Starting phenix.real_space_refine on Wed Mar 4 00:01:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ojh_12951/03_2026/7ojh_12951.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ojh_12951/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ojh_12951/03_2026/7ojh_12951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ojh_12951/03_2026/7ojh_12951.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ojh_12951/03_2026/7ojh_12951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ojh_12951/03_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-5986/lib/python3.9/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: 1.85, per 1000 atoms: 0.21 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 213.9 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: 0.30 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: 1.41 Time building geometry restraints manager: 0.86 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 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: 3.540 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 8.650 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.960 ------------------------------------------------------------------------------- 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 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 covalent geometry : bond 0.01069 ( 9197) covalent geometry : angle 0.89768 (12479) SS BOND : bond 0.00381 ( 3) SS BOND : angle 3.68189 ( 6) hydrogen bonds : bond 0.16460 ( 512) hydrogen bonds : angle 6.03792 ( 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 : 0.389 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: 0.1105 time to fit residues: 31.2848 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 : 0.323 ------------------------------------------------------------------------------- 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... 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 = 0.3768 r_free = 0.3768 target = 0.145452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120349 restraints weight = 11733.281| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.69 r_work: 0.3361 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9200 Z= 0.141 Angle : 0.571 8.987 12485 Z= 0.306 Chirality : 0.040 0.164 1441 Planarity : 0.004 0.034 1530 Dihedral : 8.796 59.479 1435 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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 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: 1.07 (0.26), residues: 1122 helix: 2.10 (0.21), residues: 654 sheet: 0.04 (0.78), residues: 48 loop : -1.55 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 236 TYR 0.011 0.001 TYR A 44 PHE 0.017 0.002 PHE B 293 TRP 0.011 0.001 TRP A 379 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9197) covalent geometry : angle 0.56377 (12479) SS BOND : bond 0.00391 ( 3) SS BOND : angle 4.20661 ( 6) hydrogen bonds : bond 0.04895 ( 512) hydrogen bonds : angle 4.40533 ( 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 131 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.310 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 124 average time/residue: 0.0883 time to fit residues: 15.5344 Evaluate side-chains 95 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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: 5.9990 chunk 82 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.133591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.107186 restraints weight = 12026.890| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.74 r_work: 0.3154 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 9200 Z= 0.289 Angle : 0.679 6.860 12485 Z= 0.356 Chirality : 0.047 0.223 1441 Planarity : 0.005 0.032 1530 Dihedral : 8.719 62.698 1435 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.79 % Allowed : 7.95 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.59 (0.26), residues: 1122 helix: 1.58 (0.20), residues: 666 sheet: 0.37 (0.73), residues: 50 loop : -1.70 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 246 TYR 0.019 0.002 TYR A 654 PHE 0.017 0.002 PHE B 507 TRP 0.022 0.003 TRP B 564 HIS 0.005 0.002 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00719 ( 9197) covalent geometry : angle 0.67686 (12479) SS BOND : bond 0.00266 ( 3) SS BOND : angle 2.57273 ( 6) hydrogen bonds : bond 0.06043 ( 512) hydrogen bonds : angle 4.28587 ( 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 121 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: B 207 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8602 (tp) REVERT: B 341 PHE cc_start: 0.8206 (m-10) cc_final: 0.7907 (m-80) outliers start: 27 outliers final: 19 residues processed: 113 average time/residue: 0.0944 time to fit residues: 14.9254 Evaluate side-chains 97 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 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 108 ILE Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 534 VAL 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: 0.0980 chunk 36 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.137560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.111644 restraints weight = 11983.526| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.72 r_work: 0.3246 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9200 Z= 0.104 Angle : 0.486 7.646 12485 Z= 0.257 Chirality : 0.038 0.168 1441 Planarity : 0.003 0.036 1530 Dihedral : 7.880 65.865 1435 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.65 % Allowed : 10.64 % Favored : 87.71 % 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: 1.34 (0.26), residues: 1122 helix: 2.31 (0.20), residues: 650 sheet: 0.92 (0.76), residues: 50 loop : -1.52 (0.31), 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 0.020 0.001 PHE B 293 TRP 0.018 0.001 TRP B 564 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9197) covalent geometry : angle 0.48476 (12479) SS BOND : bond 0.00228 ( 3) SS BOND : angle 1.34625 ( 6) hydrogen bonds : bond 0.03744 ( 512) hydrogen bonds : angle 3.96173 ( 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 103 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.214 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 99 average time/residue: 0.0803 time to fit residues: 11.8389 Evaluate side-chains 88 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 23 optimal weight: 0.0980 chunk 47 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.138577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112550 restraints weight = 12090.515| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.74 r_work: 0.3229 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9200 Z= 0.113 Angle : 0.473 8.097 12485 Z= 0.249 Chirality : 0.038 0.174 1441 Planarity : 0.003 0.035 1530 Dihedral : 7.560 69.681 1434 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.07 % Allowed : 10.74 % Favored : 87.19 % 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: 1.51 (0.26), residues: 1122 helix: 2.47 (0.21), residues: 652 sheet: 1.45 (0.79), residues: 50 loop : -1.57 (0.30), residues: 420 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 0.011 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9197) covalent geometry : angle 0.47251 (12479) SS BOND : bond 0.00151 ( 3) SS BOND : angle 1.28234 ( 6) hydrogen bonds : bond 0.03779 ( 512) hydrogen bonds : angle 3.83918 ( 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 107 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: B 172 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7847 (tttm) REVERT: B 207 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8613 (tt) outliers start: 20 outliers final: 12 residues processed: 101 average time/residue: 0.0849 time to fit residues: 12.3989 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 ------------------------------------------------------------------------------- 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 172 LYS Chi-restraints excluded: chain B residue 207 LEU 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 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 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 98 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.138636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112595 restraints weight = 12087.742| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.73 r_work: 0.3230 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9200 Z= 0.113 Angle : 0.473 9.490 12485 Z= 0.249 Chirality : 0.038 0.141 1441 Planarity : 0.003 0.036 1530 Dihedral : 7.697 71.023 1434 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.55 % Allowed : 12.60 % 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: 1.58 (0.26), residues: 1122 helix: 2.52 (0.20), residues: 652 sheet: 1.60 (0.79), residues: 50 loop : -1.55 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 193 TYR 0.010 0.001 TYR B 336 PHE 0.020 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 covalent geometry : bond 0.00260 ( 9197) covalent geometry : angle 0.47275 (12479) SS BOND : bond 0.00142 ( 3) SS BOND : angle 1.17371 ( 6) hydrogen bonds : bond 0.03684 ( 512) hydrogen bonds : angle 3.76435 ( 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: 15 poor density : 85 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: B 172 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7855 (tttm) REVERT: B 207 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8623 (tt) outliers start: 15 outliers final: 10 residues processed: 95 average time/residue: 0.0789 time to fit residues: 11.1930 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 : 0.300 ------------------------------------------------------------------------------- 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 172 LYS Chi-restraints excluded: chain B residue 207 LEU 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 180 THR Chi-restraints excluded: chain A residue 233 LYS 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: 0.3980 chunk 78 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 0.0470 chunk 108 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111778 restraints weight = 12051.129| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.78 r_work: 0.3245 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9200 Z= 0.098 Angle : 0.455 9.733 12485 Z= 0.240 Chirality : 0.037 0.143 1441 Planarity : 0.003 0.037 1530 Dihedral : 7.491 73.778 1433 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.45 % Allowed : 13.12 % 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 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: 1.73 (0.26), residues: 1122 helix: 2.61 (0.21), residues: 654 sheet: 1.84 (0.78), residues: 50 loop : -1.47 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.010 0.001 TYR B 336 PHE 0.016 0.001 PHE B 293 TRP 0.011 0.001 TRP A 379 HIS 0.002 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 9197) covalent geometry : angle 0.45496 (12479) SS BOND : bond 0.00114 ( 3) SS BOND : angle 0.94897 ( 6) hydrogen bonds : bond 0.03316 ( 512) hydrogen bonds : angle 3.68012 ( 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 102 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: B 172 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7840 (tttm) outliers start: 14 outliers final: 12 residues processed: 97 average time/residue: 0.0798 time to fit residues: 11.5464 Evaluate side-chains 92 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 172 LYS 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 180 THR Chi-restraints excluded: chain A residue 233 LYS 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 111 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 0.0060 chunk 98 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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 = 0.136908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110273 restraints weight = 12011.615| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.83 r_work: 0.3208 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9200 Z= 0.115 Angle : 0.485 11.717 12485 Z= 0.252 Chirality : 0.038 0.142 1441 Planarity : 0.003 0.036 1530 Dihedral : 7.469 73.918 1433 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.55 % Allowed : 13.53 % Favored : 84.92 % 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: 1.68 (0.26), residues: 1122 helix: 2.57 (0.21), residues: 656 sheet: 1.82 (0.77), residues: 50 loop : -1.52 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 191 TYR 0.009 0.001 TYR B 336 PHE 0.033 0.001 PHE A 293 TRP 0.009 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9197) covalent geometry : angle 0.48451 (12479) SS BOND : bond 0.00115 ( 3) SS BOND : angle 1.12318 ( 6) hydrogen bonds : bond 0.03567 ( 512) hydrogen bonds : angle 3.68361 ( 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 92 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: B 172 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7916 (tttm) REVERT: B 207 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8649 (tt) REVERT: A 172 LYS cc_start: 0.8568 (mmmm) cc_final: 0.7830 (mtmm) outliers start: 15 outliers final: 13 residues processed: 86 average time/residue: 0.0916 time to fit residues: 11.4256 Evaluate side-chains 90 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 172 LYS Chi-restraints excluded: chain B residue 207 LEU 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 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 481 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.135295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108732 restraints weight = 12006.968| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.80 r_work: 0.3181 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9200 Z= 0.151 Angle : 0.524 12.041 12485 Z= 0.271 Chirality : 0.039 0.144 1441 Planarity : 0.003 0.036 1530 Dihedral : 7.590 73.521 1433 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.86 % Allowed : 13.33 % 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 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: 1.55 (0.26), residues: 1122 helix: 2.46 (0.20), residues: 654 sheet: 1.73 (0.77), residues: 50 loop : -1.53 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.010 0.001 TYR B 336 PHE 0.028 0.001 PHE A 293 TRP 0.007 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9197) covalent geometry : angle 0.52377 (12479) SS BOND : bond 0.00104 ( 3) SS BOND : angle 1.30315 ( 6) hydrogen bonds : bond 0.04167 ( 512) hydrogen bonds : angle 3.73178 ( 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 96 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: B 172 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7939 (tttm) REVERT: B 207 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8681 (tt) REVERT: A 172 LYS cc_start: 0.8559 (mmmm) cc_final: 0.7807 (mtmm) outliers start: 18 outliers final: 12 residues processed: 90 average time/residue: 0.0886 time to fit residues: 11.4760 Evaluate side-chains 89 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 172 LYS Chi-restraints excluded: chain B residue 207 LEU 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 108 ILE 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 563 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.136443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109976 restraints weight = 11953.600| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.80 r_work: 0.3206 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 : 0.003 0.040 9200 Z= 0.116 Angle : 0.498 12.308 12485 Z= 0.258 Chirality : 0.038 0.141 1441 Planarity : 0.003 0.035 1530 Dihedral : 7.536 75.393 1433 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.45 % Allowed : 13.84 % Favored : 84.71 % 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: 1.67 (0.26), residues: 1122 helix: 2.56 (0.20), residues: 652 sheet: 1.90 (0.78), residues: 50 loop : -1.48 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 191 TYR 0.009 0.001 TYR B 459 PHE 0.024 0.001 PHE A 293 TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9197) covalent geometry : angle 0.49756 (12479) SS BOND : bond 0.00145 ( 3) SS BOND : angle 1.12774 ( 6) hydrogen bonds : bond 0.03674 ( 512) hydrogen bonds : angle 3.70711 ( 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 95 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: B 172 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7941 (tttm) REVERT: B 207 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8653 (tt) REVERT: B 592 CYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7218 (m) REVERT: B 616 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8589 (mttt) REVERT: A 160 ARG cc_start: 0.7805 (tpp80) cc_final: 0.7484 (mmm-85) REVERT: A 172 LYS cc_start: 0.8565 (mmmm) cc_final: 0.7821 (mtmm) outliers start: 14 outliers final: 10 residues processed: 91 average time/residue: 0.0999 time to fit residues: 12.8457 Evaluate side-chains 94 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 172 LYS Chi-restraints excluded: chain B residue 207 LEU 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 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 481 MET 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: 0.9980 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.136878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111887 restraints weight = 11914.146| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.69 r_work: 0.3187 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9200 Z= 0.149 Angle : 0.532 15.406 12485 Z= 0.273 Chirality : 0.039 0.144 1441 Planarity : 0.004 0.034 1530 Dihedral : 7.577 74.945 1433 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.34 % Allowed : 14.05 % Favored : 84.61 % 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: 1.51 (0.26), residues: 1122 helix: 2.42 (0.20), residues: 654 sheet: 1.85 (0.77), residues: 50 loop : -1.56 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 163 TYR 0.009 0.001 TYR B 336 PHE 0.022 0.001 PHE A 293 TRP 0.007 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9197) covalent geometry : angle 0.53100 (12479) SS BOND : bond 0.00111 ( 3) SS BOND : angle 1.30254 ( 6) hydrogen bonds : bond 0.04141 ( 512) hydrogen bonds : angle 3.73438 ( 1488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.72 seconds wall clock time: 39 minutes 35.95 seconds (2375.95 seconds total)