Starting phenix.real_space_refine on Sun Jul 27 13:36:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ojh_12951/07_2025/7ojh_12951.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ojh_12951/07_2025/7ojh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ojh_12951/07_2025/7ojh_12951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ojh_12951/07_2025/7ojh_12951.map" model { file = "/net/cci-nas-00/data/ceres_data/7ojh_12951/07_2025/7ojh_12951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ojh_12951/07_2025/7ojh_12951.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.86, per 1000 atoms: 0.76 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: 2.21 Conformation dependent library (CDL) restraints added in 985.6 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: 0.87 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: 2.67 Time building geometry restraints manager: 2.59 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: 4973 13.01 - 26.01: 396 26.01 - 39.02: 143 39.02 - 52.03: 43 52.03 - 65.03: 13 Dihedral angle restraints: 5568 sinusoidal: 2294 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 5565 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 654 or resid 701)) selection = (chain 'B' and (resid 34 through 654 or resid 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: 3.040 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.080 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 11.822 65.035 3459 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (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 TRP 0.007 0.001 TRP B 564 HIS 0.004 0.001 HIS A 267 PHE 0.012 0.001 PHE B 39 TYR 0.008 0.001 TYR B 469 ARG 0.003 0.001 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.16460 ( 512) hydrogen bonds : angle 6.03792 ( 1488) SS BOND : bond 0.00381 ( 3) SS BOND : angle 3.68189 ( 6) covalent geometry : bond 0.01069 ( 9197) covalent geometry : angle 0.89768 (12479) *********************** 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 : 0.985 Fit side-chains revert: symmetry clash 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: 0.2337 time to fit residues: 66.1718 Evaluate side-chains 104 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN A 126 GLN A 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.143552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118004 restraints weight = 11697.664| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.71 r_work: 0.3327 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9200 Z= 0.161 Angle : 0.585 7.968 12485 Z= 0.313 Chirality : 0.041 0.178 1441 Planarity : 0.004 0.034 1530 Dihedral : 8.707 59.716 1435 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.17 % Allowed : 7.02 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1122 helix: 1.92 (0.20), residues: 668 sheet: 0.08 (0.77), residues: 48 loop : -1.63 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.004 0.001 HIS A 40 PHE 0.018 0.002 PHE B 293 TYR 0.011 0.001 TYR A 44 ARG 0.004 0.001 ARG B 236 Details of bonding type rmsd hydrogen bonds : bond 0.04889 ( 512) hydrogen bonds : angle 4.36891 ( 1488) SS BOND : bond 0.01950 ( 3) SS BOND : angle 3.55485 ( 6) covalent geometry : bond 0.00368 ( 9197) covalent geometry : angle 0.58029 (12479) *********************** 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 135 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.927 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 128 average time/residue: 0.2073 time to fit residues: 37.3605 Evaluate side-chains 100 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 65 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 97 optimal weight: 0.0570 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.140210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114346 restraints weight = 11893.275| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.70 r_work: 0.3257 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9200 Z= 0.151 Angle : 0.536 7.933 12485 Z= 0.285 Chirality : 0.040 0.208 1441 Planarity : 0.004 0.033 1530 Dihedral : 7.667 64.191 1435 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.96 % Allowed : 9.30 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1122 helix: 2.21 (0.21), residues: 654 sheet: 0.50 (0.76), residues: 50 loop : -1.59 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.004 0.001 HIS A 40 PHE 0.031 0.002 PHE A 293 TYR 0.011 0.001 TYR B 336 ARG 0.006 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 512) hydrogen bonds : angle 4.05446 ( 1488) SS BOND : bond 0.00865 ( 3) SS BOND : angle 1.78336 ( 6) covalent geometry : bond 0.00358 ( 9197) covalent geometry : angle 0.53464 (12479) *********************** 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 115 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: B 207 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8600 (tp) REVERT: B 341 PHE cc_start: 0.7875 (m-10) cc_final: 0.7629 (m-80) outliers start: 19 outliers final: 11 residues processed: 110 average time/residue: 0.1989 time to fit residues: 31.8655 Evaluate side-chains 93 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 207 LEU 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 233 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.136103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.111103 restraints weight = 11949.480| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.68 r_work: 0.3184 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9200 Z= 0.184 Angle : 0.557 6.586 12485 Z= 0.294 Chirality : 0.041 0.141 1441 Planarity : 0.004 0.034 1530 Dihedral : 7.683 65.569 1435 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.48 % Allowed : 9.30 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1122 helix: 1.94 (0.20), residues: 668 sheet: 0.96 (0.75), residues: 50 loop : -1.76 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.004 0.001 HIS A 40 PHE 0.016 0.002 PHE A 293 TYR 0.012 0.002 TYR B 336 ARG 0.002 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 512) hydrogen bonds : angle 3.97962 ( 1488) SS BOND : bond 0.00076 ( 3) SS BOND : angle 1.87535 ( 6) covalent geometry : bond 0.00445 ( 9197) covalent geometry : angle 0.55550 (12479) *********************** 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 117 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: B 207 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8586 (tt) REVERT: A 287 TYR cc_start: 0.6500 (m-80) cc_final: 0.6283 (m-80) outliers start: 24 outliers final: 16 residues processed: 112 average time/residue: 0.1995 time to fit residues: 31.9409 Evaluate side-chains 100 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 207 LEU 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 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 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 565 LEU 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 17 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 617 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.104570 restraints weight = 11960.500| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.80 r_work: 0.3135 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9200 Z= 0.233 Angle : 0.595 7.980 12485 Z= 0.311 Chirality : 0.043 0.142 1441 Planarity : 0.004 0.035 1530 Dihedral : 8.271 68.091 1434 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.69 % Allowed : 10.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1122 helix: 1.76 (0.20), residues: 666 sheet: 1.16 (0.74), residues: 50 loop : -1.80 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 379 HIS 0.004 0.001 HIS A 40 PHE 0.014 0.002 PHE B 507 TYR 0.011 0.002 TYR B 336 ARG 0.004 0.001 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.05345 ( 512) hydrogen bonds : angle 4.03763 ( 1488) SS BOND : bond 0.00138 ( 3) SS BOND : angle 2.09440 ( 6) covalent geometry : bond 0.00574 ( 9197) covalent geometry : angle 0.59312 (12479) *********************** 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 107 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: B 207 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8629 (tp) REVERT: A 287 TYR cc_start: 0.6508 (m-80) cc_final: 0.6282 (m-80) outliers start: 26 outliers final: 20 residues processed: 102 average time/residue: 0.1969 time to fit residues: 29.5501 Evaluate side-chains 98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 107 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 504 ASP 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 180 THR 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 563 SER Chi-restraints excluded: chain A residue 565 LEU 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 59 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.135283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108956 restraints weight = 11789.401| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.77 r_work: 0.3220 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9200 Z= 0.112 Angle : 0.496 9.731 12485 Z= 0.261 Chirality : 0.038 0.141 1441 Planarity : 0.003 0.036 1530 Dihedral : 7.822 71.301 1434 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.55 % Allowed : 12.19 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1122 helix: 2.18 (0.20), residues: 666 sheet: 1.55 (0.78), residues: 50 loop : -1.71 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 PHE 0.017 0.001 PHE B 293 TYR 0.009 0.001 TYR B 336 ARG 0.002 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 512) hydrogen bonds : angle 3.84657 ( 1488) SS BOND : bond 0.00156 ( 3) SS BOND : angle 1.24373 ( 6) covalent geometry : bond 0.00253 ( 9197) covalent geometry : angle 0.49557 (12479) *********************** 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: 15 poor density : 85 time to evaluate : 1.131 Fit side-chains REVERT: B 592 CYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7259 (m) REVERT: A 172 LYS cc_start: 0.8507 (mmmm) cc_final: 0.7781 (mtmm) REVERT: A 287 TYR cc_start: 0.6389 (m-80) cc_final: 0.6137 (m-80) outliers start: 15 outliers final: 7 residues processed: 98 average time/residue: 0.2317 time to fit residues: 32.7151 Evaluate side-chains 85 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 LEU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 0.0570 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106699 restraints weight = 12017.941| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.80 r_work: 0.3159 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9200 Z= 0.173 Angle : 0.535 10.667 12485 Z= 0.279 Chirality : 0.040 0.142 1441 Planarity : 0.004 0.036 1530 Dihedral : 7.838 71.928 1433 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.86 % Allowed : 12.50 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1122 helix: 2.08 (0.20), residues: 666 sheet: 1.58 (0.78), residues: 50 loop : -1.75 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 PHE 0.019 0.001 PHE B 293 TYR 0.010 0.001 TYR A 336 ARG 0.003 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 512) hydrogen bonds : angle 3.84286 ( 1488) SS BOND : bond 0.00150 ( 3) SS BOND : angle 1.58436 ( 6) covalent geometry : bond 0.00423 ( 9197) covalent geometry : angle 0.53381 (12479) *********************** 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 98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: B 207 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8664 (tt) REVERT: A 172 LYS cc_start: 0.8499 (mmmm) cc_final: 0.7800 (mtmm) REVERT: A 287 TYR cc_start: 0.6441 (m-80) cc_final: 0.6190 (m-80) outliers start: 18 outliers final: 16 residues processed: 92 average time/residue: 0.1980 time to fit residues: 26.3838 Evaluate side-chains 93 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 107 LEU Chi-restraints excluded: chain B residue 207 LEU 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 68 ASN Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 LEU 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 99 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.134996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.108615 restraints weight = 12008.003| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.78 r_work: 0.3184 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9200 Z= 0.130 Angle : 0.502 11.165 12485 Z= 0.263 Chirality : 0.039 0.142 1441 Planarity : 0.003 0.037 1530 Dihedral : 7.698 74.205 1433 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.96 % Allowed : 12.60 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1122 helix: 2.18 (0.20), residues: 668 sheet: 1.75 (0.79), residues: 50 loop : -1.70 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 PHE 0.016 0.001 PHE B 293 TYR 0.009 0.001 TYR A 336 ARG 0.002 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 512) hydrogen bonds : angle 3.78952 ( 1488) SS BOND : bond 0.00141 ( 3) SS BOND : angle 1.30661 ( 6) covalent geometry : bond 0.00309 ( 9197) covalent geometry : angle 0.50122 (12479) *********************** 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 104 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: B 207 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8668 (tt) REVERT: A 172 LYS cc_start: 0.8523 (mmmm) cc_final: 0.7802 (mtmm) REVERT: A 287 TYR cc_start: 0.6341 (m-80) cc_final: 0.6051 (m-80) outliers start: 19 outliers final: 15 residues processed: 100 average time/residue: 0.2030 time to fit residues: 29.3777 Evaluate side-chains 94 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 68 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 481 MET 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 25 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110508 restraints weight = 11859.927| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.78 r_work: 0.3236 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9200 Z= 0.103 Angle : 0.492 11.919 12485 Z= 0.256 Chirality : 0.037 0.139 1441 Planarity : 0.003 0.037 1530 Dihedral : 7.603 76.471 1433 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.45 % Allowed : 13.74 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.26), residues: 1122 helix: 2.57 (0.21), residues: 650 sheet: 1.91 (0.79), residues: 50 loop : -1.55 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 PHE 0.014 0.001 PHE A 506 TYR 0.009 0.001 TYR A 336 ARG 0.002 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 512) hydrogen bonds : angle 3.71654 ( 1488) SS BOND : bond 0.00162 ( 3) SS BOND : angle 1.18718 ( 6) covalent geometry : bond 0.00232 ( 9197) covalent geometry : angle 0.49096 (12479) *********************** 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 103 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.118 Fit side-chains REVERT: B 207 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8654 (tt) REVERT: B 592 CYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7267 (m) REVERT: A 163 ARG cc_start: 0.7364 (mtp180) cc_final: 0.7151 (ttp-170) REVERT: A 172 LYS cc_start: 0.8518 (mmmm) cc_final: 0.7823 (mtmm) REVERT: A 287 TYR cc_start: 0.6259 (m-80) cc_final: 0.5982 (m-80) outliers start: 14 outliers final: 10 residues processed: 100 average time/residue: 0.2062 time to fit residues: 31.0934 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 : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 0.0570 chunk 24 optimal weight: 3.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107804 restraints weight = 12064.917| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.74 r_work: 0.3171 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9200 Z= 0.168 Angle : 0.567 13.088 12485 Z= 0.289 Chirality : 0.040 0.145 1441 Planarity : 0.004 0.037 1530 Dihedral : 7.704 74.968 1433 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.86 % Allowed : 14.05 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.26), residues: 1122 helix: 2.41 (0.20), residues: 650 sheet: 1.85 (0.78), residues: 50 loop : -1.60 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 PHE 0.024 0.001 PHE A 293 TYR 0.011 0.001 TYR A 336 ARG 0.002 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.04399 ( 512) hydrogen bonds : angle 3.79009 ( 1488) SS BOND : bond 0.00115 ( 3) SS BOND : angle 1.46332 ( 6) covalent geometry : bond 0.00410 ( 9197) covalent geometry : angle 0.56662 (12479) ********************** 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 95 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: B 207 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8660 (tt) REVERT: A 287 TYR cc_start: 0.6367 (m-80) cc_final: 0.6056 (m-80) outliers start: 18 outliers final: 15 residues processed: 92 average time/residue: 0.1971 time to fit residues: 26.2856 Evaluate side-chains 90 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 481 MET 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 24 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 0.0670 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109719 restraints weight = 11997.798| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.82 r_work: 0.3207 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4366 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= 0.110 Angle : 0.534 13.623 12485 Z= 0.270 Chirality : 0.038 0.138 1441 Planarity : 0.003 0.037 1530 Dihedral : 7.590 77.442 1433 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.76 % Allowed : 14.36 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.26), residues: 1122 helix: 2.57 (0.21), residues: 650 sheet: 1.97 (0.79), residues: 50 loop : -1.52 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 PHE 0.021 0.001 PHE A 293 TYR 0.009 0.001 TYR B 459 ARG 0.003 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 512) hydrogen bonds : angle 3.72248 ( 1488) SS BOND : bond 0.00141 ( 3) SS BOND : angle 1.08046 ( 6) covalent geometry : bond 0.00253 ( 9197) covalent geometry : angle 0.53312 (12479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5165.95 seconds wall clock time: 90 minutes 24.75 seconds (5424.75 seconds total)