Starting phenix.real_space_refine on Thu Jul 2 17:05:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ojh_12951/07_2026/7ojh_12951.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ojh_12951/07_2026/7ojh_12951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ojh_12951/07_2026/7ojh_12951.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ojh_12951/07_2026/7ojh_12951.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ojh_12951/07_2026/7ojh_12951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ojh_12951/07_2026/7ojh_12951.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ojh_12951/07_2026/7ojh_12951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ojh_12951/07_2026/7ojh_12951.map" } resolution = 3.1 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= 0.005 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 58 5.16 5 C 5839 2.51 5 N 1471 2.21 5 O 1625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8999 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4425 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 18, 'TRANS': 550} Chain breaks: 3 Chain: "A" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4425 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 18, 'TRANS': 550} Chain breaks: 3 Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'ATP': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {'ATP': 1, 'CLR': 1, 'TTC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.65, per 1000 atoms: 0.18 Number of scatterers: 8999 At special positions: 0 Unit cell: (90.42, 95.7, 122.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 6 15.00 O 1625 8.00 N 1471 7.00 C 5839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS A 603 " distance=2.04 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " 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 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 237.1 milliseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 6 sheets defined 65.6% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 187 through 201 Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 269 through 280 removed outlier: 4.501A pdb=" N LEU B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 339 through 354 removed outlier: 3.949A pdb=" N LYS B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 Processing helix chain 'B' and resid 392 through 413 Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 441 through 444 Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.668A pdb=" N VAL B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 478 removed outlier: 3.561A pdb=" N TYR B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 497 Proline residue: B 485 - end of helix removed outlier: 5.063A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 529 removed outlier: 3.849A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 508 " --> pdb=" O ASP B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 551 removed outlier: 3.731A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 4.228A pdb=" N VAL B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 4.186A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 571 Processing helix chain 'B' and resid 572 through 586 removed outlier: 4.041A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 618 Processing helix chain 'B' and resid 623 through 650 removed outlier: 3.587A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 632 " --> pdb=" O LYS B 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 95 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 269 through 280 removed outlier: 4.501A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 339 through 354 removed outlier: 3.948A pdb=" N LYS A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'A' and resid 392 through 413 Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 441 through 444 Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.668A pdb=" N VAL A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.562A pdb=" N TYR A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 497 Proline residue: A 485 - end of helix removed outlier: 5.063A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 529 removed outlier: 3.849A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 508 " --> pdb=" O ASP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.731A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 removed outlier: 4.228A pdb=" N VAL A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 4.186A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 571 Processing helix chain 'A' and resid 572 through 586 removed outlier: 4.041A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 618 Processing helix chain 'A' and resid 623 through 650 removed outlier: 3.586A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 62 through 71 removed outlier: 6.974A pdb=" N ILE B 63 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ARG B 45 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER B 65 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS B 43 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE B 67 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.206A pdb=" N LEU B 207 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N SER B 241 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU B 209 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 256 through 260 removed outlier: 3.559A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 62 through 71 removed outlier: 6.974A pdb=" N ILE A 63 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ARG A 45 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER A 65 " --> pdb=" O CYS A 43 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N CYS A 43 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE A 67 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 78 removed outlier: 6.206A pdb=" N LEU A 207 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N SER A 241 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 209 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 256 through 260 removed outlier: 3.558A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1488 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: 1.29 Time building geometry restraints manager: 0.79 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: 2790 1.34 - 1.46: 2209 1.46 - 1.58: 4082 1.58 - 1.70: 22 1.70 - 1.82: 94 Bond restraints: 9197 Sorted by residual: bond pdb=" C5 ATP B 701 " pdb=" N7 ATP B 701 " ideal model delta sigma weight residual 1.387 1.525 -0.138 1.00e-02 1.00e+04 1.91e+02 bond pdb=" C5 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.387 1.525 -0.138 1.00e-02 1.00e+04 1.89e+02 bond pdb=" C6 ATP A 701 " pdb=" N6 ATP A 701 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.10e-02 8.26e+03 1.07e+02 bond pdb=" C6 ATP B 701 " pdb=" N6 ATP B 701 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.10e-02 8.26e+03 1.07e+02 bond pdb=" C4 ATP B 701 " pdb=" N9 ATP B 701 " ideal model delta sigma weight residual 1.374 1.273 0.101 1.00e-02 1.00e+04 1.01e+02 ... (remaining 9192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 12358 3.30 - 6.60: 80 6.60 - 9.89: 27 9.89 - 13.19: 5 13.19 - 16.49: 9 Bond angle restraints: 12479 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 123.38 16.49 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 123.41 16.46 1.00e+00 1.00e+00 2.71e+02 angle pdb=" C4 ATP B 701 " pdb=" N9 ATP B 701 " pdb=" C8 ATP B 701 " ideal model delta sigma weight residual 105.72 121.17 -15.45 1.00e+00 1.00e+00 2.39e+02 angle pdb=" C4 ATP A 701 " pdb=" N9 ATP A 701 " pdb=" C8 ATP A 701 " ideal model delta sigma weight residual 105.72 121.12 -15.40 1.00e+00 1.00e+00 2.37e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 122.59 14.24 1.00e+00 1.00e+00 2.03e+02 ... (remaining 12474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.01: 4853 13.01 - 26.01: 377 26.01 - 39.02: 113 39.02 - 52.03: 24 52.03 - 65.03: 10 Dihedral angle restraints: 5377 sinusoidal: 2103 harmonic: 3274 Sorted by residual: dihedral pdb=" CA GLN A 181 " pdb=" C GLN A 181 " pdb=" N PHE A 182 " pdb=" CA PHE A 182 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA GLN B 181 " pdb=" C GLN B 181 " pdb=" N PHE B 182 " pdb=" CA PHE B 182 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLY B 553 " pdb=" C GLY B 553 " pdb=" N LEU B 554 " pdb=" CA LEU B 554 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 5374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1387 0.095 - 0.189: 43 0.189 - 0.284: 9 0.284 - 0.378: 1 0.378 - 0.473: 1 Chirality restraints: 1441 Sorted by residual: chirality pdb=" C21 TTC A 702 " pdb=" C16 TTC A 702 " pdb=" C20 TTC A 702 " pdb=" O24 TTC A 702 " both_signs ideal model delta sigma weight residual False -2.50 -2.97 0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" C17 CLR B 702 " pdb=" C13 CLR B 702 " pdb=" C16 CLR B 702 " pdb=" C20 CLR B 702 " both_signs ideal model delta sigma weight residual False 2.55 2.88 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C17 CLR A 703 " pdb=" C13 CLR A 703 " pdb=" C16 CLR A 703 " pdb=" C20 CLR A 703 " both_signs ideal model delta sigma weight residual False 2.55 2.84 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1438 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 TTC A 702 " 0.009 2.00e-02 2.50e+03 1.08e-02 6.44e+00 pdb=" C11 TTC A 702 " 0.001 2.00e-02 2.50e+03 pdb=" C13 TTC A 702 " 0.009 2.00e-02 2.50e+03 pdb=" C14 TTC A 702 " 0.008 2.00e-02 2.50e+03 pdb=" C15 TTC A 702 " 0.004 2.00e-02 2.50e+03 pdb=" C16 TTC A 702 " 0.019 2.00e-02 2.50e+03 pdb=" C17 TTC A 702 " 0.007 2.00e-02 2.50e+03 pdb=" C19 TTC A 702 " -0.007 2.00e-02 2.50e+03 pdb=" C2 TTC A 702 " 0.004 2.00e-02 2.50e+03 pdb=" C21 TTC A 702 " -0.033 2.00e-02 2.50e+03 pdb=" C27 TTC A 702 " -0.022 2.00e-02 2.50e+03 pdb=" C3 TTC A 702 " 0.010 2.00e-02 2.50e+03 pdb=" C4 TTC A 702 " 0.002 2.00e-02 2.50e+03 pdb=" C5 TTC A 702 " 0.001 2.00e-02 2.50e+03 pdb=" C6 TTC A 702 " 0.004 2.00e-02 2.50e+03 pdb=" C7 TTC A 702 " -0.005 2.00e-02 2.50e+03 pdb=" C8 TTC A 702 " 0.001 2.00e-02 2.50e+03 pdb=" C9 TTC A 702 " -0.002 2.00e-02 2.50e+03 pdb=" N10 TTC A 702 " -0.007 2.00e-02 2.50e+03 pdb=" N12 TTC A 702 " 0.006 2.00e-02 2.50e+03 pdb=" O18 TTC A 702 " -0.001 2.00e-02 2.50e+03 pdb=" O26 TTC A 702 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 601 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO B 602 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 602 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 602 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 601 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO A 602 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 602 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 602 " -0.018 5.00e-02 4.00e+02 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1864 2.77 - 3.30: 8792 3.30 - 3.84: 14104 3.84 - 4.37: 17043 4.37 - 4.90: 29736 Nonbonded interactions: 71539 Sorted by model distance: nonbonded pdb=" OG SER B 384 " pdb=" OD1 ASP B 477 " model vdw 2.240 3.040 nonbonded pdb=" OG SER A 384 " pdb=" OD1 ASP A 477 " model vdw 2.240 3.040 nonbonded pdb=" CE MET A 549 " pdb=" O24 TTC A 702 " model vdw 2.252 3.460 nonbonded pdb=" OH TYR B 44 " pdb=" OD1 ASP B 98 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR A 44 " pdb=" OD1 ASP A 98 " model vdw 2.310 3.040 ... (remaining 71534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 34 through 701) selection = (chain 'B' and resid 34 through 701) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.470 Find NCS groups from input model: 0.140 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.011 0.195 9200 Z= 0.596 Angle : 0.901 16.490 12485 Z= 0.598 Chirality : 0.047 0.473 1441 Planarity : 0.003 0.033 1530 Dihedral : 11.007 65.035 3268 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.52 % Allowed : 3.00 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.25), residues: 1122 helix: 1.41 (0.20), residues: 668 sheet: -0.59 (0.73), residues: 48 loop : -1.66 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 147 TYR 0.008 0.001 TYR B 469 PHE 0.012 0.001 PHE B 39 TRP 0.007 0.001 TRP B 564 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.01069 / 0.60 ( 9197) covalent geometry : angle 0.89768 / 0.60 (12479) SS BOND : bond 0.00381 / 0.21 ( 3) SS BOND : angle 3.68189 / 1.95 ( 6) hydrogen bonds : bond 0.16460 / 11.47 ( 512) hydrogen bonds : angle 6.03792 / 4.29 ( 1488) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 0.206 Fit side-chains REVERT: B 296 ASP cc_start: 0.7260 (t70) cc_final: 0.6748 (t0) outliers start: 5 outliers final: 2 residues processed: 212 average time/residue: 0.0816 time to fit residues: 23.2956 Evaluate side-chains 103 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 351 GLN A 126 GLN A 289 ASN A 391 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.145346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120109 restraints weight = 11731.084| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.69 r_work: 0.3360 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9200 Z= 0.141 Angle : 0.568 8.686 12485 Z= 0.303 Chirality : 0.040 0.180 1441 Planarity : 0.004 0.034 1530 Dihedral : 6.424 59.793 1244 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.27 % Allowed : 7.02 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1122 helix: 2.11 (0.21), residues: 654 sheet: 0.04 (0.77), residues: 48 loop : -1.56 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 193 TYR 0.011 0.001 TYR B 336 PHE 0.018 0.002 PHE B 293 TRP 0.012 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9197) covalent geometry : angle 0.56369 / 0.30 (12479) SS BOND : bond 0.01338 / 0.82 ( 3) SS BOND : angle 3.37033 / 1.60 ( 6) hydrogen bonds : bond 0.04726 / 3.20 ( 512) hydrogen bonds : angle 4.36667 / 3.16 ( 1488) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.211 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 123 average time/residue: 0.0658 time to fit residues: 11.8227 Evaluate side-chains 96 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106908 restraints weight = 12029.707| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.73 r_work: 0.3173 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 9200 Z= 0.285 Angle : 0.680 6.943 12485 Z= 0.357 Chirality : 0.047 0.226 1441 Planarity : 0.005 0.031 1530 Dihedral : 6.170 59.731 1244 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.89 % Allowed : 8.26 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1122 helix: 1.57 (0.20), residues: 666 sheet: 0.41 (0.73), residues: 50 loop : -1.76 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 191 TYR 0.020 0.002 TYR A 654 PHE 0.042 0.002 PHE A 293 TRP 0.022 0.002 TRP B 564 HIS 0.005 0.002 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.28 ( 9197) covalent geometry : angle 0.67789 / 0.36 (12479) SS BOND : bond 0.00389 / 0.24 ( 3) SS BOND : angle 2.59448 / 1.37 ( 6) hydrogen bonds : bond 0.06160 / 4.19 ( 512) hydrogen bonds : angle 4.29569 / 3.10 ( 1488) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 PHE cc_start: 0.8230 (m-10) cc_final: 0.7932 (m-80) outliers start: 28 outliers final: 17 residues processed: 116 average time/residue: 0.0727 time to fit residues: 12.1690 Evaluate side-chains 96 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 565 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0670 chunk 36 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112872 restraints weight = 12003.346| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.73 r_work: 0.3239 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9200 Z= 0.101 Angle : 0.483 7.291 12485 Z= 0.256 Chirality : 0.038 0.148 1441 Planarity : 0.003 0.036 1530 Dihedral : 5.445 54.421 1244 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.86 % Allowed : 10.64 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.26), residues: 1122 helix: 2.32 (0.20), residues: 650 sheet: 0.91 (0.76), residues: 50 loop : -1.53 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 236 TYR 0.011 0.001 TYR B 336 PHE 0.018 0.001 PHE B 293 TRP 0.016 0.001 TRP B 564 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 9197) covalent geometry : angle 0.48189 / 0.26 (12479) SS BOND : bond 0.00326 / 0.19 ( 3) SS BOND : angle 1.29414 / 0.66 ( 6) hydrogen bonds : bond 0.03803 / 2.60 ( 512) hydrogen bonds : angle 3.95194 / 2.88 ( 1488) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7061 (mtt) outliers start: 18 outliers final: 11 residues processed: 99 average time/residue: 0.0710 time to fit residues: 10.5814 Evaluate side-chains 90 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 654 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 47 optimal weight: 0.1980 chunk 93 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.139990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113955 restraints weight = 12048.490| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.73 r_work: 0.3252 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9200 Z= 0.098 Angle : 0.456 8.227 12485 Z= 0.240 Chirality : 0.037 0.177 1441 Planarity : 0.003 0.035 1530 Dihedral : 4.979 50.511 1243 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.65 % Allowed : 11.57 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.26), residues: 1122 helix: 2.55 (0.21), residues: 654 sheet: 1.49 (0.79), residues: 50 loop : -1.53 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.010 0.001 TYR B 336 PHE 0.020 0.001 PHE B 293 TRP 0.012 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 9197) covalent geometry : angle 0.45563 / 0.24 (12479) SS BOND : bond 0.00174 / 0.10 ( 3) SS BOND : angle 1.09716 / 0.57 ( 6) hydrogen bonds : bond 0.03456 / 2.36 ( 512) hydrogen bonds : angle 3.80341 / 2.78 ( 1488) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7019 (mtt) outliers start: 16 outliers final: 11 residues processed: 106 average time/residue: 0.0717 time to fit residues: 11.2212 Evaluate side-chains 92 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 654 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.139012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112709 restraints weight = 12050.552| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.76 r_work: 0.3237 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9200 Z= 0.110 Angle : 0.468 9.894 12485 Z= 0.245 Chirality : 0.038 0.140 1441 Planarity : 0.003 0.035 1530 Dihedral : 4.769 49.728 1243 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.45 % Allowed : 11.98 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.26), residues: 1122 helix: 2.57 (0.21), residues: 654 sheet: 1.68 (0.80), residues: 50 loop : -1.51 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.010 0.001 TYR B 336 PHE 0.019 0.001 PHE B 293 TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 9197) covalent geometry : angle 0.46748 / 0.24 (12479) SS BOND : bond 0.00146 / 0.08 ( 3) SS BOND : angle 1.12280 / 0.59 ( 6) hydrogen bonds : bond 0.03611 / 2.47 ( 512) hydrogen bonds : angle 3.73642 / 2.73 ( 1488) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7069 (mtt) outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 0.0676 time to fit residues: 9.3853 Evaluate side-chains 94 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 654 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.139121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112907 restraints weight = 12056.893| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.74 r_work: 0.3266 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9200 Z= 0.106 Angle : 0.469 10.458 12485 Z= 0.243 Chirality : 0.037 0.139 1441 Planarity : 0.003 0.036 1530 Dihedral : 4.637 49.459 1243 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.34 % Allowed : 12.50 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.26), residues: 1122 helix: 2.62 (0.21), residues: 654 sheet: 1.76 (0.79), residues: 50 loop : -1.51 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 96 TYR 0.010 0.001 TYR B 336 PHE 0.018 0.001 PHE B 293 TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9197) covalent geometry : angle 0.46881 / 0.24 (12479) SS BOND : bond 0.00130 / 0.07 ( 3) SS BOND : angle 1.05926 / 0.55 ( 6) hydrogen bonds : bond 0.03513 / 2.40 ( 512) hydrogen bonds : angle 3.69065 / 2.69 ( 1488) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.266 Fit side-chains REVERT: B 592 CYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7162 (m) REVERT: A 71 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7053 (mtt) outliers start: 13 outliers final: 10 residues processed: 88 average time/residue: 0.0735 time to fit residues: 9.4452 Evaluate side-chains 88 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 654 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 19 optimal weight: 0.0270 chunk 69 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114786 restraints weight = 11944.711| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.78 r_work: 0.3262 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9200 Z= 0.094 Angle : 0.458 11.385 12485 Z= 0.237 Chirality : 0.037 0.139 1441 Planarity : 0.003 0.035 1530 Dihedral : 4.486 48.724 1242 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.45 % Allowed : 12.71 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.27), residues: 1122 helix: 2.71 (0.21), residues: 652 sheet: 1.84 (0.79), residues: 50 loop : -1.45 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.009 0.001 TYR B 336 PHE 0.015 0.001 PHE B 293 TRP 0.010 0.001 TRP A 379 HIS 0.002 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 ( 9197) covalent geometry : angle 0.45715 / 0.24 (12479) SS BOND : bond 0.00166 / 0.10 ( 3) SS BOND : angle 1.00310 / 0.51 ( 6) hydrogen bonds : bond 0.03210 / 2.19 ( 512) hydrogen bonds : angle 3.65235 / 2.67 ( 1488) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.321 Fit side-chains REVERT: B 592 CYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7217 (m) REVERT: A 71 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7088 (mtt) REVERT: A 172 LYS cc_start: 0.8567 (mmmm) cc_final: 0.7817 (mtmm) outliers start: 14 outliers final: 10 residues processed: 93 average time/residue: 0.0706 time to fit residues: 9.8874 Evaluate side-chains 91 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 654 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 0.0270 chunk 59 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.137262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.110753 restraints weight = 11989.714| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.81 r_work: 0.3236 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9200 Z= 0.118 Angle : 0.488 11.874 12485 Z= 0.251 Chirality : 0.038 0.142 1441 Planarity : 0.003 0.035 1530 Dihedral : 4.509 48.795 1242 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.45 % Allowed : 13.22 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.27), residues: 1122 helix: 2.67 (0.21), residues: 654 sheet: 1.84 (0.79), residues: 50 loop : -1.51 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.009 0.001 TYR B 336 PHE 0.015 0.001 PHE B 293 TRP 0.008 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 9197) covalent geometry : angle 0.48719 / 0.25 (12479) SS BOND : bond 0.00121 / 0.06 ( 3) SS BOND : angle 1.03476 / 0.54 ( 6) hydrogen bonds : bond 0.03639 / 2.48 ( 512) hydrogen bonds : angle 3.64239 / 2.66 ( 1488) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7207 (mtt) REVERT: A 172 LYS cc_start: 0.8554 (mmmm) cc_final: 0.7821 (mtmm) outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 0.0682 time to fit residues: 8.8697 Evaluate side-chains 89 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 654 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.137722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111250 restraints weight = 11932.037| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.80 r_work: 0.3244 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9200 Z= 0.108 Angle : 0.490 12.838 12485 Z= 0.250 Chirality : 0.037 0.141 1441 Planarity : 0.003 0.035 1530 Dihedral : 4.458 48.865 1242 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.34 % Allowed : 13.43 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.26), residues: 1122 helix: 2.69 (0.21), residues: 654 sheet: 1.99 (0.80), residues: 50 loop : -1.50 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 191 TYR 0.009 0.001 TYR B 336 PHE 0.015 0.001 PHE B 293 TRP 0.009 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 9197) covalent geometry : angle 0.48938 / 0.25 (12479) SS BOND : bond 0.00127 / 0.07 ( 3) SS BOND : angle 1.01224 / 0.52 ( 6) hydrogen bonds : bond 0.03497 / 2.38 ( 512) hydrogen bonds : angle 3.62883 / 2.65 ( 1488) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7180 (mtt) REVERT: A 160 ARG cc_start: 0.7761 (tpp80) cc_final: 0.7451 (mmm-85) REVERT: A 172 LYS cc_start: 0.8556 (mmmm) cc_final: 0.7821 (mtmm) outliers start: 13 outliers final: 12 residues processed: 87 average time/residue: 0.0692 time to fit residues: 8.7203 Evaluate side-chains 91 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 654 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 617 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.132138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.105209 restraints weight = 11941.132| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.83 r_work: 0.3137 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9200 Z= 0.233 Angle : 0.604 17.000 12485 Z= 0.307 Chirality : 0.042 0.146 1441 Planarity : 0.004 0.035 1530 Dihedral : 4.942 52.548 1242 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.45 % Allowed : 13.33 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.26), residues: 1122 helix: 2.27 (0.20), residues: 652 sheet: 1.84 (0.79), residues: 50 loop : -1.70 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 163 TYR 0.010 0.002 TYR A 336 PHE 0.019 0.002 PHE B 293 TRP 0.010 0.002 TRP B 624 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.23 ( 9197) covalent geometry : angle 0.60246 / 0.31 (12479) SS BOND : bond 0.00092 / 0.05 ( 3) SS BOND : angle 1.76701 / 0.94 ( 6) hydrogen bonds : bond 0.05107 / 3.47 ( 512) hydrogen bonds : angle 3.82238 / 2.78 ( 1488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1879.38 seconds wall clock time: 32 minutes 51.32 seconds (1971.32 seconds total)