Starting phenix.real_space_refine on Wed Mar 4 22:02:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w2j_32262/03_2026/7w2j_32262.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w2j_32262/03_2026/7w2j_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_32262/03_2026/7w2j_32262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w2j_32262/03_2026/7w2j_32262.map" model { file = "/net/cci-nas-00/data/ceres_data/7w2j_32262/03_2026/7w2j_32262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w2j_32262/03_2026/7w2j_32262.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 4.75, per 1000 atoms: 0.29 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: 1.71 Conformation dependent library (CDL) restraints added in 594.3 milliseconds 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: 0.39 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: 2.56 Time building geometry restraints manager: 2.10 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: 0.03 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.710 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.950 ------------------------------------------------------------------------------- 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 : 17.82 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.011 0.001 ARG A 397 TYR 0.030 0.003 TYR D 368 PHE 0.034 0.004 PHE E 79 TRP 0.052 0.003 TRP A 111 HIS 0.016 0.002 HIS D 503 Details of bonding type rmsd covalent geometry : bond 0.02956 (16972) covalent geometry : angle 1.48512 (23202) hydrogen bonds : bond 0.25783 ( 498) hydrogen bonds : angle 10.23269 ( 1434) metal coordination : bond 0.87980 ( 6) metal coordination : angle 29.16381 ( 18) 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 : 0.577 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: 0.5573 (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: 0.1196 time to fit residues: 40.4354 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 : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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** A 503 HIS C 124 ASN C 238 GLN ** 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** 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 = 0.3796 r_free = 0.3796 target = 0.159113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148565 restraints weight = 21916.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 121)---------------| | r_work = 0.3643 r_free = 0.3643 target = 0.145295 restraints weight = 25325.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.144467 restraints weight = 29402.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144824 restraints weight = 25580.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144408 restraints weight = 22818.686| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.176 17010 Z= 0.231 Angle : 1.474 60.938 23220 Z= 0.478 Chirality : 0.078 2.196 2478 Planarity : 0.006 0.063 2986 Dihedral : 10.083 115.897 2432 Min Nonbonded Distance : 1.533 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.84 % Favored : 93.77 % Rotamer: Outliers : 0.82 % Allowed : 9.39 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.18), residues: 2072 helix: -0.57 (0.20), residues: 696 sheet: -0.66 (0.39), residues: 170 loop : -1.66 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 397 TYR 0.018 0.002 TYR C 120 PHE 0.015 0.001 PHE D 270 TRP 0.022 0.002 TRP D 111 HIS 0.005 0.001 HIS D 503 Details of bonding type rmsd covalent geometry : bond 0.00495 (16972) covalent geometry : angle 1.18258 (23202) hydrogen bonds : bond 0.04809 ( 498) hydrogen bonds : angle 6.49240 ( 1434) metal coordination : bond 0.02321 ( 6) metal coordination : angle 31.60423 ( 18) Misc. bond : bond 0.03967 ( 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 230 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6939 (mp10) REVERT: B 150 TYR cc_start: 0.5346 (t80) cc_final: 0.4828 (t80) REVERT: C 224 ASP cc_start: 0.7715 (p0) cc_final: 0.7455 (p0) REVERT: C 449 LYS cc_start: 0.6572 (pptt) cc_final: 0.5563 (ptpp) REVERT: D 61 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6845 (mp10) REVERT: D 211 ASP cc_start: 0.8428 (t70) cc_final: 0.7335 (t0) REVERT: F 224 ASP cc_start: 0.7729 (p0) cc_final: 0.7461 (p0) outliers start: 14 outliers final: 6 residues processed: 224 average time/residue: 0.1019 time to fit residues: 37.2101 Evaluate side-chains 193 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 121 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 178 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 169 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.164227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.157298 restraints weight = 22018.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.157067 restraints weight = 34406.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156690 restraints weight = 28934.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.156545 restraints weight = 22828.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.156630 restraints weight = 19623.678| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.167 17010 Z= 0.178 Angle : 1.497 85.612 23220 Z= 0.460 Chirality : 0.060 1.383 2478 Planarity : 0.005 0.057 2986 Dihedral : 10.023 119.228 2432 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.09 % Favored : 92.62 % Rotamer: Outliers : 1.82 % Allowed : 12.85 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.18), residues: 2072 helix: -0.25 (0.20), residues: 704 sheet: -0.37 (0.39), residues: 166 loop : -1.57 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 133 TYR 0.018 0.002 TYR A 79 PHE 0.016 0.002 PHE E 144 TRP 0.015 0.002 TRP B 128 HIS 0.006 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00418 (16972) covalent geometry : angle 1.14931 (23202) hydrogen bonds : bond 0.04157 ( 498) hydrogen bonds : angle 6.01147 ( 1434) metal coordination : bond 0.00616 ( 6) metal coordination : angle 34.44789 ( 18) Misc. bond : bond 0.04287 ( 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 231 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 221 ASN cc_start: 0.8518 (t0) cc_final: 0.8220 (t0) REVERT: A 257 MET cc_start: 0.6117 (mtm) cc_final: 0.5845 (mtp) REVERT: A 440 VAL cc_start: 0.7053 (m) cc_final: 0.6810 (m) REVERT: B 150 TYR cc_start: 0.5474 (t80) cc_final: 0.5017 (t80) REVERT: C 118 MET cc_start: 0.7877 (tpt) cc_final: 0.7469 (tpt) REVERT: C 224 ASP cc_start: 0.7671 (p0) cc_final: 0.7380 (p0) REVERT: D 61 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6781 (mp10) REVERT: D 257 MET cc_start: 0.6117 (mtm) cc_final: 0.5893 (mtp) REVERT: D 440 VAL cc_start: 0.6960 (m) cc_final: 0.6722 (m) REVERT: E 150 TYR cc_start: 0.5417 (t80) cc_final: 0.4952 (t80) REVERT: F 118 MET cc_start: 0.7874 (tpt) cc_final: 0.7486 (tpt) REVERT: F 224 ASP cc_start: 0.7664 (p0) cc_final: 0.7344 (p0) outliers start: 31 outliers final: 17 residues processed: 215 average time/residue: 0.1043 time to fit residues: 36.3743 Evaluate side-chains 204 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 D residue 61 GLN 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 E residue 132 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 120 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 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 = 0.3701 r_free = 0.3701 target = 0.150783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140985 restraints weight = 22881.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.137442 restraints weight = 27384.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.137103 restraints weight = 34363.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136828 restraints weight = 29080.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.136644 restraints weight = 28291.225| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.169 17010 Z= 0.263 Angle : 1.570 84.793 23220 Z= 0.496 Chirality : 0.064 1.475 2478 Planarity : 0.006 0.064 2986 Dihedral : 10.401 128.529 2432 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.54 % Favored : 91.07 % Rotamer: Outliers : 3.70 % Allowed : 14.03 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 2072 helix: -0.35 (0.20), residues: 706 sheet: -0.35 (0.39), residues: 170 loop : -1.64 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 133 TYR 0.021 0.002 TYR B 150 PHE 0.026 0.002 PHE E 144 TRP 0.015 0.002 TRP B 128 HIS 0.009 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00631 (16972) covalent geometry : angle 1.22091 (23202) hydrogen bonds : bond 0.04606 ( 498) hydrogen bonds : angle 6.06423 ( 1434) metal coordination : bond 0.00240 ( 6) metal coordination : angle 35.46379 ( 18) Misc. bond : bond 0.04966 ( 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 254 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 MET cc_start: 0.8363 (tpt) cc_final: 0.8159 (tpt) REVERT: C 224 ASP cc_start: 0.7742 (p0) cc_final: 0.7514 (p0) REVERT: D 61 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6897 (mp10) REVERT: F 118 MET cc_start: 0.8362 (tpt) cc_final: 0.8160 (tpt) REVERT: F 182 HIS cc_start: 0.5822 (m-70) cc_final: 0.5454 (m170) REVERT: F 224 ASP cc_start: 0.7783 (p0) cc_final: 0.7546 (p0) outliers start: 63 outliers final: 37 residues processed: 233 average time/residue: 0.0956 time to fit residues: 36.9920 Evaluate side-chains 223 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 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 408 THR 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 154 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 chunk 119 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 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 = 0.3744 r_free = 0.3744 target = 0.155056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136009 restraints weight = 22529.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.134976 restraints weight = 27936.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.135846 restraints weight = 26828.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136025 restraints weight = 21929.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136067 restraints weight = 21158.382| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 17010 Z= 0.167 Angle : 1.481 83.496 23220 Z= 0.450 Chirality : 0.060 1.429 2478 Planarity : 0.005 0.060 2986 Dihedral : 10.009 121.866 2432 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.03 % Favored : 93.77 % Rotamer: Outliers : 2.29 % Allowed : 16.20 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.19), residues: 2072 helix: -0.08 (0.20), residues: 708 sheet: -0.02 (0.41), residues: 166 loop : -1.44 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 133 TYR 0.017 0.002 TYR A 79 PHE 0.017 0.001 PHE D 270 TRP 0.012 0.001 TRP D 111 HIS 0.005 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00393 (16972) covalent geometry : angle 1.13077 (23202) hydrogen bonds : bond 0.03713 ( 498) hydrogen bonds : angle 5.74283 ( 1434) metal coordination : bond 0.00194 ( 6) metal coordination : angle 34.38239 ( 18) Misc. bond : bond 0.03361 ( 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 246 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6907 (t0) cc_final: 0.6687 (t0) REVERT: A 226 CYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7145 (p) REVERT: A 440 VAL cc_start: 0.6809 (m) cc_final: 0.6597 (m) REVERT: C 224 ASP cc_start: 0.7591 (p0) cc_final: 0.7371 (p0) REVERT: C 449 LYS cc_start: 0.6539 (pptt) cc_final: 0.5459 (ptpp) REVERT: D 61 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6708 (mp10) REVERT: D 221 ASN cc_start: 0.8545 (t0) cc_final: 0.8178 (t0) REVERT: D 226 CYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7221 (p) REVERT: F 182 HIS cc_start: 0.5834 (m-70) cc_final: 0.5379 (m170) REVERT: F 224 ASP cc_start: 0.7598 (p0) cc_final: 0.7355 (p0) outliers start: 39 outliers final: 31 residues processed: 236 average time/residue: 0.1206 time to fit residues: 43.5026 Evaluate side-chains 224 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 408 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.153543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.133719 restraints weight = 22770.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133446 restraints weight = 29232.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.134591 restraints weight = 25558.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.134655 restraints weight = 19877.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134749 restraints weight = 19787.578| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2110 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= 0.194 Angle : 1.495 84.064 23220 Z= 0.459 Chirality : 0.062 1.448 2478 Planarity : 0.005 0.063 2986 Dihedral : 10.019 123.870 2432 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.53 % Favored : 92.28 % Rotamer: Outliers : 3.81 % Allowed : 15.85 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.19), residues: 2072 helix: -0.01 (0.20), residues: 708 sheet: 0.09 (0.41), residues: 166 loop : -1.42 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 397 TYR 0.018 0.002 TYR F 135 PHE 0.018 0.002 PHE E 144 TRP 0.012 0.001 TRP B 128 HIS 0.006 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00465 (16972) covalent geometry : angle 1.14464 (23202) hydrogen bonds : bond 0.03897 ( 498) hydrogen bonds : angle 5.74328 ( 1434) metal coordination : bond 0.00127 ( 6) metal coordination : angle 34.57439 ( 18) Misc. bond : bond 0.03688 ( 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 258 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 193 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6762 (mp10) REVERT: A 221 ASN cc_start: 0.8585 (t0) cc_final: 0.8178 (t0) REVERT: A 226 CYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7258 (p) REVERT: C 224 ASP cc_start: 0.7649 (p0) cc_final: 0.7416 (p0) REVERT: D 13 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7480 (tt) REVERT: D 61 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6743 (mp10) REVERT: D 221 ASN cc_start: 0.8563 (t0) cc_final: 0.8159 (t0) REVERT: D 226 CYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7249 (p) REVERT: F 224 ASP cc_start: 0.7676 (p0) cc_final: 0.7436 (p0) outliers start: 65 outliers final: 46 residues processed: 239 average time/residue: 0.1044 time to fit residues: 40.3158 Evaluate side-chains 240 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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 384 MET 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 253 LEU Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain D residue 13 ILE 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 Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 408 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 23 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 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 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 = 0.154194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.144539 restraints weight = 22746.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141751 restraints weight = 25806.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140731 restraints weight = 31127.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140778 restraints weight = 31576.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140678 restraints weight = 27159.907| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 17010 Z= 0.192 Angle : 1.494 83.870 23220 Z= 0.457 Chirality : 0.062 1.454 2478 Planarity : 0.005 0.065 2986 Dihedral : 10.005 124.638 2432 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.76 % Favored : 93.05 % Rotamer: Outliers : 3.81 % Allowed : 16.55 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.19), residues: 2072 helix: 0.04 (0.20), residues: 706 sheet: 0.22 (0.42), residues: 166 loop : -1.41 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 397 TYR 0.020 0.002 TYR F 135 PHE 0.018 0.002 PHE A 270 TRP 0.012 0.001 TRP E 128 HIS 0.006 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00460 (16972) covalent geometry : angle 1.14256 (23202) hydrogen bonds : bond 0.03846 ( 498) hydrogen bonds : angle 5.70403 ( 1434) metal coordination : bond 0.00143 ( 6) metal coordination : angle 34.61292 ( 18) Misc. bond : bond 0.03947 ( 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 261 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6671 (mp10) REVERT: A 221 ASN cc_start: 0.8539 (t0) cc_final: 0.8203 (t0) REVERT: A 226 CYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7141 (p) REVERT: C 118 MET cc_start: 0.8051 (tpt) cc_final: 0.7766 (tpt) REVERT: C 182 HIS cc_start: 0.5724 (m-70) cc_final: 0.5193 (m90) REVERT: C 456 MET cc_start: 0.5499 (tpt) cc_final: 0.5138 (tpt) REVERT: D 61 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6612 (mp10) REVERT: D 221 ASN cc_start: 0.8514 (t0) cc_final: 0.8197 (t0) REVERT: D 226 CYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7130 (p) REVERT: D 440 VAL cc_start: 0.6927 (m) cc_final: 0.6718 (m) REVERT: F 224 ASP cc_start: 0.7514 (p0) cc_final: 0.7313 (p0) outliers start: 65 outliers final: 48 residues processed: 242 average time/residue: 0.1046 time to fit residues: 41.0102 Evaluate side-chains 238 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL 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 294 THR Chi-restraints excluded: chain D residue 298 LEU 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 Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 408 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 138 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 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 = 0.3713 r_free = 0.3713 target = 0.152513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141944 restraints weight = 22843.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140942 restraints weight = 35316.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140733 restraints weight = 32541.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140486 restraints weight = 24536.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140741 restraints weight = 22924.660| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.157 17010 Z= 0.234 Angle : 1.528 84.310 23220 Z= 0.477 Chirality : 0.063 1.455 2478 Planarity : 0.006 0.069 2986 Dihedral : 10.116 125.919 2432 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.83 % Favored : 90.97 % Rotamer: Outliers : 3.99 % Allowed : 17.37 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.19), residues: 2072 helix: -0.05 (0.20), residues: 706 sheet: 0.12 (0.42), residues: 166 loop : -1.47 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 397 TYR 0.024 0.002 TYR D 271 PHE 0.023 0.002 PHE E 144 TRP 0.013 0.002 TRP E 128 HIS 0.007 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00564 (16972) covalent geometry : angle 1.18102 (23202) hydrogen bonds : bond 0.04160 ( 498) hydrogen bonds : angle 5.79533 ( 1434) metal coordination : bond 0.00173 ( 6) metal coordination : angle 34.84759 ( 18) Misc. bond : bond 0.04312 ( 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 256 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 188 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6767 (mp10) REVERT: A 226 CYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7156 (p) REVERT: C 45 TYR cc_start: 0.7878 (t80) cc_final: 0.7322 (t80) REVERT: C 182 HIS cc_start: 0.5754 (m-70) cc_final: 0.5220 (m90) REVERT: D 61 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6717 (mp10) REVERT: D 226 CYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7122 (p) REVERT: F 45 TYR cc_start: 0.7861 (t80) cc_final: 0.7316 (t80) outliers start: 68 outliers final: 52 residues processed: 239 average time/residue: 0.1031 time to fit residues: 40.1419 Evaluate side-chains 243 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL 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 197 SER Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 266 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 384 MET 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 266 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 298 LEU 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 125 ILE 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 Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 408 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 181 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.152018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.138316 restraints weight = 22853.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137427 restraints weight = 29414.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137837 restraints weight = 28315.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137335 restraints weight = 24138.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137473 restraints weight = 23917.827| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 17010 Z= 0.174 Angle : 1.485 83.585 23220 Z= 0.454 Chirality : 0.061 1.447 2478 Planarity : 0.005 0.068 2986 Dihedral : 10.014 121.847 2432 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.47 % Favored : 93.34 % Rotamer: Outliers : 3.64 % Allowed : 17.72 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.19), residues: 2072 helix: 0.12 (0.20), residues: 714 sheet: 0.37 (0.42), residues: 162 loop : -1.36 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 397 TYR 0.025 0.002 TYR C 135 PHE 0.017 0.001 PHE A 270 TRP 0.013 0.001 TRP A 111 HIS 0.005 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00417 (16972) covalent geometry : angle 1.13116 (23202) hydrogen bonds : bond 0.03673 ( 498) hydrogen bonds : angle 5.65694 ( 1434) metal coordination : bond 0.00119 ( 6) metal coordination : angle 34.55837 ( 18) Misc. bond : bond 0.03963 ( 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 264 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 202 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6715 (mp10) REVERT: A 226 CYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7090 (p) REVERT: C 182 HIS cc_start: 0.5774 (m-70) cc_final: 0.5240 (m90) REVERT: C 456 MET cc_start: 0.5575 (tpt) cc_final: 0.4668 (tpp) REVERT: D 61 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6483 (mp10) REVERT: D 223 MET cc_start: 0.8210 (mmm) cc_final: 0.8005 (mmt) REVERT: D 226 CYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7057 (p) REVERT: F 45 TYR cc_start: 0.7825 (t80) cc_final: 0.7364 (t80) REVERT: F 456 MET cc_start: 0.5627 (tpt) cc_final: 0.4798 (tpp) outliers start: 62 outliers final: 50 residues processed: 245 average time/residue: 0.1040 time to fit residues: 41.7399 Evaluate side-chains 248 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 197 SER Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 266 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 450 ILE 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 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 11 VAL 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 197 SER Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 266 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 298 LEU 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 122 ILE 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 Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 408 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 104 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 347 HIS ** 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 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 = 0.3723 r_free = 0.3723 target = 0.153565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.144191 restraints weight = 22868.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.143169 restraints weight = 28301.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141838 restraints weight = 26486.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.141613 restraints weight = 25418.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.141638 restraints weight = 24301.833| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.151 17010 Z= 0.223 Angle : 1.520 83.969 23220 Z= 0.474 Chirality : 0.063 1.458 2478 Planarity : 0.006 0.072 2986 Dihedral : 10.153 125.312 2432 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.03 % Favored : 90.78 % Rotamer: Outliers : 3.64 % Allowed : 17.61 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.19), residues: 2072 helix: -0.02 (0.20), residues: 712 sheet: 0.18 (0.42), residues: 166 loop : -1.41 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 397 TYR 0.026 0.002 TYR F 135 PHE 0.021 0.002 PHE E 144 TRP 0.012 0.002 TRP B 128 HIS 0.007 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00541 (16972) covalent geometry : angle 1.17007 (23202) hydrogen bonds : bond 0.04042 ( 498) hydrogen bonds : angle 5.74509 ( 1434) metal coordination : bond 0.00146 ( 6) metal coordination : angle 34.87450 ( 18) Misc. bond : bond 0.04529 ( 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 253 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 191 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6715 (mp10) REVERT: A 226 CYS cc_start: 0.8586 (OUTLIER) cc_final: 0.7171 (p) REVERT: A 514 MET cc_start: 0.8293 (mtt) cc_final: 0.7859 (mtt) REVERT: D 61 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6716 (mp10) REVERT: D 226 CYS cc_start: 0.8575 (OUTLIER) cc_final: 0.7141 (p) REVERT: F 456 MET cc_start: 0.5542 (tpt) cc_final: 0.5192 (tpt) outliers start: 62 outliers final: 55 residues processed: 235 average time/residue: 0.1005 time to fit residues: 38.7612 Evaluate side-chains 249 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 190 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL 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 197 SER Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 266 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 450 ILE 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 122 ILE 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 80 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain D residue 11 VAL 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 266 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 298 LEU 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 122 ILE 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 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 Chi-restraints excluded: chain F residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 141 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS ** 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 306 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.155687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.142503 restraints weight = 22780.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.141706 restraints weight = 35402.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.142134 restraints weight = 31859.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.142184 restraints weight = 27243.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143144 restraints weight = 23250.369| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 17010 Z= 0.151 Angle : 1.448 83.384 23220 Z= 0.439 Chirality : 0.060 1.444 2478 Planarity : 0.005 0.067 2986 Dihedral : 9.885 117.142 2432 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.41 % Favored : 94.40 % Rotamer: Outliers : 3.17 % Allowed : 18.08 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.19), residues: 2072 helix: 0.20 (0.20), residues: 734 sheet: 0.53 (0.43), residues: 162 loop : -1.30 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 397 TYR 0.019 0.002 TYR F 135 PHE 0.014 0.001 PHE D 270 TRP 0.016 0.001 TRP A 111 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00353 (16972) covalent geometry : angle 1.09658 (23202) hydrogen bonds : bond 0.03318 ( 498) hydrogen bonds : angle 5.52010 ( 1434) metal coordination : bond 0.00119 ( 6) metal coordination : angle 33.97106 ( 18) Misc. bond : bond 0.04017 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.14 seconds wall clock time: 38 minutes 53.94 seconds (2333.94 seconds total)