Starting phenix.real_space_refine on Sun Jun 15 01:16:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w2j_32262/06_2025/7w2j_32262.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w2j_32262/06_2025/7w2j_32262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w2j_32262/06_2025/7w2j_32262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w2j_32262/06_2025/7w2j_32262.map" model { file = "/net/cci-nas-00/data/ceres_data/7w2j_32262/06_2025/7w2j_32262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w2j_32262/06_2025/7w2j_32262.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 P 4 5.49 5 S 90 5.16 5 C 10438 2.51 5 N 2856 2.21 5 O 3122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16522 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4143 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 36, 'TRANS': 500} Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 4 Chain: "C" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3149 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 25, 'TRANS': 392} Chain breaks: 1 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'HEC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1743 SG CYS A 226 52.601 34.063 74.352 1.00 8.79 S ATOM 1714 SG CYS A 222 51.682 31.454 77.344 1.00 8.19 S ATOM 1674 SG CYS A 216 53.050 28.269 73.790 1.00 25.28 S Restraints were copied for chains: D, E, F Time building chain proxies: 12.92, per 1000 atoms: 0.78 Number of scatterers: 16522 At special positions: 0 Unit cell: (103.077, 127.745, 119.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 12 26.01 S 90 16.00 P 4 15.00 O 3122 8.00 N 2856 7.00 C 10438 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.53 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb=" F3S D 602 " pdb="FE1 F3S D 602 " - pdb=" SG CYS D 226 " pdb="FE3 F3S D 602 " - pdb=" SG CYS D 222 " pdb="FE4 F3S D 602 " - pdb=" SG CYS D 216 " Number of angles added : 18 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 16 sheets defined 39.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.545A pdb=" N LYS A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.564A pdb=" N THR A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 removed outlier: 3.604A pdb=" N PHE A 123 " --> pdb=" O PRO A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.919A pdb=" N ARG A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.350A pdb=" N ALA A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 350 through 353 Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.982A pdb=" N ARG A 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 440 through 462 removed outlier: 4.363A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.881A pdb=" N SER A 492 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.682A pdb=" N MET A 514 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.939A pdb=" N MET A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 541 removed outlier: 4.230A pdb=" N ASP A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 74 through 83 removed outlier: 3.616A pdb=" N ALA B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 removed outlier: 4.248A pdb=" N LYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 124 removed outlier: 4.140A pdb=" N ILE B 124 " --> pdb=" O LEU B 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 124' Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'C' and resid 41 through 51 removed outlier: 3.544A pdb=" N ALA C 47 " --> pdb=" O GLY C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 removed outlier: 3.530A pdb=" N ALA C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 141 removed outlier: 3.508A pdb=" N LYS C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 185 through 196 removed outlier: 3.546A pdb=" N GLY C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 245 through 256 removed outlier: 3.504A pdb=" N THR C 255 " --> pdb=" O GLN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 278 Processing helix chain 'C' and resid 279 through 293 removed outlier: 3.609A pdb=" N ILE C 283 " --> pdb=" O PRO C 279 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 341 removed outlier: 3.752A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 408 through 423 removed outlier: 4.190A pdb=" N ALA C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.564A pdb=" N GLN C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'C' and resid 452 through 471 removed outlier: 3.560A pdb=" N MET C 456 " --> pdb=" O SER C 452 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 459 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 Processing helix chain 'D' and resid 43 through 54 Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.545A pdb=" N LYS D 59 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 105 through 110 removed outlier: 3.563A pdb=" N THR D 108 " --> pdb=" O GLY D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 123 removed outlier: 3.603A pdb=" N PHE D 123 " --> pdb=" O PRO D 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 124 through 130 Processing helix chain 'D' and resid 138 through 154 Proline residue: D 144 - end of helix Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.919A pdb=" N ARG D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 245 removed outlier: 4.350A pdb=" N ALA D 237 " --> pdb=" O ASN D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 301 Processing helix chain 'D' and resid 350 through 353 Processing helix chain 'D' and resid 355 through 360 removed outlier: 3.983A pdb=" N ARG D 358 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER D 359 " --> pdb=" O ASP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 384 Processing helix chain 'D' and resid 388 through 401 Processing helix chain 'D' and resid 440 through 462 removed outlier: 4.364A pdb=" N VAL D 444 " --> pdb=" O VAL D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 492 removed outlier: 3.881A pdb=" N SER D 492 " --> pdb=" O PRO D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 514 removed outlier: 3.682A pdb=" N MET D 514 " --> pdb=" O GLY D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 531 removed outlier: 3.940A pdb=" N MET D 526 " --> pdb=" O SER D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 541 removed outlier: 4.229A pdb=" N ASP D 535 " --> pdb=" O LEU D 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 56 Processing helix chain 'E' and resid 74 through 83 removed outlier: 3.616A pdb=" N ALA E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 removed outlier: 4.249A pdb=" N LYS E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA E 92 " --> pdb=" O THR E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 124 removed outlier: 4.141A pdb=" N ILE E 124 " --> pdb=" O LEU E 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 121 through 124' Processing helix chain 'E' and resid 125 through 130 Processing helix chain 'F' and resid 41 through 51 removed outlier: 3.545A pdb=" N ALA F 47 " --> pdb=" O GLY F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 106 removed outlier: 3.530A pdb=" N ALA F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 127 through 141 removed outlier: 3.508A pdb=" N LYS F 132 " --> pdb=" O ASP F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 163 through 172 Processing helix chain 'F' and resid 185 through 196 removed outlier: 3.545A pdb=" N GLY F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP F 196 " --> pdb=" O ARG F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 206 Processing helix chain 'F' and resid 245 through 256 removed outlier: 3.504A pdb=" N THR F 255 " --> pdb=" O GLN F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 272 Processing helix chain 'F' and resid 274 through 278 Processing helix chain 'F' and resid 279 through 293 removed outlier: 3.609A pdb=" N ILE F 283 " --> pdb=" O PRO F 279 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER F 292 " --> pdb=" O THR F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 341 removed outlier: 3.751A pdb=" N GLU F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 383 Processing helix chain 'F' and resid 408 through 423 removed outlier: 4.188A pdb=" N ALA F 413 " --> pdb=" O ASP F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 441 removed outlier: 3.564A pdb=" N GLN F 437 " --> pdb=" O ASP F 433 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 451 Processing helix chain 'F' and resid 452 through 471 removed outlier: 3.561A pdb=" N MET F 456 " --> pdb=" O SER F 452 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU F 459 " --> pdb=" O VAL F 455 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA F 467 " --> pdb=" O GLY F 463 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE F 468 " --> pdb=" O ILE F 464 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL F 471 " --> pdb=" O ALA F 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.378A pdb=" N VAL A 33 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE A 249 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 35 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 284 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.378A pdb=" N VAL A 33 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE A 249 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 35 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 284 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N PHE A 507 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE A 285 " --> pdb=" O PHE A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 332 removed outlier: 3.690A pdb=" N ILE A 405 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 331 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR A 406 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 367 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN A 408 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN A 365 " --> pdb=" O ASN A 408 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 366 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 70 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA7, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AA8, first strand: chain 'C' and resid 385 through 387 Processing sheet with id=AA9, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.377A pdb=" N VAL D 33 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE D 249 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU D 35 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER D 7 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA D 282 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP D 9 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR D 284 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA D 282 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR D 266 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR D 271 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL D 254 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.377A pdb=" N VAL D 33 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE D 249 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU D 35 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER D 7 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA D 282 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP D 9 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR D 284 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N PHE D 507 " --> pdb=" O LYS D 283 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE D 285 " --> pdb=" O PHE D 507 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 87 through 89 Processing sheet with id=AB3, first strand: chain 'D' and resid 327 through 332 removed outlier: 3.691A pdb=" N ILE D 405 " --> pdb=" O MET D 329 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE D 331 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR D 406 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY D 367 " --> pdb=" O TYR D 406 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN D 408 " --> pdb=" O GLN D 365 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN D 365 " --> pdb=" O ASN D 408 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 366 " --> pdb=" O ILE D 349 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 70 through 72 Processing sheet with id=AB5, first strand: chain 'F' and resid 224 through 225 Processing sheet with id=AB6, first strand: chain 'F' and resid 257 through 258 Processing sheet with id=AB7, first strand: chain 'F' and resid 385 through 387 510 hydrogen bonds defined for protein. 1434 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: 4.89 Time building geometry restraints manager: 5.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.77: 16809 1.77 - 2.33: 157 2.33 - 2.89: 0 2.89 - 3.45: 0 3.45 - 4.01: 6 Bond restraints: 16972 Sorted by residual: bond pdb=" S4 F3S D 602 " pdb="FE1 F3S D 602 " ideal model delta sigma weight residual 2.233 4.007 -1.774 2.00e-02 2.50e+03 7.87e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 4.007 -1.774 2.00e-02 2.50e+03 7.86e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.759 -1.501 2.00e-02 2.50e+03 5.63e+03 bond pdb=" S1 F3S D 602 " pdb="FE4 F3S D 602 " ideal model delta sigma weight residual 2.258 3.758 -1.500 2.00e-02 2.50e+03 5.63e+03 bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.463 -1.163 2.00e-02 2.50e+03 3.38e+03 ... (remaining 16967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.47: 23176 10.47 - 20.95: 6 20.95 - 31.42: 6 31.42 - 41.90: 8 41.90 - 52.37: 6 Bond angle restraints: 23202 Sorted by residual: angle pdb=" S3 F3S D 602 " pdb="FE1 F3S D 602 " pdb=" S4 F3S D 602 " ideal model delta sigma weight residual 112.59 60.22 52.37 3.00e+00 1.11e-01 3.05e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 60.24 52.35 3.00e+00 1.11e-01 3.05e+02 angle pdb=" S1 F3S D 602 " pdb="FE4 F3S D 602 " pdb=" S3 F3S D 602 " ideal model delta sigma weight residual 114.75 66.85 47.90 3.00e+00 1.11e-01 2.55e+02 angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 66.85 47.90 3.00e+00 1.11e-01 2.55e+02 angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S2 F3S A 602 " ideal model delta sigma weight residual 103.63 61.46 42.17 3.00e+00 1.11e-01 1.98e+02 ... (remaining 23197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.58: 9424 26.58 - 53.16: 494 53.16 - 79.74: 42 79.74 - 106.31: 20 106.31 - 132.89: 2 Dihedral angle restraints: 9982 sinusoidal: 3928 harmonic: 6054 Sorted by residual: dihedral pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta harmonic sigma weight residual -180.00 -132.52 -47.48 0 5.00e+00 4.00e-02 9.02e+01 dihedral pdb=" CA PHE D 80 " pdb=" C PHE D 80 " pdb=" N PRO D 81 " pdb=" CA PRO D 81 " ideal model delta harmonic sigma weight residual -180.00 -132.58 -47.42 0 5.00e+00 4.00e-02 8.99e+01 dihedral pdb=" CA PHE F 156 " pdb=" C PHE F 156 " pdb=" N PRO F 157 " pdb=" CA PRO F 157 " ideal model delta harmonic sigma weight residual 180.00 -139.15 -40.85 0 5.00e+00 4.00e-02 6.68e+01 ... (remaining 9979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.894: 2476 3.894 - 7.787: 0 7.787 - 11.681: 0 11.681 - 15.574: 0 15.574 - 19.468: 2 Chirality restraints: 2478 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -8.70 19.47 2.00e-01 2.50e+01 9.48e+03 chirality pdb=" S2 F3S D 602 " pdb="FE1 F3S D 602 " pdb="FE3 F3S D 602 " pdb="FE4 F3S D 602 " both_signs ideal model delta sigma weight residual False 10.77 -8.70 19.47 2.00e-01 2.50e+01 9.47e+03 chirality pdb=" CB ILE B 133 " pdb=" CA ILE B 133 " pdb=" CG1 ILE B 133 " pdb=" CG2 ILE B 133 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2475 not shown) Planarity restraints: 2986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 502 " -0.019 2.00e-02 2.50e+03 4.68e-02 4.93e+01 pdb=" C2C HEC C 502 " 0.127 2.00e-02 2.50e+03 pdb=" C3C HEC C 502 " -0.006 2.00e-02 2.50e+03 pdb=" C4C HEC C 502 " -0.002 2.00e-02 2.50e+03 pdb=" CAC HEC C 502 " -0.034 2.00e-02 2.50e+03 pdb=" CHC HEC C 502 " -0.024 2.00e-02 2.50e+03 pdb=" CHD HEC C 502 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC C 502 " -0.036 2.00e-02 2.50e+03 pdb=" NC HEC C 502 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC F 502 " -0.018 2.00e-02 2.50e+03 4.66e-02 4.89e+01 pdb=" C2C HEC F 502 " 0.127 2.00e-02 2.50e+03 pdb=" C3C HEC F 502 " -0.006 2.00e-02 2.50e+03 pdb=" C4C HEC F 502 " -0.003 2.00e-02 2.50e+03 pdb=" CAC HEC F 502 " -0.034 2.00e-02 2.50e+03 pdb=" CHC HEC F 502 " -0.024 2.00e-02 2.50e+03 pdb=" CHD HEC F 502 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC F 502 " -0.036 2.00e-02 2.50e+03 pdb=" NC HEC F 502 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC F 503 " 0.013 2.00e-02 2.50e+03 2.95e-02 1.95e+01 pdb=" C2C HEC F 503 " -0.080 2.00e-02 2.50e+03 pdb=" C3C HEC F 503 " 0.005 2.00e-02 2.50e+03 pdb=" C4C HEC F 503 " -0.000 2.00e-02 2.50e+03 pdb=" CAC HEC F 503 " 0.022 2.00e-02 2.50e+03 pdb=" CHC HEC F 503 " 0.015 2.00e-02 2.50e+03 pdb=" CHD HEC F 503 " -0.002 2.00e-02 2.50e+03 pdb=" CMC HEC F 503 " 0.022 2.00e-02 2.50e+03 pdb=" NC HEC F 503 " 0.006 2.00e-02 2.50e+03 ... (remaining 2983 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 246 2.59 - 3.17: 15383 3.17 - 3.74: 25522 3.74 - 4.32: 37186 4.32 - 4.90: 59514 Nonbonded interactions: 137851 Sorted by model distance: nonbonded pdb=" SG CYS A 226 " pdb=" S1 F3S A 602 " model vdw 2.011 3.760 nonbonded pdb=" SG CYS D 226 " pdb=" S1 F3S D 602 " model vdw 2.012 3.760 nonbonded pdb=" SG CYS A 222 " pdb=" S3 F3S A 602 " model vdw 2.013 3.760 nonbonded pdb=" SG CYS D 222 " pdb=" S3 F3S D 602 " model vdw 2.013 3.760 nonbonded pdb=" OH TYR A 68 " pdb=" O PRO A 224 " model vdw 2.090 3.040 ... (remaining 137846 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 44.500 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.035 1.774 17010 Z= 1.787 Angle : 1.692 52.370 23220 Z= 0.621 Chirality : 0.556 19.468 2478 Planarity : 0.006 0.078 2986 Dihedral : 15.658 132.892 6122 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.96 % Favored : 88.66 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.17), residues: 2072 helix: -1.63 (0.19), residues: 670 sheet: -1.40 (0.36), residues: 182 loop : -1.91 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 111 HIS 0.016 0.002 HIS D 503 PHE 0.034 0.004 PHE E 79 TYR 0.030 0.003 TYR D 368 ARG 0.011 0.001 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.25783 ( 498) hydrogen bonds : angle 10.23269 ( 1434) metal coordination : bond 0.87980 ( 6) metal coordination : angle 29.16381 ( 18) covalent geometry : bond 0.02956 (16972) covalent geometry : angle 1.48512 (23202) Misc. bond : bond 0.19219 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 PHE cc_start: 0.4663 (t80) cc_final: 0.4278 (t80) REVERT: B 148 LEU cc_start: 0.8433 (mt) cc_final: 0.8193 (mt) REVERT: B 150 TYR cc_start: 0.5574 (t80) cc_final: 0.5275 (t80) REVERT: C 410 GLU cc_start: 0.6098 (tp30) cc_final: 0.5835 (tp30) REVERT: E 86 PHE cc_start: 0.4701 (t80) cc_final: 0.4272 (t80) REVERT: E 148 LEU cc_start: 0.8457 (mt) cc_final: 0.8233 (mt) REVERT: E 150 TYR cc_start: 0.5648 (t80) cc_final: 0.5356 (t80) REVERT: F 135 TYR cc_start: 0.6874 (t80) cc_final: 0.6654 (t80) REVERT: F 410 GLU cc_start: 0.6060 (tp30) cc_final: 0.5821 (tp30) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3032 time to fit residues: 101.8552 Evaluate side-chains 180 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 8.9990 chunk 156 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 0.0570 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS C 124 ASN C 238 GLN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 HIS F 124 ASN ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.153941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143970 restraints weight = 22485.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140822 restraints weight = 25680.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.139579 restraints weight = 33452.927| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 17010 Z= 0.236 Angle : 1.454 57.956 23220 Z= 0.483 Chirality : 0.071 1.892 2478 Planarity : 0.006 0.067 2986 Dihedral : 10.157 117.892 2432 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.23 % Favored : 93.29 % Rotamer: Outliers : 0.82 % Allowed : 9.68 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.18), residues: 2072 helix: -0.60 (0.20), residues: 694 sheet: -0.71 (0.39), residues: 170 loop : -1.69 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 111 HIS 0.005 0.001 HIS A 503 PHE 0.016 0.001 PHE A 270 TYR 0.017 0.002 TYR C 120 ARG 0.007 0.001 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 498) hydrogen bonds : angle 6.53947 ( 1434) metal coordination : bond 0.01437 ( 6) metal coordination : angle 29.95169 ( 18) covalent geometry : bond 0.00511 (16972) covalent geometry : angle 1.19204 (23202) Misc. bond : bond 0.04498 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: B 150 TYR cc_start: 0.5349 (t80) cc_final: 0.4838 (t80) REVERT: C 224 ASP cc_start: 0.7809 (p0) cc_final: 0.7553 (p0) REVERT: D 61 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6939 (mp10) REVERT: E 86 PHE cc_start: 0.3987 (t80) cc_final: 0.3766 (t80) REVERT: E 150 TYR cc_start: 0.5272 (t80) cc_final: 0.4783 (t80) REVERT: F 224 ASP cc_start: 0.7758 (p0) cc_final: 0.7506 (p0) outliers start: 14 outliers final: 6 residues processed: 216 average time/residue: 0.2573 time to fit residues: 88.6529 Evaluate side-chains 188 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 79 optimal weight: 0.4980 chunk 165 optimal weight: 5.9990 chunk 6 optimal weight: 0.0980 chunk 192 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 170 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 GLN ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.173471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.167913 restraints weight = 21238.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.163154 restraints weight = 36701.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.161669 restraints weight = 28513.455| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 17010 Z= 0.144 Angle : 1.467 86.969 23220 Z= 0.447 Chirality : 0.059 1.404 2478 Planarity : 0.005 0.058 2986 Dihedral : 9.815 112.829 2432 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 1.70 % Allowed : 12.56 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.18), residues: 2072 helix: -0.17 (0.20), residues: 718 sheet: -0.32 (0.39), residues: 166 loop : -1.48 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 128 HIS 0.005 0.001 HIS C 105 PHE 0.014 0.001 PHE A 270 TYR 0.017 0.001 TYR A 79 ARG 0.006 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 498) hydrogen bonds : angle 5.87973 ( 1434) metal coordination : bond 0.00481 ( 6) metal coordination : angle 33.99995 ( 18) covalent geometry : bond 0.00328 (16972) covalent geometry : angle 1.12081 (23202) Misc. bond : bond 0.04706 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 1.488 Fit side-chains REVERT: A 61 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6652 (mp10) REVERT: A 211 ASP cc_start: 0.8258 (t70) cc_final: 0.7129 (t0) REVERT: A 221 ASN cc_start: 0.8395 (t0) cc_final: 0.8123 (t0) REVERT: A 440 VAL cc_start: 0.6825 (m) cc_final: 0.6605 (m) REVERT: C 118 MET cc_start: 0.7659 (tpt) cc_final: 0.7293 (tpt) REVERT: C 182 HIS cc_start: 0.5795 (m-70) cc_final: 0.5546 (m-70) REVERT: C 224 ASP cc_start: 0.7678 (p0) cc_final: 0.7363 (p0) REVERT: C 449 LYS cc_start: 0.6652 (pptt) cc_final: 0.5616 (ptpp) REVERT: D 61 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6729 (mp10) REVERT: D 211 ASP cc_start: 0.8274 (t70) cc_final: 0.7179 (t0) REVERT: D 221 ASN cc_start: 0.8435 (t0) cc_final: 0.8184 (t0) REVERT: F 118 MET cc_start: 0.7656 (tpt) cc_final: 0.7301 (tpt) REVERT: F 190 ARG cc_start: 0.6182 (tpp80) cc_final: 0.5972 (tpp80) REVERT: F 224 ASP cc_start: 0.7644 (p0) cc_final: 0.7344 (p0) outliers start: 29 outliers final: 19 residues processed: 236 average time/residue: 0.2946 time to fit residues: 109.6609 Evaluate side-chains 213 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 155 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.152222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3570 r_free = 0.3570 target = 0.139039 restraints weight = 22600.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.135944 restraints weight = 28293.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135146 restraints weight = 30406.372| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.181 17010 Z= 0.243 Angle : 1.540 84.812 23220 Z= 0.483 Chirality : 0.063 1.441 2478 Planarity : 0.006 0.062 2986 Dihedral : 10.215 124.224 2432 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.58 % Favored : 92.04 % Rotamer: Outliers : 3.11 % Allowed : 13.79 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.19), residues: 2072 helix: -0.23 (0.20), residues: 706 sheet: -0.24 (0.39), residues: 170 loop : -1.52 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 128 HIS 0.008 0.001 HIS E 118 PHE 0.023 0.002 PHE E 144 TYR 0.019 0.002 TYR E 150 ARG 0.006 0.001 ARG D 397 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 498) hydrogen bonds : angle 5.94324 ( 1434) metal coordination : bond 0.00154 ( 6) metal coordination : angle 34.99948 ( 18) covalent geometry : bond 0.00583 (16972) covalent geometry : angle 1.19277 (23202) Misc. bond : bond 0.05374 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7504 (tt) REVERT: A 61 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6888 (mp10) REVERT: C 118 MET cc_start: 0.8327 (tpt) cc_final: 0.8057 (tpt) REVERT: C 224 ASP cc_start: 0.7717 (p0) cc_final: 0.7472 (p0) REVERT: D 61 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6870 (mp10) REVERT: D 221 ASN cc_start: 0.8577 (t0) cc_final: 0.8261 (t0) REVERT: D 223 MET cc_start: 0.8227 (mmm) cc_final: 0.7895 (mmt) REVERT: F 118 MET cc_start: 0.8329 (tpt) cc_final: 0.8064 (tpt) REVERT: F 182 HIS cc_start: 0.5903 (m-70) cc_final: 0.5558 (m170) REVERT: F 224 ASP cc_start: 0.7709 (p0) cc_final: 0.7487 (p0) outliers start: 53 outliers final: 34 residues processed: 220 average time/residue: 0.2605 time to fit residues: 94.7660 Evaluate side-chains 222 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 253 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 35 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 79 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.152401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.139194 restraints weight = 23081.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.138578 restraints weight = 34181.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138852 restraints weight = 31363.145| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 17010 Z= 0.159 Angle : 1.466 83.633 23220 Z= 0.443 Chirality : 0.060 1.450 2478 Planarity : 0.005 0.059 2986 Dihedral : 9.886 119.013 2432 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.65 % Favored : 94.16 % Rotamer: Outliers : 2.58 % Allowed : 14.96 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.19), residues: 2072 helix: 0.03 (0.20), residues: 710 sheet: 0.18 (0.41), residues: 162 loop : -1.33 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 111 HIS 0.004 0.001 HIS E 118 PHE 0.020 0.001 PHE C 64 TYR 0.017 0.001 TYR A 79 ARG 0.004 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 498) hydrogen bonds : angle 5.64493 ( 1434) metal coordination : bond 0.00132 ( 6) metal coordination : angle 34.19365 ( 18) covalent geometry : bond 0.00371 (16972) covalent geometry : angle 1.11486 (23202) Misc. bond : bond 0.03805 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6577 (mp10) REVERT: A 221 ASN cc_start: 0.8559 (t0) cc_final: 0.8233 (t0) REVERT: C 182 HIS cc_start: 0.5676 (m-70) cc_final: 0.5450 (m-70) REVERT: C 224 ASP cc_start: 0.7573 (p0) cc_final: 0.7321 (p0) REVERT: C 449 LYS cc_start: 0.6708 (pptt) cc_final: 0.5650 (ptpp) REVERT: D 61 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6655 (mp10) REVERT: D 223 MET cc_start: 0.8139 (mmm) cc_final: 0.7851 (mmt) REVERT: F 190 ARG cc_start: 0.6202 (tpp80) cc_final: 0.5975 (tpp80) REVERT: F 224 ASP cc_start: 0.7568 (p0) cc_final: 0.7311 (p0) outliers start: 44 outliers final: 30 residues processed: 236 average time/residue: 0.3189 time to fit residues: 122.3507 Evaluate side-chains 222 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 123 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.154401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144720 restraints weight = 22793.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.140001 restraints weight = 27141.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139781 restraints weight = 34908.022| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 17010 Z= 0.186 Angle : 1.486 83.995 23220 Z= 0.453 Chirality : 0.061 1.452 2478 Planarity : 0.005 0.063 2986 Dihedral : 9.949 121.379 2432 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.14 % Favored : 92.66 % Rotamer: Outliers : 3.11 % Allowed : 15.55 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.19), residues: 2072 helix: 0.09 (0.20), residues: 710 sheet: 0.25 (0.41), residues: 162 loop : -1.32 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 128 HIS 0.006 0.001 HIS E 118 PHE 0.019 0.002 PHE C 64 TYR 0.031 0.002 TYR D 271 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 498) hydrogen bonds : angle 5.65191 ( 1434) metal coordination : bond 0.00136 ( 6) metal coordination : angle 34.29209 ( 18) covalent geometry : bond 0.00443 (16972) covalent geometry : angle 1.13892 (23202) Misc. bond : bond 0.03728 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6653 (mp10) REVERT: A 226 CYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7057 (p) REVERT: A 257 MET cc_start: 0.6299 (mtm) cc_final: 0.6092 (mtp) REVERT: C 224 ASP cc_start: 0.7539 (p0) cc_final: 0.7316 (p0) REVERT: C 449 LYS cc_start: 0.6788 (pptt) cc_final: 0.5844 (ptpp) REVERT: D 61 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6705 (mp10) REVERT: D 221 ASN cc_start: 0.8524 (t0) cc_final: 0.8238 (t0) REVERT: D 223 MET cc_start: 0.8145 (mmm) cc_final: 0.7878 (mmt) REVERT: D 226 CYS cc_start: 0.8568 (OUTLIER) cc_final: 0.7151 (p) REVERT: F 190 ARG cc_start: 0.6019 (tpp80) cc_final: 0.5819 (tpp80) REVERT: F 224 ASP cc_start: 0.7542 (p0) cc_final: 0.7290 (p0) outliers start: 53 outliers final: 38 residues processed: 229 average time/residue: 0.2644 time to fit residues: 98.4600 Evaluate side-chains 229 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 152 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 70 optimal weight: 0.0670 chunk 154 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 161 optimal weight: 0.0670 chunk 80 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.153999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 119)---------------| | r_work = 0.3560 r_free = 0.3560 target = 0.139158 restraints weight = 22791.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.138493 restraints weight = 23092.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.138198 restraints weight = 23241.062| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 17010 Z= 0.192 Angle : 1.489 84.121 23220 Z= 0.456 Chirality : 0.061 1.450 2478 Planarity : 0.005 0.065 2986 Dihedral : 9.995 122.943 2432 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.56 % Favored : 93.24 % Rotamer: Outliers : 3.29 % Allowed : 16.20 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.19), residues: 2072 helix: 0.14 (0.20), residues: 706 sheet: 0.34 (0.42), residues: 162 loop : -1.34 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 128 HIS 0.006 0.001 HIS E 118 PHE 0.020 0.002 PHE C 64 TYR 0.022 0.002 TYR D 271 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 498) hydrogen bonds : angle 5.64356 ( 1434) metal coordination : bond 0.00136 ( 6) metal coordination : angle 34.40744 ( 18) covalent geometry : bond 0.00459 (16972) covalent geometry : angle 1.14060 (23202) Misc. bond : bond 0.04350 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 189 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7527 (tt) REVERT: A 61 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6686 (mp10) REVERT: A 226 CYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7094 (p) REVERT: A 257 MET cc_start: 0.6376 (mtm) cc_final: 0.6152 (mtp) REVERT: A 440 VAL cc_start: 0.6828 (m) cc_final: 0.6616 (m) REVERT: C 118 MET cc_start: 0.8163 (tpt) cc_final: 0.7766 (tpt) REVERT: C 182 HIS cc_start: 0.5856 (m-70) cc_final: 0.5507 (m170) REVERT: C 224 ASP cc_start: 0.7566 (p0) cc_final: 0.7347 (p0) REVERT: C 449 LYS cc_start: 0.6715 (pptt) cc_final: 0.5611 (ptpp) REVERT: D 61 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6681 (mp10) REVERT: D 226 CYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7070 (p) REVERT: D 440 VAL cc_start: 0.6882 (m) cc_final: 0.6669 (m) REVERT: F 118 MET cc_start: 0.8156 (tpt) cc_final: 0.7771 (tpt) REVERT: F 224 ASP cc_start: 0.7634 (p0) cc_final: 0.7402 (p0) REVERT: F 456 MET cc_start: 0.5652 (tpt) cc_final: 0.5314 (tpt) outliers start: 56 outliers final: 43 residues processed: 229 average time/residue: 0.2410 time to fit residues: 87.3917 Evaluate side-chains 233 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 343 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 115 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.153423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134845 restraints weight = 22245.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134816 restraints weight = 27231.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135604 restraints weight = 22905.381| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 17010 Z= 0.190 Angle : 1.490 84.043 23220 Z= 0.455 Chirality : 0.061 1.453 2478 Planarity : 0.005 0.067 2986 Dihedral : 9.970 123.015 2432 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.05 % Favored : 92.76 % Rotamer: Outliers : 3.29 % Allowed : 16.73 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.19), residues: 2072 helix: 0.17 (0.20), residues: 708 sheet: 0.36 (0.42), residues: 162 loop : -1.32 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 128 HIS 0.006 0.001 HIS B 118 PHE 0.020 0.002 PHE C 64 TYR 0.024 0.002 TYR A 271 ARG 0.006 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 498) hydrogen bonds : angle 5.62359 ( 1434) metal coordination : bond 0.00140 ( 6) metal coordination : angle 34.42796 ( 18) covalent geometry : bond 0.00455 (16972) covalent geometry : angle 1.14090 (23202) Misc. bond : bond 0.04829 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7518 (tt) REVERT: A 61 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6781 (mp10) REVERT: A 226 CYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7155 (p) REVERT: A 257 MET cc_start: 0.6377 (mtm) cc_final: 0.6166 (mtp) REVERT: C 182 HIS cc_start: 0.5801 (m-70) cc_final: 0.5395 (m170) REVERT: C 224 ASP cc_start: 0.7644 (p0) cc_final: 0.7424 (p0) REVERT: D 61 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6687 (mp10) REVERT: D 226 CYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7125 (p) REVERT: F 224 ASP cc_start: 0.7655 (p0) cc_final: 0.7424 (p0) REVERT: F 456 MET cc_start: 0.5676 (tpt) cc_final: 0.5310 (tpt) outliers start: 56 outliers final: 43 residues processed: 230 average time/residue: 0.2428 time to fit residues: 89.6014 Evaluate side-chains 235 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 343 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 58 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 127 optimal weight: 0.0980 chunk 36 optimal weight: 0.2980 chunk 191 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 123 GLN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN E 123 GLN ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.154517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.140982 restraints weight = 22744.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140420 restraints weight = 31623.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140760 restraints weight = 30667.017| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 17010 Z= 0.148 Angle : 1.443 83.463 23220 Z= 0.435 Chirality : 0.060 1.443 2478 Planarity : 0.005 0.065 2986 Dihedral : 9.762 117.188 2432 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.89 % Favored : 94.02 % Rotamer: Outliers : 2.46 % Allowed : 18.02 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 2072 helix: 0.22 (0.20), residues: 736 sheet: 0.53 (0.43), residues: 162 loop : -1.24 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 128 HIS 0.004 0.001 HIS F 105 PHE 0.021 0.001 PHE C 64 TYR 0.026 0.002 TYR C 135 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 498) hydrogen bonds : angle 5.45802 ( 1434) metal coordination : bond 0.00126 ( 6) metal coordination : angle 33.86843 ( 18) covalent geometry : bond 0.00341 (16972) covalent geometry : angle 1.09326 (23202) Misc. bond : bond 0.04437 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8262 (t70) cc_final: 0.7078 (t0) REVERT: A 226 CYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7123 (p) REVERT: C 224 ASP cc_start: 0.7515 (p0) cc_final: 0.7291 (p0) REVERT: C 449 LYS cc_start: 0.6711 (pptt) cc_final: 0.5701 (ptpp) REVERT: C 456 MET cc_start: 0.5594 (tpt) cc_final: 0.4708 (tpp) REVERT: D 61 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6583 (mp10) REVERT: D 211 ASP cc_start: 0.8194 (t70) cc_final: 0.6962 (t0) REVERT: D 226 CYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7046 (p) REVERT: F 115 TYR cc_start: 0.7739 (m-80) cc_final: 0.7349 (m-80) REVERT: F 224 ASP cc_start: 0.7542 (p0) cc_final: 0.7300 (p0) REVERT: F 456 MET cc_start: 0.5569 (tpt) cc_final: 0.4724 (tpp) outliers start: 42 outliers final: 37 residues processed: 239 average time/residue: 0.2395 time to fit residues: 92.5092 Evaluate side-chains 231 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 343 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 107 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 94 optimal weight: 0.0870 chunk 133 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN E 164 HIS F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.157210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143269 restraints weight = 22680.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142432 restraints weight = 37332.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143023 restraints weight = 33768.222| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 17010 Z= 0.144 Angle : 1.429 83.274 23220 Z= 0.432 Chirality : 0.060 1.452 2478 Planarity : 0.005 0.064 2986 Dihedral : 9.491 112.971 2432 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 2.17 % Allowed : 19.25 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.19), residues: 2072 helix: 0.46 (0.20), residues: 734 sheet: 0.07 (0.41), residues: 170 loop : -1.14 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 128 HIS 0.004 0.001 HIS E 164 PHE 0.021 0.001 PHE C 64 TYR 0.024 0.001 TYR A 271 ARG 0.006 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 498) hydrogen bonds : angle 5.37894 ( 1434) metal coordination : bond 0.00091 ( 6) metal coordination : angle 33.35926 ( 18) covalent geometry : bond 0.00333 (16972) covalent geometry : angle 1.08606 (23202) Misc. bond : bond 0.04714 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7381 (tt) REVERT: A 226 CYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7114 (p) REVERT: A 456 MET cc_start: 0.6847 (mmm) cc_final: 0.6462 (mtt) REVERT: C 115 TYR cc_start: 0.7716 (m-80) cc_final: 0.7470 (m-80) REVERT: C 224 ASP cc_start: 0.7497 (p0) cc_final: 0.7265 (p0) REVERT: C 456 MET cc_start: 0.5642 (tpt) cc_final: 0.4762 (tpp) REVERT: D 96 TYR cc_start: 0.8653 (t80) cc_final: 0.8181 (t80) REVERT: D 226 CYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7083 (p) REVERT: D 456 MET cc_start: 0.6848 (mmm) cc_final: 0.6471 (mtt) REVERT: E 128 TRP cc_start: 0.5723 (t60) cc_final: 0.5093 (t60) REVERT: F 115 TYR cc_start: 0.7704 (m-80) cc_final: 0.7452 (m-80) REVERT: F 224 ASP cc_start: 0.7532 (p0) cc_final: 0.7271 (p0) REVERT: F 456 MET cc_start: 0.5437 (tpt) cc_final: 0.4529 (tpp) outliers start: 37 outliers final: 30 residues processed: 230 average time/residue: 0.2668 time to fit residues: 95.6124 Evaluate side-chains 221 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 343 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 25 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 111 optimal weight: 0.0370 chunk 54 optimal weight: 0.4980 chunk 166 optimal weight: 50.0000 chunk 191 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 ASN ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.157626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143772 restraints weight = 22578.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142948 restraints weight = 32803.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143227 restraints weight = 30455.869| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 17010 Z= 0.144 Angle : 1.420 83.381 23220 Z= 0.428 Chirality : 0.060 1.446 2478 Planarity : 0.005 0.064 2986 Dihedral : 9.414 111.201 2432 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.31 % Favored : 94.59 % Rotamer: Outliers : 2.52 % Allowed : 18.96 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.19), residues: 2072 helix: 0.63 (0.21), residues: 724 sheet: 0.14 (0.42), residues: 170 loop : -1.12 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 111 HIS 0.003 0.001 HIS A 278 PHE 0.023 0.001 PHE C 64 TYR 0.018 0.001 TYR C 135 ARG 0.009 0.001 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 498) hydrogen bonds : angle 5.35943 ( 1434) metal coordination : bond 0.00098 ( 6) metal coordination : angle 32.99726 ( 18) covalent geometry : bond 0.00331 (16972) covalent geometry : angle 1.08317 (23202) Misc. bond : bond 0.04586 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5122.61 seconds wall clock time: 92 minutes 11.40 seconds (5531.40 seconds total)