Starting phenix.real_space_refine on Sat Aug 23 10:14:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ifz_35427/08_2025/8ifz_35427.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifz_35427/08_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_35427/08_2025/8ifz_35427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifz_35427/08_2025/8ifz_35427.map" model { file = "/net/cci-nas-00/data/ceres_data/8ifz_35427/08_2025/8ifz_35427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifz_35427/08_2025/8ifz_35427.cif" } resolution = 2.85 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= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.93, per 1000 atoms: 0.30 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: 0.55 Conformation dependent library (CDL) restraints added in 314.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.23 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: 1.01 Time building geometry restraints manager: 0.74 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: 12.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.310 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.230 ------------------------------------------------------------------------------- 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 : 5.91 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (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 ARG 0.005 0.001 ARG A 161 TYR 0.017 0.002 TYR A 385 PHE 0.017 0.002 PHE A 327 TRP 0.012 0.001 TRP B 353 HIS 0.007 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 6686) covalent geometry : angle 0.59849 ( 9073) SS BOND : bond 0.00236 ( 4) SS BOND : angle 0.67997 ( 8) hydrogen bonds : bond 0.31864 ( 203) hydrogen bonds : angle 8.59541 ( 576) link_NAG-ASN : bond 0.00518 ( 5) link_NAG-ASN : angle 1.75317 ( 15) *********************** 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 : 0.287 Fit side-chains revert: symmetry clash 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: 0.7206 (mmt) outliers start: 16 outliers final: 9 residues processed: 119 average time/residue: 0.7226 time to fit residues: 89.7092 Evaluate side-chains 61 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN 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 472 GLN A 552 GLN A 601 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.074243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.055218 restraints weight = 24655.345| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 4.27 r_work: 0.3100 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6695 Z= 0.150 Angle : 0.639 9.377 9096 Z= 0.326 Chirality : 0.045 0.156 957 Planarity : 0.005 0.076 1163 Dihedral : 8.275 87.134 991 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.33 % Allowed : 29.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.30), residues: 785 helix: -0.70 (0.28), residues: 372 sheet: 2.05 (0.78), residues: 48 loop : -1.42 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 79 TYR 0.015 0.001 TYR B 495 PHE 0.011 0.001 PHE A 504 TRP 0.010 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6686) covalent geometry : angle 0.63632 ( 9073) SS BOND : bond 0.00240 ( 4) SS BOND : angle 0.61986 ( 8) hydrogen bonds : bond 0.04872 ( 203) hydrogen bonds : angle 5.45058 ( 576) link_NAG-ASN : bond 0.00281 ( 5) link_NAG-ASN : angle 1.63539 ( 15) *********************** 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 89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7576 (p90) REVERT: A 117 LEU cc_start: 0.9414 (mm) cc_final: 0.9089 (mm) REVERT: A 223 MET cc_start: 0.8894 (mpp) cc_final: 0.8620 (mmm) REVERT: A 249 MET cc_start: 0.8642 (mmm) cc_final: 0.8185 (tpt) REVERT: A 270 MET cc_start: 0.9177 (tpp) cc_final: 0.8907 (tpp) REVERT: A 435 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8528 (mp0) REVERT: A 502 CYS cc_start: 0.8820 (m) cc_final: 0.7947 (t) outliers start: 30 outliers final: 6 residues processed: 86 average time/residue: 0.5553 time to fit residues: 50.3293 Evaluate side-chains 53 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS 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 66 optimal weight: 7.9990 chunk 12 optimal weight: 0.1980 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.0270 chunk 41 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.073810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.054862 restraints weight = 24458.031| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 4.20 r_work: 0.3094 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6695 Z= 0.116 Angle : 0.588 10.585 9096 Z= 0.295 Chirality : 0.043 0.163 957 Planarity : 0.004 0.055 1163 Dihedral : 7.313 78.207 984 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.18 % Allowed : 28.14 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.30), residues: 785 helix: -0.66 (0.27), residues: 380 sheet: 2.13 (0.79), residues: 45 loop : -1.23 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 79 TYR 0.012 0.001 TYR B 495 PHE 0.010 0.001 PHE A 523 TRP 0.007 0.001 TRP B 436 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6686) covalent geometry : angle 0.58494 ( 9073) SS BOND : bond 0.00571 ( 4) SS BOND : angle 1.04614 ( 8) hydrogen bonds : bond 0.04099 ( 203) hydrogen bonds : angle 4.98496 ( 576) link_NAG-ASN : bond 0.00261 ( 5) link_NAG-ASN : angle 1.54366 ( 15) *********************** 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 81 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 52 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7534 (p90) REVERT: A 71 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8768 (p) REVERT: A 117 LEU cc_start: 0.9336 (mm) cc_final: 0.9085 (mm) REVERT: A 190 MET cc_start: 0.8901 (tmm) cc_final: 0.8672 (tmm) REVERT: A 223 MET cc_start: 0.8856 (mpp) cc_final: 0.8620 (mmm) REVERT: A 249 MET cc_start: 0.8724 (mmm) cc_final: 0.8316 (mmt) REVERT: A 270 MET cc_start: 0.9135 (tpp) cc_final: 0.8862 (tpp) REVERT: A 502 CYS cc_start: 0.8803 (m) cc_final: 0.7934 (t) REVERT: A 609 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8887 (pm20) outliers start: 29 outliers final: 7 residues processed: 77 average time/residue: 0.5203 time to fit residues: 42.2240 Evaluate side-chains 52 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain A residue 71 SER 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 287 HIS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 609 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 0.0030 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN A 34 ASN A 287 HIS A 300 GLN A 322 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.072979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.053906 restraints weight = 24958.366| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 4.21 r_work: 0.3068 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3661 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= 0.122 Angle : 0.588 11.189 9096 Z= 0.296 Chirality : 0.044 0.202 957 Planarity : 0.004 0.051 1163 Dihedral : 6.541 56.534 983 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.75 % Allowed : 28.43 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.30), residues: 785 helix: -0.48 (0.28), residues: 381 sheet: 2.10 (0.78), residues: 45 loop : -1.19 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.013 0.001 TYR B 495 PHE 0.012 0.001 PHE A 523 TRP 0.008 0.001 TRP A 349 HIS 0.006 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6686) covalent geometry : angle 0.57932 ( 9073) SS BOND : bond 0.00421 ( 4) SS BOND : angle 1.81349 ( 8) hydrogen bonds : bond 0.03705 ( 203) hydrogen bonds : angle 4.72454 ( 576) link_NAG-ASN : bond 0.00239 ( 5) link_NAG-ASN : angle 2.19627 ( 15) *********************** 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 74 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7474 (p90) REVERT: A 94 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9348 (tm) REVERT: A 98 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9363 (mm) REVERT: A 117 LEU cc_start: 0.9300 (mm) cc_final: 0.9068 (mm) REVERT: A 174 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8940 (mptm) REVERT: A 223 MET cc_start: 0.8839 (mpp) cc_final: 0.8618 (mmm) REVERT: A 249 MET cc_start: 0.8737 (mmm) cc_final: 0.8420 (tpp) REVERT: A 270 MET cc_start: 0.9107 (tpp) cc_final: 0.8831 (tpp) REVERT: A 344 CYS cc_start: 0.5353 (OUTLIER) cc_final: 0.4989 (m) REVERT: A 474 MET cc_start: 0.8512 (mmm) cc_final: 0.8301 (mpp) REVERT: A 496 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8310 (p) REVERT: A 502 CYS cc_start: 0.8849 (m) cc_final: 0.8019 (t) outliers start: 26 outliers final: 9 residues processed: 71 average time/residue: 0.4736 time to fit residues: 35.7353 Evaluate side-chains 57 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 94 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 362 THR 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 496 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.072524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.053463 restraints weight = 25348.663| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 4.23 r_work: 0.3059 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6695 Z= 0.117 Angle : 0.560 8.573 9096 Z= 0.282 Chirality : 0.043 0.150 957 Planarity : 0.004 0.050 1163 Dihedral : 5.739 57.355 983 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.32 % Allowed : 28.14 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.30), residues: 785 helix: -0.35 (0.28), residues: 382 sheet: 2.10 (0.77), residues: 45 loop : -1.14 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.013 0.001 TYR B 495 PHE 0.010 0.001 PHE A 523 TRP 0.007 0.001 TRP A 203 HIS 0.009 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6686) covalent geometry : angle 0.55212 ( 9073) SS BOND : bond 0.00367 ( 4) SS BOND : angle 1.38064 ( 8) hydrogen bonds : bond 0.03501 ( 203) hydrogen bonds : angle 4.61037 ( 576) link_NAG-ASN : bond 0.00300 ( 5) link_NAG-ASN : angle 2.14475 ( 15) *********************** 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 72 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: B 456 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7485 (p90) REVERT: A 94 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9362 (tm) REVERT: A 223 MET cc_start: 0.8793 (mpp) cc_final: 0.8575 (mmm) REVERT: A 249 MET cc_start: 0.8741 (mmm) cc_final: 0.8193 (tpt) REVERT: A 323 MET cc_start: 0.8662 (mmm) cc_final: 0.8256 (mtm) REVERT: A 474 MET cc_start: 0.8587 (mmm) cc_final: 0.8303 (mpp) REVERT: A 482 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8773 (mmt90) REVERT: A 496 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8250 (p) outliers start: 23 outliers final: 8 residues processed: 71 average time/residue: 0.4821 time to fit residues: 36.2781 Evaluate side-chains 52 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 B residue 525 CYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 203 TRP 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.071429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.052466 restraints weight = 24819.247| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 4.12 r_work: 0.3036 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6695 Z= 0.142 Angle : 0.580 9.207 9096 Z= 0.296 Chirality : 0.044 0.156 957 Planarity : 0.004 0.050 1163 Dihedral : 5.367 59.709 981 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.74 % Allowed : 29.44 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.30), residues: 785 helix: -0.17 (0.28), residues: 378 sheet: 2.00 (0.78), residues: 45 loop : -1.19 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.019 0.001 TYR A 497 PHE 0.012 0.001 PHE A 523 TRP 0.010 0.001 TRP A 349 HIS 0.005 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6686) covalent geometry : angle 0.57461 ( 9073) SS BOND : bond 0.00465 ( 4) SS BOND : angle 1.42368 ( 8) hydrogen bonds : bond 0.03721 ( 203) hydrogen bonds : angle 4.65206 ( 576) link_NAG-ASN : bond 0.00174 ( 5) link_NAG-ASN : angle 1.73596 ( 15) *********************** 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 63 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.229 Fit side-chains REVERT: A 162 LEU cc_start: 0.9529 (mm) cc_final: 0.9274 (mm) REVERT: A 223 MET cc_start: 0.8747 (mpp) cc_final: 0.8544 (mmm) REVERT: A 249 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8148 (tpt) REVERT: A 323 MET cc_start: 0.8695 (mmm) cc_final: 0.8336 (mtm) REVERT: A 482 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8779 (mmt180) outliers start: 19 outliers final: 9 residues processed: 61 average time/residue: 0.5772 time to fit residues: 37.1597 Evaluate side-chains 51 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 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 249 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 482 ARG 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 18 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 56 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.072177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.053399 restraints weight = 24701.571| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 4.06 r_work: 0.3063 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6695 Z= 0.104 Angle : 0.581 9.692 9096 Z= 0.287 Chirality : 0.043 0.161 957 Planarity : 0.004 0.050 1163 Dihedral : 4.853 56.379 977 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.45 % Allowed : 29.29 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.30), residues: 785 helix: -0.12 (0.28), residues: 379 sheet: 1.98 (0.77), residues: 45 loop : -1.10 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.008 0.001 TYR B 495 PHE 0.008 0.001 PHE A 523 TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6686) covalent geometry : angle 0.57723 ( 9073) SS BOND : bond 0.00444 ( 4) SS BOND : angle 1.11187 ( 8) hydrogen bonds : bond 0.03181 ( 203) hydrogen bonds : angle 4.46801 ( 576) link_NAG-ASN : bond 0.00234 ( 5) link_NAG-ASN : angle 1.54614 ( 15) *********************** 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 62 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.185 Fit side-chains REVERT: A 223 MET cc_start: 0.8733 (mpp) cc_final: 0.8530 (mmm) REVERT: A 249 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8109 (tpt) REVERT: A 323 MET cc_start: 0.8631 (mmm) cc_final: 0.8312 (mtm) REVERT: A 482 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8819 (mmt90) REVERT: A 502 CYS cc_start: 0.8820 (m) cc_final: 0.8145 (t) outliers start: 17 outliers final: 5 residues processed: 61 average time/residue: 0.5180 time to fit residues: 33.4804 Evaluate side-chains 48 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 249 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 482 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.0870 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 0.0980 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.072125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.053352 restraints weight = 24874.914| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 4.07 r_work: 0.3068 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4556 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= 0.104 Angle : 0.589 10.303 9096 Z= 0.289 Chirality : 0.043 0.161 957 Planarity : 0.004 0.050 1163 Dihedral : 4.767 55.255 977 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.31 % Allowed : 29.73 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.30), residues: 785 helix: 0.05 (0.28), residues: 372 sheet: 1.84 (0.76), residues: 45 loop : -1.08 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.008 0.001 TYR B 495 PHE 0.012 0.001 PHE A 504 TRP 0.006 0.001 TRP A 349 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6686) covalent geometry : angle 0.58581 ( 9073) SS BOND : bond 0.00344 ( 4) SS BOND : angle 1.06332 ( 8) hydrogen bonds : bond 0.03026 ( 203) hydrogen bonds : angle 4.36962 ( 576) link_NAG-ASN : bond 0.00216 ( 5) link_NAG-ASN : angle 1.40144 ( 15) *********************** 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 57 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.283 Fit side-chains REVERT: B 474 GLN cc_start: 0.9133 (tt0) cc_final: 0.8766 (tp-100) REVERT: A 223 MET cc_start: 0.8759 (mpp) cc_final: 0.8542 (mmm) REVERT: A 249 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8357 (tpp) REVERT: A 323 MET cc_start: 0.8562 (mmm) cc_final: 0.8243 (mtm) REVERT: A 482 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8845 (mmt180) REVERT: A 502 CYS cc_start: 0.8807 (m) cc_final: 0.8180 (t) outliers start: 16 outliers final: 9 residues processed: 56 average time/residue: 0.5994 time to fit residues: 35.5179 Evaluate side-chains 53 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 203 TRP 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 283 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 482 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.068215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.049508 restraints weight = 25339.619| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 4.01 r_work: 0.2961 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6695 Z= 0.268 Angle : 0.713 10.692 9096 Z= 0.361 Chirality : 0.047 0.167 957 Planarity : 0.004 0.053 1163 Dihedral : 5.485 52.446 977 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.60 % Allowed : 29.29 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.30), residues: 785 helix: -0.05 (0.28), residues: 380 sheet: 1.78 (0.79), residues: 45 loop : -1.32 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 161 TYR 0.026 0.002 TYR B 495 PHE 0.020 0.002 PHE A 523 TRP 0.017 0.002 TRP A 203 HIS 0.004 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00617 ( 6686) covalent geometry : angle 0.70851 ( 9073) SS BOND : bond 0.00535 ( 4) SS BOND : angle 1.53544 ( 8) hydrogen bonds : bond 0.04897 ( 203) hydrogen bonds : angle 4.94472 ( 576) link_NAG-ASN : bond 0.00329 ( 5) link_NAG-ASN : angle 1.90774 ( 15) *********************** 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 58 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.281 Fit side-chains REVERT: A 249 MET cc_start: 0.8630 (mmm) cc_final: 0.8281 (tpp) REVERT: A 344 CYS cc_start: 0.5236 (p) cc_final: 0.4807 (p) REVERT: A 482 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8781 (mtt-85) outliers start: 18 outliers final: 8 residues processed: 56 average time/residue: 0.5479 time to fit residues: 32.5321 Evaluate side-chains 48 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 203 TRP Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 482 ARG 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 60 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 49 optimal weight: 0.0570 chunk 61 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.070405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.051798 restraints weight = 24149.603| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 4.01 r_work: 0.3030 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4862 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= 0.113 Angle : 0.618 11.589 9096 Z= 0.303 Chirality : 0.043 0.177 957 Planarity : 0.004 0.062 1163 Dihedral : 5.037 53.537 977 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.59 % Allowed : 30.59 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.30), residues: 785 helix: 0.02 (0.28), residues: 386 sheet: 1.60 (0.76), residues: 45 loop : -1.00 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 161 TYR 0.008 0.001 TYR B 495 PHE 0.010 0.001 PHE A 523 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6686) covalent geometry : angle 0.61533 ( 9073) SS BOND : bond 0.00466 ( 4) SS BOND : angle 1.10749 ( 8) hydrogen bonds : bond 0.03314 ( 203) hydrogen bonds : angle 4.52105 ( 576) link_NAG-ASN : bond 0.00227 ( 5) link_NAG-ASN : angle 1.32363 ( 15) ********************** 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 55 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.277 Fit side-chains REVERT: B 474 GLN cc_start: 0.9159 (tt0) cc_final: 0.8822 (tp-100) REVERT: A 223 MET cc_start: 0.8816 (mpp) cc_final: 0.8472 (mmm) REVERT: A 249 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8053 (tpt) REVERT: A 482 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8759 (mtt180) outliers start: 11 outliers final: 6 residues processed: 54 average time/residue: 0.5870 time to fit residues: 33.5705 Evaluate side-chains 50 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 203 TRP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 482 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 265 HIS A 322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.069849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.051305 restraints weight = 24482.964| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 4.02 r_work: 0.3021 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6695 Z= 0.132 Angle : 0.626 11.548 9096 Z= 0.308 Chirality : 0.044 0.170 957 Planarity : 0.004 0.058 1163 Dihedral : 4.993 52.279 977 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.73 % Allowed : 30.74 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.30), residues: 785 helix: 0.08 (0.28), residues: 382 sheet: 1.68 (0.77), residues: 45 loop : -1.00 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 161 TYR 0.014 0.001 TYR B 495 PHE 0.012 0.001 PHE A 523 TRP 0.009 0.001 TRP A 349 HIS 0.002 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6686) covalent geometry : angle 0.62359 ( 9073) SS BOND : bond 0.00422 ( 4) SS BOND : angle 1.03875 ( 8) hydrogen bonds : bond 0.03465 ( 203) hydrogen bonds : angle 4.48485 ( 576) link_NAG-ASN : bond 0.00174 ( 5) link_NAG-ASN : angle 1.30058 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2329.72 seconds wall clock time: 40 minutes 24.15 seconds (2424.15 seconds total)