Starting phenix.real_space_refine
on Wed Jan 14 00:06:21 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8gzq_34401/01_2026/8gzq_34401.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gzq_34401/01_2026/8gzq_34401.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gzq_34401/01_2026/8gzq_34401.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gzq_34401/01_2026/8gzq_34401.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gzq_34401/01_2026/8gzq_34401.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gzq_34401/01_2026/8gzq_34401.map"
  }
  resolution = 3.9
  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=   0.000 sd=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      68      5.49       5
     S      39      5.16       5
     C    6285      2.51       5
     N    1918      2.21       5
     O    2060      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10372
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 852, 6423
          Classifications: {'peptide': 852}
          Incomplete info: {'truncation_to_alanine': 139}
          Link IDs: {'PTRANS': 40, 'TRANS': 811}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 503
          Unresolved non-hydrogen angles: 600
          Unresolved non-hydrogen dihedrals: 408
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLU:plan': 37, 'ARG:plan': 13, 'GLN:plan1': 6, 'ASN:plan1': 6, 'HIS:plan': 1, 'ASP:plan': 12}
          Unresolved non-hydrogen planarities: 296
    Chain: "B"
      Number of atoms: 2513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 408, 2513
          Classifications: {'peptide': 408}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 225}
          Link IDs: {'PTRANS': 25, 'TRANS': 382}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 765
          Unresolved non-hydrogen angles: 955
          Unresolved non-hydrogen dihedrals: 592
          Unresolved non-hydrogen chiralities: 82
          Planarities with less than four sites: {'GLU:plan': 25, 'ARG:plan': 19, 'ASP:plan': 27, 'GLN:plan1': 9, 'HIS:plan': 1, 'ASN:plan1': 11, 'PHE:plan': 6, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 393
    Chain: "S"
      Number of atoms: 1406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 1406
          Classifications: {'RNA': 66}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 27}
          Link IDs: {'rna2p': 7, 'rna3p': 58}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "S"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5166  SG  CYS A 728      58.412  41.457  34.079  1.00 92.91           S
  ATOM   6106  SG  CYS A 847      61.688  43.262  34.948  1.00111.96           S
  ATOM   3115  SG  CYS A 446      18.025  60.139  39.318  1.00135.00           S
  ATOM   3131  SG  CYS A 449      18.877  57.138  38.017  1.00131.52           S

  Time building chain proxies: 2.50, per 1000 atoms: 0.24
  Number of scatterers: 10372
  At special positions: 0
  Unit cell: (122.618, 96.9345, 108.533, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      39     16.00
     P      68     15.00
     O    2060      8.00
     N    1918      7.00
     C    6285      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 396.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" NE2 HIS A 714 "
        pdb="ZN    ZN A1001 " - pdb=" NE2 HIS A 712 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 847 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 728 "
      pdb="  ZN A1002 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 446 "
        pdb="ZN    ZN A1002 " - pdb=" NE2 HIS A 441 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 449 "
      Number of angles added : 2


  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2348

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 8 sheets defined
      49.0% alpha, 9.0% beta
      22 base pairs and 34 stacking pairs defined.
    Time for finding SS restraints: 1.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 19
    Processing helix  chain 'A' and resid 21 through 29
    Processing helix  chain 'A' and resid 38 through 48
    Processing helix  chain 'A' and resid 57 through 68
      removed outlier: 3.769A  pdb=" N   PHE A  65 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ARG A  68 " --> pdb=" O   TRP A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 93
      removed outlier: 3.790A  pdb=" N   GLY A  93 " --> pdb=" O   TYR A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 122
      No H-bonds generated for 'chain 'A' and resid 120 through 122'
    Processing helix  chain 'A' and resid 153 through 169
    Processing helix  chain 'A' and resid 170 through 172
      No H-bonds generated for 'chain 'A' and resid 170 through 172'
    Processing helix  chain 'A' and resid 186 through 201
    Processing helix  chain 'A' and resid 226 through 241
    Processing helix  chain 'A' and resid 272 through 287
      removed outlier: 5.210A  pdb=" N   GLU A 278 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      removed outlier: 5.622A  pdb=" N   ARG A 279 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
    Processing helix  chain 'A' and resid 327 through 332
      Proline residue:  A 330  - end of helix
      No H-bonds generated for 'chain 'A' and resid 327 through 332'
    Processing helix  chain 'A' and resid 334 through 342
      removed outlier: 3.715A  pdb=" N   ALA A 341 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 358
    Processing helix  chain 'A' and resid 366 through 385
    Processing helix  chain 'A' and resid 394 through 404
    Processing helix  chain 'A' and resid 418 through 427
    Processing helix  chain 'A' and resid 428 through 444
    Processing helix  chain 'A' and resid 472 through 489
    Processing helix  chain 'A' and resid 489 through 494
    Processing helix  chain 'A' and resid 498 through 503
    Processing helix  chain 'A' and resid 510 through 524
      removed outlier: 3.595A  pdb=" N   LEU A 514 " --> pdb=" O   GLY A 510 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   GLY A 515 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   TYR A 516 " --> pdb=" O   HIS A 512 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ILE A 524 " --> pdb=" O   ASP A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 541
      removed outlier: 3.675A  pdb=" N   ILE A 541 " --> pdb=" O   ASP A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 551
    Processing helix  chain 'A' and resid 552 through 556
      removed outlier: 3.560A  pdb=" N   MET A 556 " --> pdb=" O   THR A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 572
      removed outlier: 3.614A  pdb=" N   LEU A 563 " --> pdb=" O   GLU A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 625
    Processing helix  chain 'A' and resid 629 through 635
    Processing helix  chain 'A' and resid 639 through 656
      removed outlier: 4.584A  pdb=" N   ILE A 643 " --> pdb=" O   LEU A 639 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   VAL A 652 " --> pdb=" O   GLU A 648 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   GLU A 653 " --> pdb=" O   THR A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 676
    Processing helix  chain 'A' and resid 677 through 685
      removed outlier: 4.102A  pdb=" N   LEU A 681 " --> pdb=" O   ALA A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 738
      removed outlier: 3.971A  pdb=" N   LEU A 734 " --> pdb=" O   PRO A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 747 through 766
      removed outlier: 3.542A  pdb=" N   CYS A 753 " --> pdb=" O   LYS A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 782
    Processing helix  chain 'A' and resid 808 through 818
      removed outlier: 3.536A  pdb=" N   VAL A 812 " --> pdb=" O   ASP A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 847
    Processing helix  chain 'A' and resid 853 through 875
      removed outlier: 5.833A  pdb=" N   LEU A 864 " --> pdb=" O   ALA A 860 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   THR A 865 " --> pdb=" O   GLN A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 882 through 886
    Processing helix  chain 'B' and resid 180 through 185
    Processing helix  chain 'B' and resid 203 through 215
      removed outlier: 3.920A  pdb=" N   ALA B 207 " --> pdb=" O   LYS B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 236
    Processing helix  chain 'B' and resid 263 through 272
    Processing helix  chain 'B' and resid 291 through 307
    Processing helix  chain 'B' and resid 349 through 354
      removed outlier: 3.816A  pdb=" N   THR B 353 " --> pdb=" O   ASN B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 379
    Processing helix  chain 'B' and resid 390 through 400
      removed outlier: 4.846A  pdb=" N   GLN B 396 " --> pdb=" O   ASP B 392 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   LYS B 397 " --> pdb=" O   THR B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 414
    Processing helix  chain 'B' and resid 451 through 461
    Processing helix  chain 'B' and resid 482 through 486
      removed outlier: 4.080A  pdb=" N   ASP B 485 " --> pdb=" O   ASN B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 499
    Processing helix  chain 'B' and resid 527 through 540
    Processing helix  chain 'B' and resid 544 through 554
      removed outlier: 3.762A  pdb=" N   GLU B 554 " --> pdb=" O   LYS B 550 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 603
      removed outlier: 3.698A  pdb=" N   SER B 603 " --> pdb=" O   ARG B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 604 through 616
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36
    Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 127
      removed outlier: 8.754A  pdb=" N   LYS A 125 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   VAL A 100 " --> pdb=" O   LYS A 125 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   MET A 127 " --> pdb=" O   VAL A 100 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   GLY A 102 " --> pdb=" O   MET A 127 " (cutoff:3.500A)
      removed outlier: 5.672A  pdb=" N   GLY A  75 " --> pdb=" O   VAL A  97 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLU A  99 " --> pdb=" O   GLY A  75 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 309
      removed outlier: 5.594A  pdb=" N   TYR A 304 " --> pdb=" O   SER A 593 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   SER A 593 " --> pdb=" O   TYR A 304 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   GLY A 306 " --> pdb=" O   ILE A 591 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TYR A 451 " --> pdb=" O   VAL A 576 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LYS A 578 " --> pdb=" O   TYR A 451 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 658 through 661
    Processing sheet with id=AA5, first strand: chain 'A' and resid 712 through 717
    Processing sheet with id=AA6, first strand: chain 'B' and resid 188 through 192
      removed outlier: 6.337A  pdb=" N   LEU B 220 " --> pdb=" O   ILE B 283 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   ASP B 285 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   LEU B 222 " --> pdb=" O   ASP B 285 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   THR B 219 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
      removed outlier: 8.211A  pdb=" N   MET B 261 " --> pdb=" O   THR B 219 " (cutoff:3.500A)
      removed outlier: 5.958A  pdb=" N   ILE B 221 " --> pdb=" O   MET B 261 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   ARG B 242 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 8.216A  pdb=" N   CYS B 262 " --> pdb=" O   ARG B 242 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 334 through 337
      removed outlier: 6.721A  pdb=" N   GLN B 334 " --> pdb=" O   TYR B 473 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   PHE B 475 " --> pdb=" O   GLN B 334 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   GLU B 336 " --> pdb=" O   PHE B 475 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   VAL B 423 " --> pdb=" O   ILE B 474 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 432 through 435

    442 hydrogen bonds defined for protein.
    1254 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      55 hydrogen bonds
      106 hydrogen bond angles
      0 basepair planarities
      22 basepair parallelities
      34 stacking parallelities
  Total time for adding SS restraints: 2.12

  Time building geometry restraints manager: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 2984
        1.33 -     1.45: 2607
        1.45 -     1.57: 4978
        1.57 -     1.70: 133
        1.70 -     1.82: 64
  Bond restraints: 10766
  Sorted by residual:
  bond pdb=" CB  TRP A 817 "
       pdb=" CG  TRP A 817 "
    ideal  model  delta    sigma   weight residual
    1.498  1.414  0.084 3.10e-02 1.04e+03 7.28e+00
  bond pdb=" CB  TRP A 762 "
       pdb=" CG  TRP A 762 "
    ideal  model  delta    sigma   weight residual
    1.498  1.421  0.077 3.10e-02 1.04e+03 6.17e+00
  bond pdb=" C   VAL A 836 "
       pdb=" N   PRO A 837 "
    ideal  model  delta    sigma   weight residual
    1.334  1.278  0.056 2.34e-02 1.83e+03 5.72e+00
  bond pdb=" CB  ASN A 609 "
       pdb=" CG  ASN A 609 "
    ideal  model  delta    sigma   weight residual
    1.516  1.462  0.054 2.50e-02 1.60e+03 4.74e+00
  bond pdb=" CB  TRP A 703 "
       pdb=" CG  TRP A 703 "
    ideal  model  delta    sigma   weight residual
    1.498  1.434  0.064 3.10e-02 1.04e+03 4.25e+00
  ... (remaining 10761 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 14073
        1.56 -     3.11: 821
        3.11 -     4.67: 112
        4.67 -     6.22: 22
        6.22 -     7.78: 10
  Bond angle restraints: 15038
  Sorted by residual:
  angle pdb=" C   ARG A 737 "
        pdb=" N   ALA A 738 "
        pdb=" CA  ALA A 738 "
      ideal   model   delta    sigma   weight residual
     122.65  117.57    5.08 1.60e+00 3.91e-01 1.01e+01
  angle pdb=" C3'   A S  19 "
        pdb=" O3'   A S  19 "
        pdb=" P     C S  20 "
      ideal   model   delta    sigma   weight residual
     120.20  124.86   -4.66 1.50e+00 4.44e-01 9.67e+00
  angle pdb=" C3'   U S  61 "
        pdb=" O3'   U S  61 "
        pdb=" P     U S  62 "
      ideal   model   delta    sigma   weight residual
     120.20  124.55   -4.35 1.50e+00 4.44e-01 8.41e+00
  angle pdb=" C   HIS A  52 "
        pdb=" N   HIS A  53 "
        pdb=" CA  HIS A  53 "
      ideal   model   delta    sigma   weight residual
     122.33  117.47    4.86 1.68e+00 3.54e-01 8.38e+00
  angle pdb=" C4'   A S  19 "
        pdb=" C3'   A S  19 "
        pdb=" O3'   A S  19 "
      ideal   model   delta    sigma   weight residual
     113.00  109.00    4.00 1.50e+00 4.44e-01 7.12e+00
  ... (remaining 15033 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.99: 6068
       33.99 -    67.97: 266
       67.97 -   101.96: 27
      101.96 -   135.94: 2
      135.94 -   169.93: 1
  Dihedral angle restraints: 6364
    sinusoidal: 2732
      harmonic: 3632
  Sorted by residual:
  dihedral pdb=" O2B GDP S 201 "
           pdb=" O3A GDP S 201 "
           pdb=" PB  GDP S 201 "
           pdb=" PA  GDP S 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00   47.70  132.30     1      2.00e+01 2.50e-03 4.02e+01
  dihedral pdb=" CA  PRO B 544 "
           pdb=" C   PRO B 544 "
           pdb=" N   VAL B 545 "
           pdb=" CA  VAL B 545 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.89  -23.11     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" O5' GDP S 201 "
           pdb=" O3A GDP S 201 "
           pdb=" PA  GDP S 201 "
           pdb=" PB  GDP S 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -179.98 -101.15  -78.83     1      2.00e+01 2.50e-03 1.93e+01
  ... (remaining 6361 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1144
       0.043 -    0.087: 439
       0.087 -    0.130: 131
       0.130 -    0.173: 18
       0.173 -    0.216: 3
  Chirality restraints: 1735
  Sorted by residual:
  chirality pdb=" P     A S   1 "
            pdb=" OP1   A S   1 "
            pdb=" OP2   A S   1 "
            pdb=" O5'   A S   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.63   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" C3'   U S  61 "
            pdb=" C4'   U S  61 "
            pdb=" O3'   U S  61 "
            pdb=" C2'   U S  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.53   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" P     C S  67 "
            pdb=" OP1   C S  67 "
            pdb=" OP2   C S  67 "
            pdb=" O5'   C S  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.62   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 1732 not shown)

  Planarity restraints: 1707
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 726 "    0.033 5.00e-02 4.00e+02   5.05e-02 4.09e+00
        pdb=" N   PRO A 727 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 727 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 727 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 502 "    0.009 2.00e-02 2.50e+03   1.84e-02 3.38e+00
        pdb=" C   SER A 502 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   SER A 502 "    0.012 2.00e-02 2.50e+03
        pdb=" N   TYR A 503 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 363 "   -0.027 5.00e-02 4.00e+02   4.17e-02 2.78e+00
        pdb=" N   PRO B 364 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 364 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 364 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1704 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.46: 24
        2.46 -     3.07: 7792
        3.07 -     3.68: 16848
        3.68 -     4.29: 22885
        4.29 -     4.90: 35965
  Nonbonded interactions: 83514
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 437 "
            pdb="ZN    ZN A1002 "
     model   vdw
     1.852 2.230
  nonbonded pdb=" O   GLN A 602 "
            pdb=" OG1 THR A 605 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" N3    G S  18 "
            pdb=" O2'   A S  45 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" N2    G S  18 "
            pdb=" N3    A S  45 "
     model   vdw
     2.328 3.200
  nonbonded pdb=" NH1 ARG A 386 "
            pdb=" O   ASN A 501 "
     model   vdw
     2.352 3.120
  ... (remaining 83509 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.900
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.330
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
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   0.084  10774  Z= 0.538
  Angle     :  0.836   7.779  15040  Z= 0.459
  Chirality :  0.049   0.216   1735
  Planarity :  0.005   0.051   1707
  Dihedral  : 17.512 169.926   4016
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  4.63 %
    Favored  : 95.10 %
  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: -1.11 (0.23), residues: 1242
  helix:  0.59 (0.22), residues: 557
  sheet: -1.39 (0.42), residues: 148
  loop : -1.98 (0.26), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 262 
 TYR   0.012   0.002   TYR A 308 
 PHE   0.016   0.003   PHE A  25 
 TRP   0.019   0.002   TRP A 703 
 HIS   0.007   0.002   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.01120 (10766)
  covalent geometry    : angle       0.83566 (15038)
  hydrogen bonds       : bond        0.12195 (  497)
  hydrogen bonds       : angle       6.51129 ( 1360)
  metal coordination   : bond        0.04507 (    7)
  metal coordination   : angle       2.30811 (    2)
  Misc. bond           : bond        0.00231 (    1)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 129
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 ASP cc_start: 0.8854 (t0) cc_final: 0.8580 (t0)
REVERT: A  246 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7402 (t80)
REVERT: A  824 MET cc_start: 0.8735 (tpt) cc_final: 0.8507 (tpt)
REVERT: B  217 LEU cc_start: 0.9056 (mt) cc_final: 0.8570 (tt)
REVERT: B  279 TYR cc_start: 0.8647 (m-80) cc_final: 0.8059 (m-10)
REVERT: B  284 MET cc_start: 0.8338 (ttt) cc_final: 0.7939 (tmm)
REVERT: B  379 ASN cc_start: 0.8761 (m-40) cc_final: 0.8429 (m110)
REVERT: B  418 PHE cc_start: 0.8834 (m-10) cc_final: 0.8559 (m-10)
REVERT: B  510 PHE cc_start: 0.9177 (t80) cc_final: 0.8968 (t80)
REVERT: B  563 TRP cc_start: 0.8498 (p-90) cc_final: 0.7600 (p-90)
  outliers start: 2
  outliers final: 1
  residues processed: 131
  average time/residue: 0.0941
  time to fit residues: 18.1766
Evaluate side-chains
  99 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  771 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0570
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    2.5504

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.068920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.048834 restraints weight = 49015.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.050312 restraints weight = 25468.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.051305 restraints weight = 16520.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.051950 restraints weight = 12310.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.052334 restraints weight = 10120.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10774  Z= 0.149
  Angle     :  0.548   5.901  15040  Z= 0.282
  Chirality :  0.040   0.190   1735
  Planarity :  0.004   0.045   1707
  Dihedral  : 18.001 166.553   2372
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  9.95 %
    Favored  : 88.69 %
  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:  0.28 (0.25), residues: 1242
  helix:  1.99 (0.23), residues: 551
  sheet: -1.01 (0.42), residues: 145
  loop : -1.42 (0.27), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 210 
 TYR   0.010   0.001   TYR B 395 
 PHE   0.014   0.001   PHE B 614 
 TRP   0.012   0.001   TRP A 859 
 HIS   0.004   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (10766)
  covalent geometry    : angle       0.54815 (15038)
  hydrogen bonds       : bond        0.03997 (  497)
  hydrogen bonds       : angle       4.65484 ( 1360)
  metal coordination   : bond        0.01559 (    7)
  metal coordination   : angle       1.64597 (    2)
  Misc. bond           : bond        0.00068 (    1)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 ASP cc_start: 0.8861 (t0) cc_final: 0.8615 (t0)
REVERT: A  127 MET cc_start: 0.8390 (mtp) cc_final: 0.8105 (mtp)
REVERT: A  252 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7577 (mp0)
REVERT: A  356 GLU cc_start: 0.8390 (pp20) cc_final: 0.8107 (pp20)
REVERT: A  533 ASP cc_start: 0.8115 (p0) cc_final: 0.7885 (p0)
REVERT: A  589 MET cc_start: 0.9246 (tpp) cc_final: 0.8686 (tpt)
REVERT: B  279 TYR cc_start: 0.8707 (m-80) cc_final: 0.7746 (m-80)
REVERT: B  379 ASN cc_start: 0.8678 (m-40) cc_final: 0.8247 (m110)
REVERT: B  418 PHE cc_start: 0.8802 (m-10) cc_final: 0.8547 (m-10)
REVERT: B  563 TRP cc_start: 0.8614 (p-90) cc_final: 0.7789 (p-90)
  outliers start: 10
  outliers final: 8
  residues processed: 111
  average time/residue: 0.0735
  time to fit residues: 13.0011
Evaluate side-chains
  106 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  496 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 95 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 63 optimal weight:   10.0000
   chunk 91 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 562 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.068346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.048149 restraints weight = 49618.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.049613 restraints weight = 25969.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.050582 restraints weight = 16953.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.051218 restraints weight = 12691.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.051613 restraints weight = 10469.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10774  Z= 0.174
  Angle     :  0.553   8.556  15040  Z= 0.280
  Chirality :  0.040   0.294   1735
  Planarity :  0.004   0.060   1707
  Dihedral  : 17.750 167.792   2372
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.08 %
    Favored  : 85.15 %
  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:  0.45 (0.25), residues: 1242
  helix:  2.18 (0.23), residues: 551
  sheet: -1.08 (0.43), residues: 142
  loop : -1.34 (0.27), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 210 
 TYR   0.009   0.001   TYR A 482 
 PHE   0.023   0.002   PHE B 510 
 TRP   0.009   0.001   TRP A 694 
 HIS   0.004   0.001   HIS A 711 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (10766)
  covalent geometry    : angle       0.55236 (15038)
  hydrogen bonds       : bond        0.03953 (  497)
  hydrogen bonds       : angle       4.53241 ( 1360)
  metal coordination   : bond        0.01947 (    7)
  metal coordination   : angle       1.68235 (    2)
  Misc. bond           : bond        0.00046 (    1)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A   79 ASP cc_start: 0.8806 (t0) cc_final: 0.8601 (t0)
REVERT: A  252 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7976 (mm-30)
REVERT: A  356 GLU cc_start: 0.8388 (pp20) cc_final: 0.8088 (pp20)
REVERT: A  589 MET cc_start: 0.9262 (tpp) cc_final: 0.8670 (tpt)
REVERT: A  765 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8643 (mmm)
REVERT: B  284 MET cc_start: 0.8019 (tmm) cc_final: 0.7749 (tmm)
REVERT: B  379 ASN cc_start: 0.8620 (m-40) cc_final: 0.8209 (m110)
REVERT: B  418 PHE cc_start: 0.8795 (m-10) cc_final: 0.8522 (m-10)
REVERT: B  563 TRP cc_start: 0.8634 (p-90) cc_final: 0.7822 (p-90)
  outliers start: 13
  outliers final: 9
  residues processed: 105
  average time/residue: 0.0734
  time to fit residues: 12.2515
Evaluate side-chains
  103 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  496 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 84 optimal weight:    0.0170
   chunk 85 optimal weight:    7.9990
   chunk 100 optimal weight:   30.0000
   chunk 82 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 128 optimal weight:    9.9990
   chunk 87 optimal weight:   50.0000
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 121 optimal weight:    0.0000
   overall best weight:    1.9826

-------------------------------------------------------------------------------
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 = 0.3398 r_free = 0.3398 target = 0.069220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.049180 restraints weight = 49177.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.050664 restraints weight = 25698.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.051655 restraints weight = 16711.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.052273 restraints weight = 12460.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.052697 restraints weight = 10299.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10774  Z= 0.118
  Angle     :  0.516   7.658  15040  Z= 0.257
  Chirality :  0.039   0.282   1735
  Planarity :  0.004   0.066   1707
  Dihedral  : 17.467 167.468   2372
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.58 %
    Favored  : 83.65 %
  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:  0.76 (0.25), residues: 1242
  helix:  2.33 (0.23), residues: 554
  sheet: -0.60 (0.44), residues: 132
  loop : -1.17 (0.27), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 210 
 TYR   0.008   0.001   TYR B 279 
 PHE   0.019   0.001   PHE B 510 
 TRP   0.007   0.001   TRP A 694 
 HIS   0.004   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (10766)
  covalent geometry    : angle       0.51564 (15038)
  hydrogen bonds       : bond        0.03419 (  497)
  hydrogen bonds       : angle       4.20372 ( 1360)
  metal coordination   : bond        0.01155 (    7)
  metal coordination   : angle       1.34050 (    2)
  Misc. bond           : bond        0.00047 (    1)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A   79 ASP cc_start: 0.8787 (t0) cc_final: 0.8561 (t0)
REVERT: A  252 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7958 (mp0)
REVERT: A  356 GLU cc_start: 0.8358 (pp20) cc_final: 0.8068 (pp20)
REVERT: A  589 MET cc_start: 0.9261 (tpp) cc_final: 0.8639 (tpt)
REVERT: A  761 MET cc_start: 0.9264 (ttp) cc_final: 0.8903 (ttt)
REVERT: A  765 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8409 (mpp)
REVERT: A  809 MET cc_start: 0.9153 (mmp) cc_final: 0.8940 (mmp)
REVERT: B  284 MET cc_start: 0.8029 (tmm) cc_final: 0.7163 (tmm)
REVERT: B  318 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8705 (p)
REVERT: B  379 ASN cc_start: 0.8555 (m-40) cc_final: 0.8177 (m-40)
REVERT: B  418 PHE cc_start: 0.8847 (m-10) cc_final: 0.8548 (m-10)
REVERT: B  563 TRP cc_start: 0.8632 (p-90) cc_final: 0.7856 (p-90)
  outliers start: 13
  outliers final: 9
  residues processed: 108
  average time/residue: 0.0681
  time to fit residues: 12.0802
Evaluate side-chains
  108 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  883 MET
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  318 THR
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  496 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 76 optimal weight:    0.8980
   chunk 90 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 2 optimal weight:   20.0000
   chunk 39 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 118 optimal weight:    5.9990
   chunk 94 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   chunk 98 optimal weight:    0.0040
   overall best weight:    1.8796

-------------------------------------------------------------------------------
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 = 0.3407 r_free = 0.3407 target = 0.069564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.049444 restraints weight = 49328.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.050929 restraints weight = 25871.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.051925 restraints weight = 16883.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.052551 restraints weight = 12599.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.052912 restraints weight = 10414.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10774  Z= 0.114
  Angle     :  0.499   6.799  15040  Z= 0.250
  Chirality :  0.039   0.257   1735
  Planarity :  0.004   0.067   1707
  Dihedral  : 17.110 167.461   2370
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.99 %
    Favored  : 83.11 %
  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:  0.82 (0.25), residues: 1242
  helix:  2.35 (0.23), residues: 561
  sheet: -0.57 (0.44), residues: 132
  loop : -1.14 (0.27), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 210 
 TYR   0.009   0.001   TYR A  89 
 PHE   0.015   0.001   PHE B 510 
 TRP   0.006   0.001   TRP A 694 
 HIS   0.004   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (10766)
  covalent geometry    : angle       0.49873 (15038)
  hydrogen bonds       : bond        0.03291 (  497)
  hydrogen bonds       : angle       4.07743 ( 1360)
  metal coordination   : bond        0.01183 (    7)
  metal coordination   : angle       1.38406 (    2)
  Misc. bond           : bond        0.00019 (    1)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 ASP cc_start: 0.8747 (t0) cc_final: 0.8542 (t0)
REVERT: A  250 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8507 (t)
REVERT: A  252 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7800 (mp0)
REVERT: A  356 GLU cc_start: 0.8379 (pp20) cc_final: 0.8111 (pp20)
REVERT: A  589 MET cc_start: 0.9258 (tpp) cc_final: 0.8611 (tpt)
REVERT: A  765 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8413 (mpp)
REVERT: B  284 MET cc_start: 0.8005 (tmm) cc_final: 0.7312 (tmm)
REVERT: B  318 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8733 (p)
REVERT: B  379 ASN cc_start: 0.8497 (m-40) cc_final: 0.8133 (m110)
REVERT: B  418 PHE cc_start: 0.8870 (m-10) cc_final: 0.8561 (m-10)
REVERT: B  563 TRP cc_start: 0.8642 (p-90) cc_final: 0.7859 (p-90)
  outliers start: 14
  outliers final: 8
  residues processed: 105
  average time/residue: 0.0628
  time to fit residues: 10.8390
Evaluate side-chains
  105 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  318 THR
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  496 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 20 optimal weight:    0.1980
   chunk 31 optimal weight:    6.9990
   chunk 73 optimal weight:    9.9990
   chunk 119 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 128 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    3.2388

-------------------------------------------------------------------------------
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 = 0.3385 r_free = 0.3385 target = 0.068390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.048220 restraints weight = 48846.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.049690 restraints weight = 25537.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.050676 restraints weight = 16656.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.051317 restraints weight = 12465.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.051725 restraints weight = 10245.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.2915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10774  Z= 0.162
  Angle     :  0.523   6.024  15040  Z= 0.264
  Chirality :  0.039   0.185   1735
  Planarity :  0.004   0.064   1707
  Dihedral  : 17.030 166.947   2370
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 14.58 %
    Favored  : 82.56 %
  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:  0.79 (0.25), residues: 1242
  helix:  2.35 (0.23), residues: 559
  sheet: -0.57 (0.44), residues: 132
  loop : -1.18 (0.27), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 871 
 TYR   0.010   0.001   TYR A 482 
 PHE   0.016   0.001   PHE B 510 
 TRP   0.006   0.001   TRP A 694 
 HIS   0.004   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (10766)
  covalent geometry    : angle       0.52225 (15038)
  hydrogen bonds       : bond        0.03610 (  497)
  hydrogen bonds       : angle       4.22714 ( 1360)
  metal coordination   : bond        0.01914 (    7)
  metal coordination   : angle       2.11335 (    2)
  Misc. bond           : bond        0.00053 (    1)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A   79 ASP cc_start: 0.8765 (t0) cc_final: 0.8422 (t0)
REVERT: A  250 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8754 (t)
REVERT: A  252 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8198 (mm-30)
REVERT: A  356 GLU cc_start: 0.8435 (pp20) cc_final: 0.8105 (pp20)
REVERT: A  589 MET cc_start: 0.9265 (tpp) cc_final: 0.8622 (tpt)
REVERT: A  765 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8361 (mpp)
REVERT: B  284 MET cc_start: 0.7930 (tmm) cc_final: 0.7568 (tmm)
REVERT: B  379 ASN cc_start: 0.8460 (m-40) cc_final: 0.8085 (m110)
REVERT: B  418 PHE cc_start: 0.8846 (m-10) cc_final: 0.8520 (m-10)
REVERT: B  563 TRP cc_start: 0.8644 (p-90) cc_final: 0.7853 (p-90)
  outliers start: 21
  outliers final: 11
  residues processed: 110
  average time/residue: 0.0680
  time to fit residues: 12.4049
Evaluate side-chains
  108 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  496 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 130 optimal weight:   20.0000
   chunk 30 optimal weight:    8.9990
   chunk 109 optimal weight:   20.0000
   chunk 42 optimal weight:    8.9990
   chunk 100 optimal weight:   30.0000
   chunk 43 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 101 optimal weight:    7.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.3366 r_free = 0.3366 target = 0.067706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.047705 restraints weight = 49313.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.049094 restraints weight = 26259.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.050021 restraints weight = 17400.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.050594 restraints weight = 13141.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.050993 restraints weight = 10958.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10774  Z= 0.210
  Angle     :  0.566   5.473  15040  Z= 0.288
  Chirality :  0.040   0.186   1735
  Planarity :  0.004   0.068   1707
  Dihedral  : 17.118 166.515   2370
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.12 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.49 (0.25), residues: 1242
  helix:  2.04 (0.22), residues: 572
  sheet: -0.68 (0.43), residues: 130
  loop : -1.36 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 871 
 TYR   0.012   0.001   TYR A 482 
 PHE   0.017   0.002   PHE B 510 
 TRP   0.007   0.001   TRP A 795 
 HIS   0.004   0.001   HIS A 801 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (10766)
  covalent geometry    : angle       0.56478 (15038)
  hydrogen bonds       : bond        0.04073 (  497)
  hydrogen bonds       : angle       4.42820 ( 1360)
  metal coordination   : bond        0.02331 (    7)
  metal coordination   : angle       2.77590 (    2)
  Misc. bond           : bond        0.00031 (    1)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A   79 ASP cc_start: 0.8633 (t0) cc_final: 0.8422 (t0)
REVERT: A  251 ILE cc_start: 0.9453 (mt) cc_final: 0.9142 (mm)
REVERT: A  252 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8001 (mp0)
REVERT: A  356 GLU cc_start: 0.8449 (pp20) cc_final: 0.8147 (pp20)
REVERT: A  529 MET cc_start: 0.8918 (mtp) cc_final: 0.8486 (mtt)
REVERT: A  589 MET cc_start: 0.9210 (tpp) cc_final: 0.8576 (tpt)
REVERT: A  765 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8358 (mpp)
REVERT: B  284 MET cc_start: 0.7962 (tmm) cc_final: 0.7612 (tmm)
REVERT: B  379 ASN cc_start: 0.8455 (m-40) cc_final: 0.8095 (m110)
REVERT: B  418 PHE cc_start: 0.8895 (m-10) cc_final: 0.8548 (m-10)
REVERT: B  489 TRP cc_start: 0.9155 (m100) cc_final: 0.8827 (m100)
REVERT: B  563 TRP cc_start: 0.8644 (p-90) cc_final: 0.7834 (p-90)
  outliers start: 22
  outliers final: 18
  residues processed: 114
  average time/residue: 0.0699
  time to fit residues: 13.1147
Evaluate side-chains
  114 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  637 HIS
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  883 MET
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  496 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 76 optimal weight:    8.9990
   chunk 90 optimal weight:    5.9990
   chunk 78 optimal weight:    4.9990
   chunk 2 optimal weight:   20.0000
   chunk 106 optimal weight:   20.0000
   chunk 32 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 111 optimal weight:    0.6980
   chunk 79 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    3.5388

-------------------------------------------------------------------------------
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 = 0.3374 r_free = 0.3374 target = 0.067981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.047856 restraints weight = 49823.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.049279 restraints weight = 26446.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.050221 restraints weight = 17427.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.050814 restraints weight = 13141.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.051206 restraints weight = 10936.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10774  Z= 0.174
  Angle     :  0.544   6.677  15040  Z= 0.275
  Chirality :  0.040   0.261   1735
  Planarity :  0.004   0.069   1707
  Dihedral  : 17.087 166.667   2370
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.80 %
    Favored  : 81.61 %
  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:  0.57 (0.25), residues: 1242
  helix:  2.08 (0.22), residues: 566
  sheet: -0.65 (0.44), residues: 132
  loop : -1.24 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 871 
 TYR   0.010   0.001   TYR A 482 
 PHE   0.017   0.001   PHE B 184 
 TRP   0.007   0.001   TRP A 694 
 HIS   0.004   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (10766)
  covalent geometry    : angle       0.54349 (15038)
  hydrogen bonds       : bond        0.03815 (  497)
  hydrogen bonds       : angle       4.39862 ( 1360)
  metal coordination   : bond        0.01958 (    7)
  metal coordination   : angle       2.47070 (    2)
  Misc. bond           : bond        0.00030 (    1)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 ASP cc_start: 0.8588 (t0) cc_final: 0.8290 (t0)
REVERT: A  251 ILE cc_start: 0.9456 (mt) cc_final: 0.9145 (mm)
REVERT: A  252 GLU cc_start: 0.8568 (mm-30) cc_final: 0.7929 (mp0)
REVERT: A  356 GLU cc_start: 0.8443 (pp20) cc_final: 0.8137 (pp20)
REVERT: A  529 MET cc_start: 0.8956 (mtp) cc_final: 0.8572 (mtt)
REVERT: A  589 MET cc_start: 0.9232 (tpp) cc_final: 0.8590 (tpt)
REVERT: A  761 MET cc_start: 0.9340 (ttp) cc_final: 0.9115 (ttp)
REVERT: A  765 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8325 (mpp)
REVERT: B  284 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7550 (tmm)
REVERT: B  379 ASN cc_start: 0.8439 (m-40) cc_final: 0.8101 (m110)
REVERT: B  418 PHE cc_start: 0.8873 (m-10) cc_final: 0.8549 (m-10)
REVERT: B  563 TRP cc_start: 0.8637 (p-90) cc_final: 0.7844 (p-90)
  outliers start: 19
  outliers final: 16
  residues processed: 110
  average time/residue: 0.0674
  time to fit residues: 12.2682
Evaluate side-chains
  114 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  874 ILE
Chi-restraints excluded: chain A residue  883 MET
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  284 MET
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  496 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 51 optimal weight:    0.0980
   chunk 42 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 68 optimal weight:    0.1980
   chunk 19 optimal weight:    9.9990
   chunk 89 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    8.9990
   chunk 118 optimal weight:    5.9990
   overall best weight:    2.8586

-------------------------------------------------------------------------------
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 = 0.3378 r_free = 0.3378 target = 0.068090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.048041 restraints weight = 48682.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.049492 restraints weight = 25465.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.050464 restraints weight = 16668.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.051103 restraints weight = 12450.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.051483 restraints weight = 10235.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10774  Z= 0.148
  Angle     :  0.529   6.654  15040  Z= 0.266
  Chirality :  0.039   0.181   1735
  Planarity :  0.004   0.068   1707
  Dihedral  : 16.989 166.916   2370
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.67 %
    Favored  : 81.61 %
  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:  0.71 (0.25), residues: 1242
  helix:  2.17 (0.22), residues: 566
  sheet: -0.54 (0.44), residues: 132
  loop : -1.15 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 871 
 TYR   0.008   0.001   TYR A 482 
 PHE   0.015   0.001   PHE B 184 
 TRP   0.007   0.001   TRP A 813 
 HIS   0.004   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (10766)
  covalent geometry    : angle       0.52831 (15038)
  hydrogen bonds       : bond        0.03563 (  497)
  hydrogen bonds       : angle       4.26951 ( 1360)
  metal coordination   : bond        0.01665 (    7)
  metal coordination   : angle       2.17634 (    2)
  Misc. bond           : bond        0.00026 (    1)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 ASP cc_start: 0.8546 (t0) cc_final: 0.8235 (t0)
REVERT: A  252 GLU cc_start: 0.8561 (mm-30) cc_final: 0.7938 (mp0)
REVERT: A  356 GLU cc_start: 0.8430 (pp20) cc_final: 0.8112 (pp20)
REVERT: A  529 MET cc_start: 0.8930 (mtp) cc_final: 0.8565 (mtt)
REVERT: A  589 MET cc_start: 0.9275 (tpp) cc_final: 0.8643 (tpt)
REVERT: A  765 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8333 (mpp)
REVERT: B  284 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7639 (tmm)
REVERT: B  379 ASN cc_start: 0.8428 (m-40) cc_final: 0.8072 (m110)
REVERT: B  418 PHE cc_start: 0.8869 (m-10) cc_final: 0.8530 (m-10)
REVERT: B  524 TYR cc_start: 0.8894 (m-80) cc_final: 0.8621 (m-80)
REVERT: B  563 TRP cc_start: 0.8623 (p-90) cc_final: 0.7833 (p-90)
  outliers start: 20
  outliers final: 16
  residues processed: 109
  average time/residue: 0.0726
  time to fit residues: 13.0137
Evaluate side-chains
  114 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  637 HIS
Chi-restraints excluded: chain A residue  735 ILE
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  874 ILE
Chi-restraints excluded: chain A residue  883 MET
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  284 MET
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  496 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 59 optimal weight:   10.0000
   chunk 66 optimal weight:    0.0050
   chunk 120 optimal weight:    5.9990
   chunk 111 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 106 optimal weight:   20.0000
   chunk 85 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    3.4002

-------------------------------------------------------------------------------
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 = 0.3378 r_free = 0.3378 target = 0.068207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.048192 restraints weight = 49126.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.049591 restraints weight = 26214.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.050538 restraints weight = 17345.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.051130 restraints weight = 13071.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.051527 restraints weight = 10885.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10774  Z= 0.168
  Angle     :  0.548   6.775  15040  Z= 0.277
  Chirality :  0.039   0.183   1735
  Planarity :  0.004   0.064   1707
  Dihedral  : 17.002 166.995   2370
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.80 %
    Favored  : 81.61 %
  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:  0.68 (0.25), residues: 1242
  helix:  2.10 (0.23), residues: 567
  sheet: -0.56 (0.44), residues: 132
  loop : -1.11 (0.27), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 871 
 TYR   0.012   0.001   TYR B 279 
 PHE   0.019   0.002   PHE B 184 
 TRP   0.008   0.001   TRP A 762 
 HIS   0.004   0.001   HIS A 801 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (10766)
  covalent geometry    : angle       0.54710 (15038)
  hydrogen bonds       : bond        0.03711 (  497)
  hydrogen bonds       : angle       4.32870 ( 1360)
  metal coordination   : bond        0.01904 (    7)
  metal coordination   : angle       2.58143 (    2)
  Misc. bond           : bond        0.00027 (    1)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 ASP cc_start: 0.8594 (t0) cc_final: 0.8266 (t0)
REVERT: A  252 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7961 (mp0)
REVERT: A  356 GLU cc_start: 0.8460 (pp20) cc_final: 0.8139 (pp20)
REVERT: A  529 MET cc_start: 0.9012 (mtp) cc_final: 0.8630 (mtt)
REVERT: A  589 MET cc_start: 0.9270 (tpp) cc_final: 0.8633 (tpt)
REVERT: A  765 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8373 (mpp)
REVERT: B  284 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7529 (tmm)
REVERT: B  379 ASN cc_start: 0.8424 (m-40) cc_final: 0.8061 (m110)
REVERT: B  418 PHE cc_start: 0.8861 (m-10) cc_final: 0.8530 (m-10)
REVERT: B  524 TYR cc_start: 0.8953 (m-80) cc_final: 0.8693 (m-80)
REVERT: B  563 TRP cc_start: 0.8629 (p-90) cc_final: 0.7844 (p-90)
  outliers start: 19
  outliers final: 16
  residues processed: 109
  average time/residue: 0.0756
  time to fit residues: 13.1576
Evaluate side-chains
  113 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  637 HIS
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  874 ILE
Chi-restraints excluded: chain A residue  883 MET
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  284 MET
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  496 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 129 optimal weight:   20.0000
   chunk 99 optimal weight:    4.9990
   chunk 119 optimal weight:   30.0000
   chunk 0 optimal weight:   30.0000
   chunk 97 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 8 optimal weight:    8.9990
   chunk 130 optimal weight:   20.0000
   chunk 69 optimal weight:    3.9990
   chunk 110 optimal weight:   20.0000
   overall best weight:    6.5990

-------------------------------------------------------------------------------
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 = 0.3335 r_free = 0.3335 target = 0.066377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.046327 restraints weight = 50079.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.047696 restraints weight = 26760.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.048584 restraints weight = 17816.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.049174 restraints weight = 13610.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.049531 restraints weight = 11346.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  10774  Z= 0.302
  Angle     :  0.666   7.207  15040  Z= 0.342
  Chirality :  0.043   0.195   1735
  Planarity :  0.005   0.064   1707
  Dihedral  : 17.327 166.706   2370
  Min Nonbonded Distance : 1.821

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 15.26 %
    Favored  : 81.34 %
  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:  0.18 (0.25), residues: 1242
  helix:  1.66 (0.22), residues: 572
  sheet: -0.72 (0.44), residues: 126
  loop : -1.40 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 871 
 TYR   0.019   0.002   TYR B 279 
 PHE   0.018   0.002   PHE B 614 
 TRP   0.012   0.002   TRP A 795 
 HIS   0.007   0.002   HIS A 801 

Details of bonding type rmsd
  covalent geometry    : bond        0.00639 (10766)
  covalent geometry    : angle       0.66522 (15038)
  hydrogen bonds       : bond        0.04964 (  497)
  hydrogen bonds       : angle       4.88071 ( 1360)
  metal coordination   : bond        0.02953 (    7)
  metal coordination   : angle       3.40215 (    2)
  Misc. bond           : bond        0.00036 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1664.30 seconds
wall clock time: 29 minutes 29.60 seconds (1769.60 seconds total)