Starting phenix.real_space_refine on Wed May 14 04:52:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ifz_35427/05_2025/8ifz_35427.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifz_35427/05_2025/8ifz_35427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ifz_35427/05_2025/8ifz_35427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifz_35427/05_2025/8ifz_35427.map" model { file = "/net/cci-nas-00/data/ceres_data/8ifz_35427/05_2025/8ifz_35427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifz_35427/05_2025/8ifz_35427.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5948 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 38 5.16 5 C 4159 2.51 5 N 1071 2.21 5 O 1237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6506 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1547 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "A" Number of atoms: 4888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4888 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 570} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.07, per 1000 atoms: 0.93 Number of scatterers: 6506 At special positions: 0 Unit cell: (73.04, 101.2, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 38 16.00 O 1237 8.00 N 1071 7.00 C 4159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 54 " " NAG A 702 " - " ASN A 432 " " NAG A 703 " - " ASN A 299 " " NAG A 704 " - " ASN A 546 " " NAG A 705 " - " ASN A 91 " Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 49.8% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.602A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 372' Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.025A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'A' and resid 21 through 54 removed outlier: 4.103A pdb=" N GLN A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 39 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.658A pdb=" N MET A 63 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.544A pdb=" N GLU A 88 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.578A pdb=" N LYS A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 109 removed outlier: 7.424A pdb=" N THR A 106 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.955A pdb=" N THR A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 4.074A pdb=" N GLN A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 removed outlier: 3.542A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.780A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.708A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.566A pdb=" N TYR A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.632A pdb=" N TYR A 207 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 208 " --> pdb=" O GLY A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 208' Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.689A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.530A pdb=" N GLN A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.684A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.694A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.897A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.634A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.524A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 513 through 532 removed outlier: 3.534A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS A 530 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.853A pdb=" N LYS A 541 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 548 through 561 removed outlier: 4.129A pdb=" N LEU A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.836A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.578A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.610A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.866A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.918A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.176A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2069 1.34 - 1.46: 1702 1.46 - 1.58: 2854 1.58 - 1.70: 1 1.70 - 1.83: 60 Bond restraints: 6686 Sorted by residual: bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" CB PRO A 500 " pdb=" CG PRO A 500 " ideal model delta sigma weight residual 1.492 1.651 -0.159 5.00e-02 4.00e+02 1.02e+01 bond pdb=" CG PRO A 500 " pdb=" CD PRO A 500 " ideal model delta sigma weight residual 1.503 1.569 -0.066 3.40e-02 8.65e+02 3.75e+00 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 ... (remaining 6681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 8870 1.72 - 3.43: 178 3.43 - 5.15: 15 5.15 - 6.86: 3 6.86 - 8.58: 7 Bond angle restraints: 9073 Sorted by residual: angle pdb=" N PRO A 500 " pdb=" CA PRO A 500 " pdb=" C PRO A 500 " ideal model delta sigma weight residual 112.47 118.67 -6.20 2.06e+00 2.36e-01 9.05e+00 angle pdb=" CB MET A 152 " pdb=" CG MET A 152 " pdb=" SD MET A 152 " ideal model delta sigma weight residual 112.70 120.60 -7.90 3.00e+00 1.11e-01 6.94e+00 angle pdb=" N ASN A 195 " pdb=" CA ASN A 195 " pdb=" C ASN A 195 " ideal model delta sigma weight residual 110.91 107.94 2.97 1.17e+00 7.31e-01 6.45e+00 angle pdb=" N VAL B 503 " pdb=" CA VAL B 503 " pdb=" C VAL B 503 " ideal model delta sigma weight residual 112.98 109.90 3.08 1.25e+00 6.40e-01 6.05e+00 angle pdb=" CA LEU A 491 " pdb=" CB LEU A 491 " pdb=" CG LEU A 491 " ideal model delta sigma weight residual 116.30 124.88 -8.58 3.50e+00 8.16e-02 6.01e+00 ... (remaining 9068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.81: 3576 22.81 - 45.62: 362 45.62 - 68.44: 68 68.44 - 91.25: 6 91.25 - 114.06: 3 Dihedral angle restraints: 4015 sinusoidal: 1689 harmonic: 2326 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -140.81 54.81 1 1.00e+01 1.00e-02 4.07e+01 dihedral pdb=" CA PRO B 373 " pdb=" C PRO B 373 " pdb=" N PHE B 374 " pdb=" CA PHE B 374 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" C1 NAG A 702 " pdb=" C5 NAG A 702 " pdb=" O5 NAG A 702 " pdb=" C4 NAG A 702 " ideal model delta sinusoidal sigma weight residual -64.11 49.95 -114.06 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 4012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 686 0.043 - 0.086: 206 0.086 - 0.130: 59 0.130 - 0.173: 4 0.173 - 0.216: 2 Chirality restraints: 957 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 54 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 432 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CG LEU A 491 " pdb=" CB LEU A 491 " pdb=" CD1 LEU A 491 " pdb=" CD2 LEU A 491 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 954 not shown) Planarity restraints: 1168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " -0.078 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO A 500 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO A 258 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 195 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C ASN A 195 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN A 195 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 196 " 0.013 2.00e-02 2.50e+03 ... (remaining 1165 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 318 2.73 - 3.27: 6213 3.27 - 3.81: 9861 3.81 - 4.36: 11978 4.36 - 4.90: 20046 Nonbonded interactions: 48416 Sorted by model distance: nonbonded pdb=" O LEU A 278 " pdb=" OG1 THR A 282 " model vdw 2.185 3.040 nonbonded pdb=" N GLU A 76 " pdb=" OE1 GLU A 76 " model vdw 2.208 3.120 nonbonded pdb=" NH2 ARG A 460 " pdb=" O TYR A 510 " model vdw 2.219 3.120 nonbonded pdb=" OH TYR A 279 " pdb=" ND2 ASN A 437 " model vdw 2.223 3.120 nonbonded pdb=" OH TYR A 279 " pdb=" O ASN A 437 " model vdw 2.241 3.040 ... (remaining 48411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.520 Find NCS groups from input model: 0.060 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 6695 Z= 0.172 Angle : 0.602 8.581 9096 Z= 0.300 Chirality : 0.044 0.216 957 Planarity : 0.006 0.119 1163 Dihedral : 17.658 114.059 2511 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 2.31 % Allowed : 33.19 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.29), residues: 785 helix: -1.26 (0.27), residues: 325 sheet: 1.21 (0.72), residues: 60 loop : -1.36 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.007 0.001 HIS A 416 PHE 0.017 0.002 PHE A 327 TYR 0.017 0.002 TYR A 385 ARG 0.005 0.001 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 5) link_NAG-ASN : angle 1.75317 ( 15) hydrogen bonds : bond 0.31864 ( 203) hydrogen bonds : angle 8.59541 ( 576) SS BOND : bond 0.00236 ( 4) SS BOND : angle 0.67997 ( 8) covalent geometry : bond 0.00428 ( 6686) covalent geometry : angle 0.59849 ( 9073) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7150 (p90) REVERT: A 474 MET cc_start: 0.7707 (mmm) cc_final: 0.7207 (mmt) outliers start: 16 outliers final: 9 residues processed: 119 average time/residue: 1.3307 time to fit residues: 165.6396 Evaluate side-chains 62 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN B 343 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 477 ASN B 487 ASN A 34 ASN A 97 GLN A 195 ASN A 322 HIS A 325 GLN A 388 GLN A 437 ASN A 472 GLN A 552 GLN A 601 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.071320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.052343 restraints weight = 24747.820| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 4.17 r_work: 0.3020 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 6695 Z= 0.265 Angle : 0.705 9.059 9096 Z= 0.367 Chirality : 0.048 0.158 957 Planarity : 0.006 0.074 1163 Dihedral : 8.651 90.043 991 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.77 % Allowed : 28.86 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.29), residues: 785 helix: -0.75 (0.27), residues: 375 sheet: 1.98 (0.77), residues: 48 loop : -1.61 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 49 HIS 0.004 0.001 HIS A 378 PHE 0.017 0.002 PHE A 523 TYR 0.029 0.002 TYR B 495 ARG 0.008 0.001 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 5) link_NAG-ASN : angle 1.67611 ( 15) hydrogen bonds : bond 0.05618 ( 203) hydrogen bonds : angle 5.66450 ( 576) SS BOND : bond 0.00406 ( 4) SS BOND : angle 0.78165 ( 8) covalent geometry : bond 0.00607 ( 6686) covalent geometry : angle 0.70266 ( 9073) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 55 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8799 (tp30) REVERT: A 117 LEU cc_start: 0.9437 (mm) cc_final: 0.9160 (mm) REVERT: A 249 MET cc_start: 0.8687 (mmm) cc_final: 0.8246 (tpt) REVERT: A 270 MET cc_start: 0.9214 (tpp) cc_final: 0.8803 (tpp) REVERT: A 474 MET cc_start: 0.8429 (mmm) cc_final: 0.8070 (mmt) REVERT: A 496 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8601 (p) REVERT: A 502 CYS cc_start: 0.8920 (m) cc_final: 0.7855 (t) outliers start: 40 outliers final: 10 residues processed: 90 average time/residue: 1.0301 time to fit residues: 98.8387 Evaluate side-chains 58 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN A 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.071641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.052624 restraints weight = 24980.246| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 4.20 r_work: 0.3035 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6695 Z= 0.137 Angle : 0.626 11.877 9096 Z= 0.315 Chirality : 0.045 0.223 957 Planarity : 0.005 0.056 1163 Dihedral : 7.702 83.067 982 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.76 % Allowed : 27.13 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.30), residues: 785 helix: -0.56 (0.28), residues: 377 sheet: 2.10 (0.79), residues: 45 loop : -1.47 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 349 HIS 0.004 0.001 HIS A 374 PHE 0.013 0.001 PHE A 73 TYR 0.013 0.001 TYR B 495 ARG 0.005 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 5) link_NAG-ASN : angle 1.42715 ( 15) hydrogen bonds : bond 0.04404 ( 203) hydrogen bonds : angle 5.13118 ( 576) SS BOND : bond 0.00932 ( 4) SS BOND : angle 2.39650 ( 8) covalent geometry : bond 0.00320 ( 6686) covalent geometry : angle 0.62040 ( 9073) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 55 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8262 (mt-10) REVERT: A 117 LEU cc_start: 0.9389 (mm) cc_final: 0.9141 (mm) REVERT: A 190 MET cc_start: 0.8913 (tmm) cc_final: 0.8706 (tmm) REVERT: A 249 MET cc_start: 0.8744 (mmm) cc_final: 0.8265 (tpt) REVERT: A 270 MET cc_start: 0.9190 (tpp) cc_final: 0.8857 (tpp) REVERT: A 323 MET cc_start: 0.8659 (mmm) cc_final: 0.8258 (mmm) REVERT: A 474 MET cc_start: 0.8439 (mmm) cc_final: 0.8230 (mmt) REVERT: A 482 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8779 (mtt180) outliers start: 33 outliers final: 13 residues processed: 85 average time/residue: 1.1082 time to fit residues: 99.9150 Evaluate side-chains 61 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.3980 chunk 36 optimal weight: 10.0000 chunk 11 optimal weight: 0.1980 chunk 75 optimal weight: 0.8980 chunk 15 optimal weight: 0.0030 chunk 42 optimal weight: 3.9990 chunk 61 optimal weight: 0.0270 chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 overall best weight: 0.2648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 300 GLN A 322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.072923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.053996 restraints weight = 24717.419| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 4.16 r_work: 0.3074 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6695 Z= 0.108 Angle : 0.600 11.887 9096 Z= 0.296 Chirality : 0.043 0.156 957 Planarity : 0.004 0.051 1163 Dihedral : 6.644 62.548 981 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.61 % Allowed : 27.99 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.30), residues: 785 helix: -0.44 (0.28), residues: 380 sheet: 1.93 (0.76), residues: 45 loop : -1.27 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS A 374 PHE 0.011 0.001 PHE A 73 TYR 0.009 0.001 TYR A 74 ARG 0.006 0.000 ARG A 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 5) link_NAG-ASN : angle 1.95195 ( 15) hydrogen bonds : bond 0.03376 ( 203) hydrogen bonds : angle 4.73228 ( 576) SS BOND : bond 0.00410 ( 4) SS BOND : angle 1.43985 ( 8) covalent geometry : bond 0.00243 ( 6686) covalent geometry : angle 0.59388 ( 9073) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.9272 (mm) cc_final: 0.9060 (mm) REVERT: A 174 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8652 (mptm) REVERT: A 180 TYR cc_start: 0.9462 (t80) cc_final: 0.9248 (t80) REVERT: A 223 MET cc_start: 0.8867 (mpp) cc_final: 0.8566 (mmm) REVERT: A 249 MET cc_start: 0.8737 (mmm) cc_final: 0.8451 (tpp) REVERT: A 270 MET cc_start: 0.9141 (tpp) cc_final: 0.8781 (tpp) REVERT: A 310 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8539 (mt-10) REVERT: A 323 MET cc_start: 0.8569 (mmm) cc_final: 0.8231 (mtm) REVERT: A 482 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8755 (mpt180) REVERT: A 496 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8732 (t) REVERT: A 502 CYS cc_start: 0.8822 (m) cc_final: 0.8037 (t) outliers start: 25 outliers final: 8 residues processed: 76 average time/residue: 1.0788 time to fit residues: 86.9782 Evaluate side-chains 57 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 496 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.069993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.050961 restraints weight = 24878.431| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 4.08 r_work: 0.2997 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6695 Z= 0.185 Angle : 0.605 8.545 9096 Z= 0.309 Chirality : 0.045 0.153 957 Planarity : 0.004 0.051 1163 Dihedral : 5.668 57.626 979 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.91 % Allowed : 27.99 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.30), residues: 785 helix: -0.33 (0.27), residues: 382 sheet: 1.99 (0.78), residues: 45 loop : -1.37 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 349 HIS 0.003 0.001 HIS A 378 PHE 0.015 0.001 PHE A 523 TYR 0.020 0.001 TYR B 495 ARG 0.003 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 5) link_NAG-ASN : angle 2.49093 ( 15) hydrogen bonds : bond 0.04318 ( 203) hydrogen bonds : angle 4.92751 ( 576) SS BOND : bond 0.00575 ( 4) SS BOND : angle 1.58794 ( 8) covalent geometry : bond 0.00430 ( 6686) covalent geometry : angle 0.59583 ( 9073) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 45 time to evaluate : 0.780 Fit side-chains REVERT: A 117 LEU cc_start: 0.9348 (mm) cc_final: 0.9135 (mm) REVERT: A 223 MET cc_start: 0.8855 (mpp) cc_final: 0.8550 (mmm) REVERT: A 249 MET cc_start: 0.8733 (mmm) cc_final: 0.8187 (tpt) REVERT: A 270 MET cc_start: 0.9111 (tpp) cc_final: 0.8891 (tpp) REVERT: A 323 MET cc_start: 0.8680 (mmm) cc_final: 0.8401 (mtm) REVERT: A 482 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8770 (mmt90) REVERT: A 496 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8650 (p) REVERT: A 527 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8889 (tp30) outliers start: 34 outliers final: 18 residues processed: 75 average time/residue: 0.9805 time to fit residues: 78.5117 Evaluate side-chains 62 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 68 optimal weight: 0.0010 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 chunk 51 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.070794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.052002 restraints weight = 24170.582| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.99 r_work: 0.3031 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6695 Z= 0.114 Angle : 0.559 8.838 9096 Z= 0.284 Chirality : 0.043 0.163 957 Planarity : 0.004 0.050 1163 Dihedral : 4.931 58.832 975 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.04 % Allowed : 29.00 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.30), residues: 785 helix: -0.24 (0.27), residues: 386 sheet: 1.82 (0.76), residues: 45 loop : -1.22 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS A 374 PHE 0.011 0.001 PHE A 504 TYR 0.012 0.001 TYR B 495 ARG 0.003 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 5) link_NAG-ASN : angle 1.90572 ( 15) hydrogen bonds : bond 0.03503 ( 203) hydrogen bonds : angle 4.68517 ( 576) SS BOND : bond 0.00478 ( 4) SS BOND : angle 1.41404 ( 8) covalent geometry : bond 0.00268 ( 6686) covalent geometry : angle 0.55295 ( 9073) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 50 time to evaluate : 0.789 Fit side-chains REVERT: A 117 LEU cc_start: 0.9311 (mm) cc_final: 0.9051 (mm) REVERT: A 223 MET cc_start: 0.8811 (mpp) cc_final: 0.8517 (mmm) REVERT: A 249 MET cc_start: 0.8723 (mmm) cc_final: 0.8148 (tpt) REVERT: A 270 MET cc_start: 0.9074 (tpp) cc_final: 0.8737 (tpp) REVERT: A 474 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8083 (mpt) REVERT: A 482 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8773 (mtt180) REVERT: A 496 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8626 (p) outliers start: 28 outliers final: 16 residues processed: 76 average time/residue: 1.0754 time to fit residues: 86.9317 Evaluate side-chains 63 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.0270 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.071044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.052472 restraints weight = 24546.603| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 4.02 r_work: 0.3040 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6695 Z= 0.111 Angle : 0.586 9.609 9096 Z= 0.290 Chirality : 0.043 0.164 957 Planarity : 0.004 0.050 1163 Dihedral : 4.770 56.520 975 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.61 % Allowed : 29.73 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.30), residues: 785 helix: -0.10 (0.28), residues: 378 sheet: 1.81 (0.75), residues: 45 loop : -1.28 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 349 HIS 0.005 0.001 HIS A 493 PHE 0.009 0.001 PHE A 523 TYR 0.018 0.001 TYR A 497 ARG 0.002 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 5) link_NAG-ASN : angle 1.64890 ( 15) hydrogen bonds : bond 0.03300 ( 203) hydrogen bonds : angle 4.54849 ( 576) SS BOND : bond 0.00543 ( 4) SS BOND : angle 1.35039 ( 8) covalent geometry : bond 0.00266 ( 6686) covalent geometry : angle 0.58102 ( 9073) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.789 Fit side-chains REVERT: A 117 LEU cc_start: 0.9310 (mm) cc_final: 0.8799 (mm) REVERT: A 223 MET cc_start: 0.8802 (mpp) cc_final: 0.8529 (mmm) REVERT: A 249 MET cc_start: 0.8729 (mmm) cc_final: 0.8139 (tpt) REVERT: A 270 MET cc_start: 0.9021 (tpp) cc_final: 0.8768 (tpp) REVERT: A 474 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8100 (mpt) REVERT: A 482 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.8835 (mmt90) REVERT: A 496 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8964 (t) outliers start: 25 outliers final: 13 residues processed: 74 average time/residue: 1.1521 time to fit residues: 90.4534 Evaluate side-chains 60 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 0.0970 chunk 37 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 0.0370 chunk 19 optimal weight: 0.0060 chunk 77 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.070154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.051599 restraints weight = 24651.948| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 4.02 r_work: 0.3023 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6695 Z= 0.126 Angle : 0.615 10.982 9096 Z= 0.306 Chirality : 0.043 0.165 957 Planarity : 0.004 0.050 1163 Dihedral : 4.768 55.632 975 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.90 % Allowed : 29.87 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.30), residues: 785 helix: 0.02 (0.28), residues: 367 sheet: 1.78 (0.75), residues: 45 loop : -1.23 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 349 HIS 0.004 0.001 HIS A 265 PHE 0.014 0.001 PHE A 464 TYR 0.018 0.001 TYR A 199 ARG 0.002 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 5) link_NAG-ASN : angle 1.53903 ( 15) hydrogen bonds : bond 0.03409 ( 203) hydrogen bonds : angle 4.60393 ( 576) SS BOND : bond 0.00474 ( 4) SS BOND : angle 1.18200 ( 8) covalent geometry : bond 0.00302 ( 6686) covalent geometry : angle 0.61148 ( 9073) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 0.903 Fit side-chains REVERT: A 117 LEU cc_start: 0.9107 (mm) cc_final: 0.8873 (mm) REVERT: A 223 MET cc_start: 0.8794 (mpp) cc_final: 0.8570 (mmm) REVERT: A 249 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8145 (tpt) REVERT: A 270 MET cc_start: 0.8980 (tpp) cc_final: 0.8729 (tpp) REVERT: A 474 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8095 (mpt) REVERT: A 482 ARG cc_start: 0.9306 (OUTLIER) cc_final: 0.8855 (mmt90) REVERT: A 496 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8897 (t) outliers start: 27 outliers final: 16 residues processed: 64 average time/residue: 1.1224 time to fit residues: 76.6729 Evaluate side-chains 60 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.0050 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 ASN A 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.070730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.052140 restraints weight = 25040.272| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 4.05 r_work: 0.3037 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6695 Z= 0.111 Angle : 0.609 11.854 9096 Z= 0.301 Chirality : 0.043 0.167 957 Planarity : 0.004 0.051 1163 Dihedral : 4.668 54.730 975 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.17 % Allowed : 30.16 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.30), residues: 785 helix: -0.05 (0.28), residues: 373 sheet: 1.68 (0.76), residues: 45 loop : -1.17 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.005 0.001 HIS A 265 PHE 0.010 0.001 PHE A 464 TYR 0.010 0.001 TYR A 497 ARG 0.002 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 5) link_NAG-ASN : angle 1.38601 ( 15) hydrogen bonds : bond 0.03112 ( 203) hydrogen bonds : angle 4.50215 ( 576) SS BOND : bond 0.00444 ( 4) SS BOND : angle 1.05159 ( 8) covalent geometry : bond 0.00265 ( 6686) covalent geometry : angle 0.60593 ( 9073) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 0.819 Fit side-chains REVERT: A 117 LEU cc_start: 0.9094 (mm) cc_final: 0.8869 (mm) REVERT: A 223 MET cc_start: 0.8785 (mpp) cc_final: 0.8556 (mmm) REVERT: A 249 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8354 (tpp) REVERT: A 474 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8103 (mpt) REVERT: A 482 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.8867 (mmt180) REVERT: A 496 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8920 (t) outliers start: 22 outliers final: 12 residues processed: 61 average time/residue: 1.0298 time to fit residues: 67.2138 Evaluate side-chains 57 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 38 optimal weight: 0.0060 chunk 30 optimal weight: 0.0980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 ASN A 534 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.071045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.052484 restraints weight = 25073.556| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 4.08 r_work: 0.3050 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6695 Z= 0.109 Angle : 0.613 12.807 9096 Z= 0.303 Chirality : 0.043 0.168 957 Planarity : 0.004 0.053 1163 Dihedral : 4.590 54.216 975 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.03 % Allowed : 30.45 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.30), residues: 785 helix: 0.09 (0.28), residues: 366 sheet: 1.52 (0.75), residues: 45 loop : -1.11 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.004 0.001 HIS A 374 PHE 0.012 0.001 PHE A 464 TYR 0.030 0.001 TYR A 199 ARG 0.002 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 5) link_NAG-ASN : angle 1.29465 ( 15) hydrogen bonds : bond 0.02984 ( 203) hydrogen bonds : angle 4.44167 ( 576) SS BOND : bond 0.00412 ( 4) SS BOND : angle 0.95396 ( 8) covalent geometry : bond 0.00258 ( 6686) covalent geometry : angle 0.61062 ( 9073) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.846 Fit side-chains REVERT: B 474 GLN cc_start: 0.9125 (tt0) cc_final: 0.8823 (tp-100) REVERT: A 117 LEU cc_start: 0.9080 (mm) cc_final: 0.8857 (mm) REVERT: A 223 MET cc_start: 0.8779 (mpp) cc_final: 0.8561 (mmm) REVERT: A 249 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8353 (tpp) REVERT: A 474 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8063 (mpt) REVERT: A 482 ARG cc_start: 0.9306 (OUTLIER) cc_final: 0.8812 (mtt-85) REVERT: A 496 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8912 (t) outliers start: 21 outliers final: 12 residues processed: 63 average time/residue: 1.0684 time to fit residues: 72.1836 Evaluate side-chains 56 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 572 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.0670 chunk 37 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 ASN A 534 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.071179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.052664 restraints weight = 25277.753| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 4.08 r_work: 0.3056 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6695 Z= 0.106 Angle : 0.609 13.318 9096 Z= 0.298 Chirality : 0.043 0.167 957 Planarity : 0.004 0.054 1163 Dihedral : 4.545 53.654 975 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.17 % Allowed : 30.88 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.30), residues: 785 helix: 0.03 (0.28), residues: 373 sheet: 1.43 (0.76), residues: 45 loop : -1.09 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.005 0.001 HIS A 265 PHE 0.009 0.001 PHE A 504 TYR 0.013 0.001 TYR A 199 ARG 0.002 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 5) link_NAG-ASN : angle 1.22217 ( 15) hydrogen bonds : bond 0.02989 ( 203) hydrogen bonds : angle 4.40461 ( 576) SS BOND : bond 0.00383 ( 4) SS BOND : angle 0.89196 ( 8) covalent geometry : bond 0.00252 ( 6686) covalent geometry : angle 0.60748 ( 9073) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4791.02 seconds wall clock time: 83 minutes 29.38 seconds (5009.38 seconds total)