT: D 510 GLU cc_start: 0.7302 (pm20) cc_final: 0.7054 (mm-30) REVERT: D 554 ARG cc_start: 0.8795 (mtp-110) cc_final: 0.8312 (mtm110) REVERT: E 5 ASP cc_start: 0.7943 (p0) cc_final: 0.7640 (p0) REVERT: E 28 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8131 (ttpt) REVERT: E 34 GLU cc_start: 0.7526 (pp20) cc_final: 0.7083 (pp20) REVERT: E 95 LYS cc_start: 0.8688 (tttt) cc_final: 0.8380 (ttmm) REVERT: E 110 GLU cc_start: 0.7938 (tt0) cc_final: 0.7637 (tt0) REVERT: E 113 GLU cc_start: 0.9045 (tp30) cc_final: 0.8664 (tm-30) REVERT: E 118 ASN cc_start: 0.8488 (m-40) cc_final: 0.8219 (m-40) REVERT: E 138 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8696 (tp30) REVERT: E 139 GLN cc_start: 0.8622 (tt0) cc_final: 0.8323 (pt0) REVERT: E 142 ARG cc_start: 0.8559 (ttt90) cc_final: 0.8292 (ttt90) REVERT: E 266 LEU cc_start: 0.9109 (mt) cc_final: 0.8885 (mt) REVERT: E 274 LEU cc_start: 0.5194 (tp) cc_final: 0.4731 (tt) REVERT: E 286 ILE cc_start: 0.7891 (tt) cc_final: 0.7602 (pt) REVERT: E 316 ILE cc_start: 0.8870 (tp) cc_final: 0.8407 (tt) REVERT: E 369 ARG cc_start: 0.8561 (ptp-170) cc_final: 0.7993 (ptp-110) REVERT: E 370 ASN cc_start: 0.9041 (m-40) cc_final: 0.8746 (m110) REVERT: E 373 LYS cc_start: 0.8340 (ptpp) cc_final: 0.7896 (ptpp) REVERT: E 381 ASN cc_start: 0.6712 (t0) cc_final: 0.6270 (t0) REVERT: E 390 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.7836 (tpp80) REVERT: E 394 GLN cc_start: 0.8699 (tp40) cc_final: 0.7587 (tp40) REVERT: E 397 GLU cc_start: 0.7338 (pp20) cc_final: 0.6608 (pp20) REVERT: E 421 GLU cc_start: 0.8784 (tt0) cc_final: 0.8149 (tt0) REVERT: F 1 MET cc_start: 0.5320 (ptp) cc_final: 0.4003 (ptp) REVERT: F 12 THR cc_start: 0.5836 (p) cc_final: 0.5583 (p) REVERT: F 39 LYS cc_start: 0.8482 (pttm) cc_final: 0.7881 (tppt) REVERT: F 49 LEU cc_start: 0.7946 (tp) cc_final: 0.7731 (tp) REVERT: F 60 ASP cc_start: 0.6931 (t0) cc_final: 0.6455 (t0) REVERT: F 71 ASN cc_start: 0.8212 (m110) cc_final: 0.7770 (p0) REVERT: F 91 ASP cc_start: 0.8887 (t0) cc_final: 0.8613 (t0) REVERT: F 95 LYS cc_start: 0.9278 (mtpt) cc_final: 0.8844 (ptpt) REVERT: F 111 PHE cc_start: 0.7920 (m-80) cc_final: 0.6810 (m-80) REVERT: F 157 ASN cc_start: 0.7640 (t0) cc_final: 0.7337 (m-40) REVERT: F 262 ASP cc_start: 0.7102 (t0) cc_final: 0.6753 (t0) REVERT: F 274 LEU cc_start: 0.7927 (tp) cc_final: 0.7524 (tp) REVERT: F 335 ASN cc_start: 0.7578 (t0) cc_final: 0.6632 (p0) REVERT: F 381 ASN cc_start: 0.8884 (t0) cc_final: 0.8474 (m-40) REVERT: F 424 ARG cc_start: 0.8594 (mmm160) cc_final: 0.7983 (mmm160) REVERT: F 443 LEU cc_start: 0.8983 (mt) cc_final: 0.8707 (mt) outliers start: 2 outliers final: 0 residues processed: 764 average time/residue: 0.1663 time to fit residues: 196.0448 Evaluate side-chains 602 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 602 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 209 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 107 optimal weight: 0.0980 chunk 193 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 168 optimal weight: 0.0770 chunk 153 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 258 HIS ** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 ASN D 565 ASN E 267 HIS ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN F 209 GLN F 234 ASN F 402 HIS F 429 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.210142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.150819 restraints weight = 45740.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.149811 restraints weight = 32977.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151124 restraints weight = 18860.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153792 restraints weight = 14932.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153774 restraints weight = 12021.565| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23642 Z= 0.152 Angle : 0.650 12.828 32097 Z= 0.325 Chirality : 0.043 0.211 3650 Planarity : 0.004 0.046 4231 Dihedral : 7.125 61.150 3495 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.13 % Allowed : 1.14 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 3005 helix: 0.81 (0.15), residues: 1299 sheet: 0.50 (0.25), residues: 406 loop : -0.67 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 603 TYR 0.024 0.002 TYR D 243 PHE 0.031 0.002 PHE F 301 TRP 0.036 0.002 TRP A 290 HIS 0.010 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00344 (23642) covalent geometry : angle 0.65034 (32097) hydrogen bonds : bond 0.03319 ( 1078) hydrogen bonds : angle 4.95082 ( 3114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 768 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3161 (mpp) cc_final: 0.1871 (pmm) REVERT: A 39 LYS cc_start: 0.8720 (pttm) cc_final: 0.8427 (mmtm) REVERT: A 63 ILE cc_start: 0.7401 (mm) cc_final: 0.7084 (mm) REVERT: A 105 ILE cc_start: 0.8328 (pt) cc_final: 0.7772 (pt) REVERT: A 116 PHE cc_start: 0.8265 (t80) cc_final: 0.7840 (t80) REVERT: A 166 LEU cc_start: 0.8241 (tp) cc_final: 0.7895 (mt) REVERT: A 204 ARG cc_start: 0.7116 (mtt-85) cc_final: 0.6580 (mmt90) REVERT: A 264 MET cc_start: 0.7562 (mtp) cc_final: 0.6581 (mmt) REVERT: A 376 MET cc_start: 0.5512 (ppp) cc_final: 0.4396 (ppp) REVERT: A 397 GLU cc_start: 0.8742 (pt0) cc_final: 0.8287 (pp20) REVERT: B 5 ASP cc_start: 0.8059 (p0) cc_final: 0.7548 (p0) REVERT: B 22 LEU cc_start: 0.8035 (pp) cc_final: 0.7835 (pp) REVERT: B 27 PHE cc_start: 0.6361 (m-80) cc_final: 0.5936 (m-80) REVERT: B 28 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8200 (ttpt) REVERT: B 34 GLU cc_start: 0.7483 (pp20) cc_final: 0.6933 (pp20) REVERT: B 53 ASP cc_start: 0.7614 (t0) cc_final: 0.6992 (t70) REVERT: B 77 ASP cc_start: 0.7248 (p0) cc_final: 0.6602 (p0) REVERT: B 80 GLU cc_start: 0.7254 (tp30) cc_final: 0.6992 (tp30) REVERT: B 95 LYS cc_start: 0.8847 (tttt) cc_final: 0.8464 (ttmm) REVERT: B 110 GLU cc_start: 0.7520 (tt0) cc_final: 0.7175 (tt0) REVERT: B 116 PHE cc_start: 0.8673 (t80) cc_final: 0.8022 (t80) REVERT: B 125 GLN cc_start: 0.8329 (pm20) cc_final: 0.8094 (pm20) REVERT: B 138 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8395 (mm-30) REVERT: B 139 GLN cc_start: 0.8114 (pt0) cc_final: 0.7595 (pp30) REVERT: B 180 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7643 (mp0) REVERT: B 197 ILE cc_start: 0.8547 (pt) cc_final: 0.8188 (pt) REVERT: B 266 LEU cc_start: 0.9214 (mt) cc_final: 0.8934 (mt) REVERT: B 369 ARG cc_start: 0.7893 (ttm110) cc_final: 0.7621 (ptp-110) REVERT: B 373 LYS cc_start: 0.8241 (tppt) cc_final: 0.7953 (ptpp) REVERT: B 381 ASN cc_start: 0.7002 (p0) cc_final: 0.5535 (t0) REVERT: B 390 ARG cc_start: 0.7648 (tpp80) cc_final: 0.6933 (tpp80) REVERT: B 394 GLN cc_start: 0.8210 (tp40) cc_final: 0.7846 (tp40) REVERT: B 397 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7400 (tm-30) REVERT: B 427 GLN cc_start: 0.8822 (tt0) cc_final: 0.8340 (tt0) REVERT: C 1 MET cc_start: 0.8164 (mmm) cc_final: 0.7849 (mmm) REVERT: C 39 ILE cc_start: 0.9303 (mt) cc_final: 0.8802 (mm) REVERT: C 243 TYR cc_start: 0.8602 (m-80) cc_final: 0.8374 (m-10) REVERT: C 276 TYR cc_start: 0.7669 (p90) cc_final: 0.7313 (p90) REVERT: C 283 LYS cc_start: 0.8819 (mttp) cc_final: 0.8374 (mtpt) REVERT: C 327 SER cc_start: 0.8856 (m) cc_final: 0.8433 (t) REVERT: C 331 MET cc_start: 0.7841 (mpp) cc_final: 0.7439 (mpp) REVERT: C 333 ASN cc_start: 0.8244 (p0) cc_final: 0.7966 (p0) REVERT: C 344 GLU cc_start: 0.7638 (tt0) cc_final: 0.7434 (tt0) REVERT: C 345 TYR cc_start: 0.8323 (p90) cc_final: 0.7986 (p90) REVERT: C 397 ASP cc_start: 0.8154 (t0) cc_final: 0.7693 (t0) REVERT: C 429 PHE cc_start: 0.8724 (m-80) cc_final: 0.8085 (m-10) REVERT: C 435 TYR cc_start: 0.7441 (m-80) cc_final: 0.7171 (m-80) REVERT: C 481 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8302 (mtmm) REVERT: C 522 LYS cc_start: 0.8320 (ptmt) cc_final: 0.8017 (ptpp) REVERT: C 564 ARG cc_start: 0.6226 (tpt170) cc_final: 0.5885 (tpt170) REVERT: C 585 GLU cc_start: 0.8049 (mp0) cc_final: 0.7809 (mp0) REVERT: D 20 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7496 (mm-30) REVERT: D 39 ILE cc_start: 0.9241 (mt) cc_final: 0.8757 (mm) REVERT: D 170 TYR cc_start: 0.8816 (p90) cc_final: 0.8515 (p90) REVERT: D 264 MET cc_start: 0.7184 (tpt) cc_final: 0.6947 (tpt) REVERT: D 283 LYS cc_start: 0.9021 (mttp) cc_final: 0.8632 (mtmt) REVERT: D 347 PHE cc_start: 0.7577 (p90) cc_final: 0.7234 (p90) REVERT: D 390 ASN cc_start: 0.8566 (t0) cc_final: 0.8257 (t0) REVERT: D 397 ASP cc_start: 0.8244 (t0) cc_final: 0.7833 (t0) REVERT: D 419 THR cc_start: 0.7899 (t) cc_final: 0.7481 (p) REVERT: D 434 GLU cc_start: 0.8666 (pt0) cc_final: 0.8414 (pt0) REVERT: D 510 GLU cc_start: 0.7413 (pm20) cc_final: 0.7172 (mm-30) REVERT: D 558 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7987 (tm-30) REVERT: D 585 GLU cc_start: 0.8441 (pm20) cc_final: 0.8222 (pm20) REVERT: E 5 ASP cc_start: 0.8049 (p0) cc_final: 0.7746 (p0) REVERT: E 28 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8290 (ttpt) REVERT: E 31 GLU cc_start: 0.8090 (mp0) cc_final: 0.7687 (mp0) REVERT: E 34 GLU cc_start: 0.7479 (pp20) cc_final: 0.7040 (pp20) REVERT: E 84 HIS cc_start: 0.7811 (m-70) cc_final: 0.7438 (m-70) REVERT: E 95 LYS cc_start: 0.8701 (tttt) cc_final: 0.8368 (ttmm) REVERT: E 98 LEU cc_start: 0.8806 (mt) cc_final: 0.8396 (mt) REVERT: E 110 GLU cc_start: 0.7973 (tt0) cc_final: 0.7675 (tt0) REVERT: E 113 GLU cc_start: 0.9079 (tp30) cc_final: 0.8683 (tp30) REVERT: E 118 ASN cc_start: 0.8595 (m-40) cc_final: 0.8325 (m-40) REVERT: E 138 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8735 (tp30) REVERT: E 139 GLN cc_start: 0.8720 (tt0) cc_final: 0.8352 (pt0) REVERT: E 142 ARG cc_start: 0.8662 (ttt90) cc_final: 0.8436 (tpt-90) REVERT: E 266 LEU cc_start: 0.9114 (mt) cc_final: 0.8888 (mt) REVERT: E 274 LEU cc_start: 0.5275 (tp) cc_final: 0.5004 (tp) REVERT: E 284 ILE cc_start: 0.8799 (mm) cc_final: 0.8595 (pt) REVERT: E 286 ILE cc_start: 0.7749 (tt) cc_final: 0.7455 (pt) REVERT: E 316 ILE cc_start: 0.8851 (tp) cc_final: 0.8376 (tt) REVERT: E 373 LYS cc_start: 0.8345 (ptpp) cc_final: 0.7922 (ptpp) REVERT: E 390 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.7948 (tpp80) REVERT: E 394 GLN cc_start: 0.8720 (tp40) cc_final: 0.7632 (tp40) REVERT: E 397 GLU cc_start: 0.7122 (pp20) cc_final: 0.6395 (pp20) REVERT: E 421 GLU cc_start: 0.8821 (tt0) cc_final: 0.8283 (tt0) REVERT: F 1 MET cc_start: 0.5382 (ptp) cc_final: 0.4775 (ptp) REVERT: F 12 THR cc_start: 0.5914 (p) cc_final: 0.5679 (p) REVERT: F 39 LYS cc_start: 0.8631 (pttm) cc_final: 0.7881 (tppt) REVERT: F 49 LEU cc_start: 0.7944 (tp) cc_final: 0.7274 (mt) REVERT: F 60 ASP cc_start: 0.7022 (t0) cc_final: 0.6508 (t0) REVERT: F 71 ASN cc_start: 0.8515 (m110) cc_final: 0.7818 (p0) REVERT: F 95 LYS cc_start: 0.9269 (mtpt) cc_final: 0.8915 (mtmt) REVERT: F 98 LEU cc_start: 0.7523 (mm) cc_final: 0.6846 (pp) REVERT: F 129 ILE cc_start: 0.8985 (mm) cc_final: 0.8747 (mm) REVERT: F 157 ASN cc_start: 0.7649 (t0) cc_final: 0.7361 (m-40) REVERT: F 262 ASP cc_start: 0.7391 (t0) cc_final: 0.7152 (t0) REVERT: F 274 LEU cc_start: 0.7960 (tp) cc_final: 0.7599 (tt) REVERT: F 335 ASN cc_start: 0.7829 (t0) cc_final: 0.6769 (p0) REVERT: F 344 LEU cc_start: 0.8123 (tt) cc_final: 0.7525 (mt) REVERT: F 381 ASN cc_start: 0.8972 (t0) cc_final: 0.8610 (m-40) REVERT: F 424 ARG cc_start: 0.8596 (mmm160) cc_final: 0.8142 (mmm160) REVERT: F 427 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7161 (tm-30) REVERT: F 443 LEU cc_start: 0.9066 (mt) cc_final: 0.8863 (mt) outliers start: 3 outliers final: 0 residues processed: 769 average time/residue: 0.1552 time to fit residues: 184.3794 Evaluate side-chains 619 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 619 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 280 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 251 optimal weight: 0.5980 chunk 245 optimal weight: 0.4980 chunk 190 optimal weight: 0.7980 chunk 289 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 277 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 429 ASN B 267 HIS ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS D 122 GLN D 252 HIS ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 HIS ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN F 234 ASN ** F 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.210494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.156694 restraints weight = 45901.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.152083 restraints weight = 22671.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.153891 restraints weight = 17006.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.154407 restraints weight = 13256.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.154610 restraints weight = 12352.377| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.7304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23642 Z= 0.141 Angle : 0.654 11.275 32097 Z= 0.327 Chirality : 0.043 0.202 3650 Planarity : 0.004 0.050 4231 Dihedral : 7.111 59.785 3495 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.08 % Allowed : 0.72 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.16), residues: 3005 helix: 0.87 (0.15), residues: 1306 sheet: 0.46 (0.25), residues: 407 loop : -0.65 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 155 TYR 0.020 0.002 TYR D 243 PHE 0.046 0.002 PHE B 447 TRP 0.032 0.002 TRP A 317 HIS 0.010 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00318 (23642) covalent geometry : angle 0.65361 (32097) hydrogen bonds : bond 0.03305 ( 1078) hydrogen bonds : angle 4.91889 ( 3114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 772 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2860 (mpp) cc_final: 0.1605 (pmm) REVERT: A 39 LYS cc_start: 0.8664 (pttm) cc_final: 0.8390 (mmtm) REVERT: A 63 ILE cc_start: 0.7415 (mm) cc_final: 0.7095 (mm) REVERT: A 91 ASP cc_start: 0.8924 (t0) cc_final: 0.8719 (t0) REVERT: A 95 LYS cc_start: 0.9407 (pttt) cc_final: 0.8920 (pttp) REVERT: A 105 ILE cc_start: 0.8334 (pt) cc_final: 0.7753 (pt) REVERT: A 116 PHE cc_start: 0.8220 (t80) cc_final: 0.7791 (t80) REVERT: A 166 LEU cc_start: 0.8192 (tp) cc_final: 0.7860 (mt) REVERT: A 204 ARG cc_start: 0.7133 (mtt-85) cc_final: 0.6661 (mmt90) REVERT: A 264 MET cc_start: 0.7183 (mtp) cc_final: 0.6433 (mmt) REVERT: A 302 MET cc_start: 0.7094 (mmp) cc_final: 0.5581 (mtp) REVERT: A 346 MET cc_start: 0.6013 (tpt) cc_final: 0.5715 (tpt) REVERT: A 376 MET cc_start: 0.5422 (ppp) cc_final: 0.4321 (ppp) REVERT: A 382 MET cc_start: 0.8170 (tpt) cc_final: 0.7867 (tpp) REVERT: A 442 LEU cc_start: 0.8862 (tp) cc_final: 0.8621 (mm) REVERT: B 1 MET cc_start: -0.1636 (ttt) cc_final: -0.2003 (ttt) REVERT: B 5 ASP cc_start: 0.8041 (p0) cc_final: 0.7543 (p0) REVERT: B 27 PHE cc_start: 0.6090 (m-80) cc_final: 0.5735 (m-80) REVERT: B 28 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8251 (ttpt) REVERT: B 34 GLU cc_start: 0.7417 (pp20) cc_final: 0.6896 (pp20) REVERT: B 53 ASP cc_start: 0.7705 (t0) cc_final: 0.7025 (t70) REVERT: B 77 ASP cc_start: 0.7226 (p0) cc_final: 0.6591 (p0) REVERT: B 80 GLU cc_start: 0.7124 (tp30) cc_final: 0.6883 (tp30) REVERT: B 95 LYS cc_start: 0.8875 (tttt) cc_final: 0.8491 (ttmm) REVERT: B 110 GLU cc_start: 0.7440 (tt0) cc_final: 0.7108 (tt0) REVERT: B 113 GLU cc_start: 0.9274 (tp30) cc_final: 0.8992 (tp30) REVERT: B 116 PHE cc_start: 0.8581 (t80) cc_final: 0.7946 (t80) REVERT: B 125 GLN cc_start: 0.8323 (pm20) cc_final: 0.8115 (pm20) REVERT: B 138 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8356 (mt-10) REVERT: B 139 GLN cc_start: 0.8185 (pt0) cc_final: 0.7713 (pp30) REVERT: B 169 TYR cc_start: 0.8208 (m-80) cc_final: 0.7890 (m-80) REVERT: B 266 LEU cc_start: 0.9132 (mt) cc_final: 0.8807 (mt) REVERT: B 286 ILE cc_start: 0.8098 (tt) cc_final: 0.7779 (pt) REVERT: B 390 ARG cc_start: 0.7700 (tpp80) cc_final: 0.6933 (tpp80) REVERT: B 397 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7271 (tm-30) REVERT: B 421 GLU cc_start: 0.8776 (tt0) cc_final: 0.8535 (tt0) REVERT: B 427 GLN cc_start: 0.8804 (tt0) cc_final: 0.8306 (tt0) REVERT: C 1 MET cc_start: 0.8148 (mmm) cc_final: 0.7877 (mmm) REVERT: C 39 ILE cc_start: 0.9280 (mt) cc_final: 0.8822 (mm) REVERT: C 243 TYR cc_start: 0.8540 (m-80) cc_final: 0.8292 (m-10) REVERT: C 276 TYR cc_start: 0.7625 (p90) cc_final: 0.7391 (p90) REVERT: C 283 LYS cc_start: 0.8835 (mttp) cc_final: 0.8421 (mtpt) REVERT: C 327 SER cc_start: 0.8759 (m) cc_final: 0.8318 (t) REVERT: C 344 GLU cc_start: 0.7614 (tt0) cc_final: 0.7385 (tt0) REVERT: C 345 TYR cc_start: 0.8258 (p90) cc_final: 0.7985 (p90) REVERT: C 397 ASP cc_start: 0.8216 (t0) cc_final: 0.7810 (t0) REVERT: C 427 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7701 (ptm-80) REVERT: C 429 PHE cc_start: 0.8892 (m-80) cc_final: 0.8526 (m-10) REVERT: C 435 TYR cc_start: 0.7539 (m-80) cc_final: 0.7331 (m-80) REVERT: C 438 MET cc_start: 0.8122 (mmm) cc_final: 0.7665 (mmm) REVERT: C 451 ILE cc_start: 0.8618 (mt) cc_final: 0.8377 (mt) REVERT: C 522 LYS cc_start: 0.8364 (ptmt) cc_final: 0.8087 (ptpp) REVERT: C 564 ARG cc_start: 0.6191 (tpt170) cc_final: 0.5817 (tpt170) REVERT: C 585 GLU cc_start: 0.7972 (mp0) cc_final: 0.7757 (mp0) REVERT: C 603 ARG cc_start: 0.8335 (mtm180) cc_final: 0.8131 (mtm-85) REVERT: D 20 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7414 (mm-30) REVERT: D 39 ILE cc_start: 0.9135 (mt) cc_final: 0.8583 (mt) REVERT: D 283 LYS cc_start: 0.9026 (mttp) cc_final: 0.8514 (mtpt) REVERT: D 322 MET cc_start: 0.7953 (tpp) cc_final: 0.7749 (tpp) REVERT: D 347 PHE cc_start: 0.7587 (p90) cc_final: 0.7156 (p90) REVERT: D 397 ASP cc_start: 0.8233 (t0) cc_final: 0.7797 (t0) REVERT: D 427 ARG cc_start: 0.7984 (mtm110) cc_final: 0.7735 (ptm160) REVERT: D 434 GLU cc_start: 0.8637 (pt0) cc_final: 0.8419 (pt0) REVERT: E 5 ASP cc_start: 0.8055 (p0) cc_final: 0.7734 (p0) REVERT: E 28 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8310 (ttpt) REVERT: E 34 GLU cc_start: 0.7398 (pp20) cc_final: 0.6939 (pp20) REVERT: E 84 HIS cc_start: 0.7723 (m-70) cc_final: 0.7461 (m-70) REVERT: E 95 LYS cc_start: 0.8715 (tttt) cc_final: 0.8351 (ttmm) REVERT: E 110 GLU cc_start: 0.7743 (tt0) cc_final: 0.7444 (tt0) REVERT: E 113 GLU cc_start: 0.9003 (tp30) cc_final: 0.8647 (tm-30) REVERT: E 118 ASN cc_start: 0.8410 (m-40) cc_final: 0.8164 (m-40) REVERT: E 138 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8712 (tp30) REVERT: E 139 GLN cc_start: 0.8651 (tt0) cc_final: 0.8234 (tt0) REVERT: E 142 ARG cc_start: 0.8559 (ttt90) cc_final: 0.8328 (tpt-90) REVERT: E 166 LEU cc_start: 0.8721 (tt) cc_final: 0.8492 (tt) REVERT: E 266 LEU cc_start: 0.9104 (mt) cc_final: 0.8845 (mt) REVERT: E 274 LEU cc_start: 0.5209 (tp) cc_final: 0.4792 (tp) REVERT: E 286 ILE cc_start: 0.7749 (tt) cc_final: 0.7441 (pt) REVERT: E 316 ILE cc_start: 0.8925 (tp) cc_final: 0.8436 (tt) REVERT: E 373 LYS cc_start: 0.8326 (ptpp) cc_final: 0.7841 (ptpp) REVERT: E 390 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.8017 (tpp80) REVERT: E 394 GLN cc_start: 0.8637 (tp40) cc_final: 0.7358 (tp40) REVERT: E 397 GLU cc_start: 0.7187 (pp20) cc_final: 0.6480 (pp20) REVERT: E 407 LYS cc_start: 0.8062 (pttt) cc_final: 0.7767 (pttt) REVERT: E 421 GLU cc_start: 0.8743 (tt0) cc_final: 0.8174 (tt0) REVERT: F 1 MET cc_start: 0.5163 (ptp) cc_final: 0.3815 (ptp) REVERT: F 12 THR cc_start: 0.5924 (p) cc_final: 0.5695 (p) REVERT: F 28 LYS cc_start: 0.7295 (mttm) cc_final: 0.7064 (mtpp) REVERT: F 39 LYS cc_start: 0.8558 (pttm) cc_final: 0.7875 (tppt) REVERT: F 45 TYR cc_start: 0.6968 (t80) cc_final: 0.6441 (t80) REVERT: F 49 LEU cc_start: 0.7984 (tp) cc_final: 0.7594 (tp) REVERT: F 59 LEU cc_start: 0.7710 (mt) cc_final: 0.7493 (mp) REVERT: F 60 ASP cc_start: 0.6984 (t0) cc_final: 0.6498 (t0) REVERT: F 71 ASN cc_start: 0.8417 (m110) cc_final: 0.7992 (p0) REVERT: F 91 ASP cc_start: 0.8900 (t0) cc_final: 0.8649 (t0) REVERT: F 92 LEU cc_start: 0.8694 (mt) cc_final: 0.8206 (mp) REVERT: F 95 LYS cc_start: 0.9259 (mtpt) cc_final: 0.8807 (ptpt) REVERT: F 129 ILE cc_start: 0.9029 (mm) cc_final: 0.8773 (mm) REVERT: F 142 ARG cc_start: 0.7898 (mtm-85) cc_final: 0.7615 (mtm-85) REVERT: F 145 LEU cc_start: 0.8018 (tp) cc_final: 0.7737 (tp) REVERT: F 148 LEU cc_start: 0.7656 (tp) cc_final: 0.6957 (mm) REVERT: F 157 ASN cc_start: 0.7671 (t0) cc_final: 0.7369 (m-40) REVERT: F 215 GLU cc_start: 0.7079 (pm20) cc_final: 0.6835 (pm20) REVERT: F 335 ASN cc_start: 0.7706 (t0) cc_final: 0.6727 (p0) REVERT: F 381 ASN cc_start: 0.8940 (t0) cc_final: 0.8591 (m-40) REVERT: F 443 LEU cc_start: 0.9005 (mt) cc_final: 0.8763 (mt) outliers start: 2 outliers final: 0 residues processed: 773 average time/residue: 0.1576 time to fit residues: 188.0341 Evaluate side-chains 621 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 621 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 126 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 429 ASN B 139 GLN B 267 HIS B 374 GLN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN D 252 HIS D 363 GLN D 565 ASN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN ** F 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.208902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.155622 restraints weight = 45385.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151294 restraints weight = 22324.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153357 restraints weight = 18151.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.153442 restraints weight = 13272.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153769 restraints weight = 11750.522| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.7575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23642 Z= 0.164 Angle : 0.682 13.454 32097 Z= 0.343 Chirality : 0.044 0.252 3650 Planarity : 0.005 0.050 4231 Dihedral : 7.137 61.432 3495 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.04 % Allowed : 0.34 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 3005 helix: 0.77 (0.15), residues: 1296 sheet: 0.29 (0.24), residues: 409 loop : -0.60 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 155 TYR 0.022 0.002 TYR D 243 PHE 0.038 0.002 PHE B 447 TRP 0.036 0.002 TRP A 290 HIS 0.010 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00370 (23642) covalent geometry : angle 0.68177 (32097) hydrogen bonds : bond 0.03453 ( 1078) hydrogen bonds : angle 4.98685 ( 3114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6010 Ramachandran restraints generated. 3005 Oldfield, 0 Emsley, 3005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 758 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2786 (mpp) cc_final: 0.1585 (pmm) REVERT: A 28 LYS cc_start: 0.7108 (mttp) cc_final: 0.6285 (ptmt) REVERT: A 39 LYS cc_start: 0.8609 (pttm) cc_final: 0.8343 (mmtm) REVERT: A 63 ILE cc_start: 0.7427 (mm) cc_final: 0.7103 (mm) REVERT: A 95 LYS cc_start: 0.9436 (pttt) cc_final: 0.9007 (pttp) REVERT: A 105 ILE cc_start: 0.8328 (pt) cc_final: 0.7747 (pt) REVERT: A 116 PHE cc_start: 0.8282 (t80) cc_final: 0.7873 (t80) REVERT: A 121 LEU cc_start: 0.4743 (pt) cc_final: 0.4542 (pt) REVERT: A 166 LEU cc_start: 0.8274 (tp) cc_final: 0.7960 (mt) REVERT: A 204 ARG cc_start: 0.7212 (mtt-85) cc_final: 0.6873 (mmt90) REVERT: A 257 GLU cc_start: 0.7765 (tp30) cc_final: 0.7510 (tp30) REVERT: A 264 MET cc_start: 0.7092 (mtp) cc_final: 0.6361 (mmt) REVERT: A 302 MET cc_start: 0.7241 (mmp) cc_final: 0.5449 (mtm) REVERT: A 346 MET cc_start: 0.6044 (tpt) cc_final: 0.5839 (tpt) REVERT: A 376 MET cc_start: 0.5405 (ppp) cc_final: 0.4518 (ppp) REVERT: A 382 MET cc_start: 0.7996 (tpt) cc_final: 0.7674 (tpp) REVERT: A 396 LEU cc_start: 0.7635 (pp) cc_final: 0.7405 (pp) REVERT: A 397 GLU cc_start: 0.8708 (pt0) cc_final: 0.8354 (pp20) REVERT: A 398 GLN cc_start: 0.8714 (mm-40) cc_final: 0.7987 (tp40) REVERT: A 442 LEU cc_start: 0.8867 (tp) cc_final: 0.8614 (mm) REVERT: B 1 MET cc_start: -0.2941 (ttt) cc_final: -0.3188 (ttt) REVERT: B 5 ASP cc_start: 0.8024 (p0) cc_final: 0.7505 (p0) REVERT: B 27 PHE cc_start: 0.6069 (m-80) cc_final: 0.5778 (m-80) REVERT: B 28 LYS cc_start: 0.8727 (mtpt) cc_final: 0.8314 (ttpt) REVERT: B 34 GLU cc_start: 0.7369 (pp20) cc_final: 0.6851 (pp20) REVERT: B 53 ASP cc_start: 0.7550 (t0) cc_final: 0.6831 (t70) REVERT: B 77 ASP cc_start: 0.7035 (p0) cc_final: 0.6317 (p0) REVERT: B 95 LYS cc_start: 0.8790 (tttt) cc_final: 0.8404 (ttmm) REVERT: B 110 GLU cc_start: 0.7466 (tt0) cc_final: 0.7123 (tt0) REVERT: B 113 GLU cc_start: 0.9258 (tp30) cc_final: 0.8880 (tm-30) REVERT: B 116 PHE cc_start: 0.8584 (t80) cc_final: 0.7996 (t80) REVERT: B 120 LYS cc_start: 0.8389 (mttm) cc_final: 0.7995 (mttm) REVERT: B 138 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8439 (mt-10) REVERT: B 139 GLN cc_start: 0.8515 (pt0) cc_final: 0.7894 (pp30) REVERT: B 166 LEU cc_start: 0.8796 (tt) cc_final: 0.8572 (tt) REVERT: B 266 LEU cc_start: 0.9162 (mt) cc_final: 0.8813 (mt) REVERT: B 274 LEU cc_start: 0.4380 (tp) cc_final: 0.4141 (tp) REVERT: B 286 ILE cc_start: 0.8107 (tt) cc_final: 0.7805 (pt) REVERT: B 333 VAL cc_start: 0.9109 (t) cc_final: 0.8770 (m) REVERT: B 390 ARG cc_start: 0.7761 (tpp80) cc_final: 0.7029 (tpp80) REVERT: B 397 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7292 (tm-30) REVERT: B 407 LYS cc_start: 0.8036 (ptmt) cc_final: 0.7723 (ttpt) REVERT: B 427 GLN cc_start: 0.8869 (tt0) cc_final: 0.8410 (tt0) REVERT: C 1 MET cc_start: 0.8151 (mmm) cc_final: 0.7909 (mmm) REVERT: C 243 TYR cc_start: 0.8569 (m-80) cc_final: 0.8355 (m-80) REVERT: C 276 TYR cc_start: 0.7611 (p90) cc_final: 0.7382 (p90) REVERT: C 283 LYS cc_start: 0.8869 (mttp) cc_final: 0.8419 (mtpt) REVERT: C 327 SER cc_start: 0.8773 (m) cc_final: 0.8326 (t) REVERT: C 333 ASN cc_start: 0.8198 (p0) cc_final: 0.7817 (p0) REVERT: C 345 TYR cc_start: 0.8262 (p90) cc_final: 0.8000 (p90) REVERT: C 397 ASP cc_start: 0.8309 (t0) cc_final: 0.7878 (t0) REVERT: C 427 ARG cc_start: 0.8311 (ptm160) cc_final: 0.7873 (ptm-80) REVERT: C 434 GLU cc_start: 0.8529 (pt0) cc_final: 0.8218 (pt0) REVERT: C 435 TYR cc_start: 0.7587 (m-80) cc_final: 0.7125 (m-80) REVERT: C 438 MET cc_start: 0.8291 (mmm) cc_final: 0.7769 (mmm) REVERT: C 564 ARG cc_start: 0.6199 (tpt170) cc_final: 0.5830 (tpt170) REVERT: D 20 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7327 (mm-30) REVERT: D 39 ILE cc_start: 0.9274 (mt) cc_final: 0.8903 (mt) REVERT: D 205 ILE cc_start: 0.9002 (mm) cc_final: 0.8719 (mm) REVERT: D 283 LYS cc_start: 0.9046 (mttp) cc_final: 0.8295 (mmmt) REVERT: D 347 PHE cc_start: 0.7635 (p90) cc_final: 0.7279 (p90) REVERT: D 397 ASP cc_start: 0.8339 (t0) cc_final: 0.7946 (t0) REVERT: D 419 THR cc_start: 0.7868 (t) cc_final: 0.7570 (p) REVERT: D 427 ARG cc_start: 0.8127 (mtm110) cc_final: 0.7590 (ptm160) REVERT: D 434 GLU cc_start: 0.8678 (pt0) cc_final: 0.8473 (pt0) REVERT: D 438 MET cc_start: 0.8188 (mmm) cc_final: 0.7830 (mmm) REVERT: D 480 LEU cc_start: 0.8902 (pp) cc_final: 0.8673 (pp) REVERT: D 603 ARG cc_start: 0.8261 (mtm180) cc_final: 0.7135 (mtm-85) REVERT: E 28 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8368 (ttpt) REVERT: E 34 GLU cc_start: 0.7333 (pp20) cc_final: 0.6869 (pp20) REVERT: E 84 HIS cc_start: 0.7838 (m-70) cc_final: 0.7569 (m-70) REVERT: E 95 LYS cc_start: 0.8726 (tttt) cc_final: 0.8356 (ttmm) REVERT: E 98 LEU cc_start: 0.8820 (mt) cc_final: 0.8139 (mt) REVERT: E 110 GLU cc_start: 0.7930 (tt0) cc_final: 0.7659 (tt0) REVERT: E 138 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8721 (tp30) REVERT: E 139 GLN cc_start: 0.8740 (tt0) cc_final: 0.8360 (tt0) REVERT: E 145 LEU cc_start: 0.8255 (mm) cc_final: 0.8044 (mp) REVERT: E 274 LEU cc_start: 0.5508 (tp) cc_final: 0.5285 (tp) REVERT: E 286 ILE cc_start: 0.7748 (tt) cc_final: 0.7425 (pt) REVERT: E 316 ILE cc_start: 0.8960 (tp) cc_final: 0.8484 (tt) REVERT: E 370 ASN cc_start: 0.9081 (m110) cc_final: 0.8564 (m110) REVERT: E 371 HIS cc_start: 0.9054 (t-90) cc_final: 0.8482 (t-90) REVERT: E 373 LYS cc_start: 0.8307 (ptpp) cc_final: 0.7986 (ptpp) REVERT: E 390 ARG cc_start: 0.8426 (mmm-85) cc_final: 0.8121 (tpp80) REVERT: E 394 GLN cc_start: 0.8633 (tp40) cc_final: 0.7405 (mm-40) REVERT: E 397 GLU cc_start: 0.7144 (pp20) cc_final: 0.6492 (pp20) REVERT: E 407 LYS cc_start: 0.8142 (pttt) cc_final: 0.7869 (pttt) REVERT: E 421 GLU cc_start: 0.8838 (tt0) cc_final: 0.8336 (tt0) REVERT: F 1 MET cc_start: 0.3433 (ptp) cc_final: 0.2886 (ptm) REVERT: F 12 THR cc_start: 0.5922 (p) cc_final: 0.5689 (p) REVERT: F 28 LYS cc_start: 0.7321 (mttm) cc_final: 0.6908 (mtpt) REVERT: F 39 LYS cc_start: 0.8523 (pttm) cc_final: 0.7915 (tppt) REVERT: F 45 TYR cc_start: 0.6771 (t80) cc_final: 0.6204 (t80) REVERT: F 59 LEU cc_start: 0.7829 (mt) cc_final: 0.7306 (mp) REVERT: F 60 ASP cc_start: 0.7121 (t0) cc_final: 0.6599 (t0) REVERT: F 71 ASN cc_start: 0.8464 (m110) cc_final: 0.8034 (p0) REVERT: F 142 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7649 (mtm-85) REVERT: F 157 ASN cc_start: 0.7711 (t0) cc_final: 0.7431 (m-40) REVERT: F 164 THR cc_start: 0.8485 (t) cc_final: 0.8240 (p) REVERT: F 217 MET cc_start: 0.6129 (tpp) cc_final: 0.5771 (tpt) REVERT: F 229 LYS cc_start: 0.8226 (mptt) cc_final: 0.7898 (mmtt) REVERT: F 234 ASN cc_start: 0.9184 (t0) cc_final: 0.8903 (t0) REVERT: F 302 MET cc_start: 0.6728 (mmp) cc_final: 0.5338 (mtp) REVERT: F 335 ASN cc_start: 0.7729 (t0) cc_final: 0.6751 (p0) REVERT: F 360 ARG cc_start: 0.8043 (ttm110) cc_final: 0.7759 (ttm-80) REVERT: F 381 ASN cc_start: 0.8914 (t0) cc_final: 0.8606 (m-40) REVERT: F 397 GLU cc_start: 0.8555 (pt0) cc_final: 0.8124 (pp20) REVERT: F 398 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8174 (tm-30) REVERT: F 443 LEU cc_start: 0.8983 (mt) cc_final: 0.8691 (mt) outliers start: 1 outliers final: 0 residues processed: 758 average time/residue: 0.1714 time to fit residues: 200.1496 Evaluate side-chains 620 residues out of total 2431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 162 optimal weight: 0.9990 chunk 128 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 219 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 174 optimal weight: 0.3980 chunk 190 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 429 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN D 252 HIS D 363 GLN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 HIS E 374 GLN ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.209174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.155473 restraints weight = 45541.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.150571 restraints weight = 22666.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.153291 restraints weight = 16519.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.153372 restraints weight = 13053.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153575 restraints weight = 11717.184| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.7712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23642 Z= 0.138 Angle : 0.674 12.337 32097 Z= 0.339 Chirality : 0.043 0.184 3650 Planarity : 0.004 0.045 4231 Dihedral : 7.021 61.038 3495 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.08 % Allowed : 0.21 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.16), residues: 3005 helix: 0.84 (0.15), residues: 1302 sheet: 0.28 (0.24), residues: 416 loop : -0.62 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 393 TYR 0.025 0.002 TYR C 265 PHE 0.025 0.002 PHE C 429 TRP 0.023 0.001 TRP A 290 HIS 0.010 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00314 (23642) covalent geometry : angle 0.67372 (32097) hydrogen bonds : bond 0.03324 ( 1078) hydrogen bonds : angle 4.93124 ( 3114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5273.26 seconds wall clock time: 91 minutes 9.60 seconds (5469.60 seconds total)