Starting phenix.real_space_refine
on Tue Jul 29 00:14:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wmi_37653/07_2025/8wmi_37653.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wmi_37653/07_2025/8wmi_37653.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wmi_37653/07_2025/8wmi_37653.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wmi_37653/07_2025/8wmi_37653.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wmi_37653/07_2025/8wmi_37653.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wmi_37653/07_2025/8wmi_37653.cif"
  }
  resolution = 3.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.025
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      4      6.06       5
     P      39      5.49       5
     S      48      5.16       5
     C    6661      2.51       5
     N    1910      2.21       5
     O    2101      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10763
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "R"
      Number of atoms: 826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 826
          Classifications: {'RNA': 39}
          Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 7, 'rna3p_pur': 5, 'rna3p_pyr': 14}
          Link IDs: {'rna2p': 19, 'rna3p': 19}
    Chain: "A"
      Number of atoms: 9933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1237, 9933
          Classifications: {'peptide': 1237}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 69, 'TRANS': 1167}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' ZN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1530  SG  CYS A  86      31.106  61.179 143.315  1.00167.47           S
  ATOM   1776  SG  CYS A 115      30.437  63.002 146.580  1.00183.20           S
  ATOM   1838  SG  CYS A 123      33.359  64.123 144.339  1.00164.06           S
  ATOM   1862  SG  CYS A 126      30.196  64.876 143.087  1.00164.08           S
  ATOM   3939  SG  CYS A 463      26.495  43.368 117.825  1.00 97.81           S
  ATOM   4001  SG  CYS A 472      25.737  44.730 121.212  1.00117.18           S
  ATOM   4015  SG  CYS A 474      28.393  41.977 120.839  1.00106.05           S
  ATOM   4037  SG  CYS A 477      29.080  45.542 119.770  1.00100.36           S
  ATOM   5851  SG  CYS A 706      16.732  34.431  91.751  1.00112.69           S
  ATOM   5866  SG  CYS A 708      17.689  31.234  90.060  1.00 99.20           S
  ATOM   5888  SG  CYS A 711      20.376  33.929  90.899  1.00 90.76           S
  ATOM   7751  SG  CYS A 965      23.001  39.486  53.614  1.00 78.96           S
  ATOM   8629  SG  CYS A1312      19.545  40.974  54.239  1.00 87.57           S
  ATOM   8661  SG  CYS A1342      22.140  37.284  54.682  1.00 78.23           S

  Time building chain proxies: 6.78, per 1000 atoms: 0.63
  Number of scatterers: 10763
  At special positions: 0
  Unit cell: (80.75, 95.2, 159.8, 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      4     29.99
     S      48     16.00
     P      39     15.00
     O    2101      8.00
     N    1910      7.00
     C    6661      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=0, symmetry=0
  Time building additional restraints: 2.42
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1701 "
        pdb="ZN    ZN A1701 " - pdb=" SG  CYS A 123 "
        pdb="ZN    ZN A1701 " - pdb=" SG  CYS A 126 "
        pdb="ZN    ZN A1701 " - pdb=" SG  CYS A  86 "
        pdb="ZN    ZN A1701 " - pdb=" SG  CYS A 115 "
      pdb="  ZN A1702 "
        pdb="ZN    ZN A1702 " - pdb=" SG  CYS A 472 "
        pdb="ZN    ZN A1702 " - pdb=" SG  CYS A 463 "
        pdb="ZN    ZN A1702 " - pdb=" SG  CYS A 474 "
        pdb="ZN    ZN A1702 " - pdb=" SG  CYS A 477 "
      pdb="  ZN A1703 "
        pdb="ZN    ZN A1703 " - pdb=" ND1 HIS A 703 "
        pdb="ZN    ZN A1703 " - pdb=" SG  CYS A 706 "
        pdb="ZN    ZN A1703 " - pdb=" SG  CYS A 708 "
        pdb="ZN    ZN A1703 " - pdb=" SG  CYS A 711 "
      pdb="  ZN A1704 "
        pdb="ZN    ZN A1704 " - pdb=" SG  CYS A 965 "
        pdb="ZN    ZN A1704 " - pdb=" SG  CYS A1312 "
        pdb="ZN    ZN A1704 " - pdb=" SG  CYS A1342 "
      Number of angles added : 15


  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2290

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 17 sheets defined
      28.8% alpha, 15.7% beta
      0 base pairs and 8 stacking pairs defined.
    Time for finding SS restraints: 3.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 26
      removed outlier: 3.559A  pdb=" N   ARG A  25 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 36
    Processing helix  chain 'A' and resid 57 through 76
      removed outlier: 4.080A  pdb=" N   LEU A  61 " --> pdb=" O   THR A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 130
    Processing helix  chain 'A' and resid 163 through 168
    Processing helix  chain 'A' and resid 211 through 225
      removed outlier: 3.650A  pdb=" N   ARG A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 277
    Processing helix  chain 'A' and resid 278 through 280
      No H-bonds generated for 'chain 'A' and resid 278 through 280'
    Processing helix  chain 'A' and resid 281 through 291
    Processing helix  chain 'A' and resid 292 through 294
      No H-bonds generated for 'chain 'A' and resid 292 through 294'
    Processing helix  chain 'A' and resid 295 through 299
      removed outlier: 3.920A  pdb=" N   LEU A 298 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL A 299 " --> pdb=" O   SER A 296 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 295 through 299'
    Processing helix  chain 'A' and resid 329 through 338
    Processing helix  chain 'A' and resid 344 through 364
    Processing helix  chain 'A' and resid 443 through 460
      removed outlier: 3.628A  pdb=" N   VAL A 447 " --> pdb=" O   PRO A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 481
    Processing helix  chain 'A' and resid 542 through 555
    Processing helix  chain 'A' and resid 586 through 594
    Processing helix  chain 'A' and resid 595 through 598
      removed outlier: 3.874A  pdb=" N   ARG A 598 " --> pdb=" O   TRP A 595 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 595 through 598'
    Processing helix  chain 'A' and resid 599 through 608
    Processing helix  chain 'A' and resid 643 through 648
      removed outlier: 3.683A  pdb=" N   VAL A 648 " --> pdb=" O   ARG A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 675 through 691
      removed outlier: 3.804A  pdb=" N   ILE A 690 " --> pdb=" O   ALA A 686 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   HIS A 691 " --> pdb=" O   VAL A 687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 715
    Processing helix  chain 'A' and resid 780 through 785
    Processing helix  chain 'A' and resid 785 through 801
      removed outlier: 3.817A  pdb=" N   CYS A 789 " --> pdb=" O   ASP A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 962
      removed outlier: 4.027A  pdb=" N   LEU A 950 " --> pdb=" O   PRO A 946 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL A 957 " --> pdb=" O   MET A 953 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1232 through 1245
      removed outlier: 3.826A  pdb=" N   ILE A1236 " --> pdb=" O   GLU A1232 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LYS A1237 " --> pdb=" O   LYS A1233 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ARG A1243 " --> pdb=" O   LYS A1239 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   VAL A1244 " --> pdb=" O   GLU A1240 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   TYR A1245 " --> pdb=" O   LEU A1241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1300 through 1304
    Processing helix  chain 'A' and resid 1342 through 1349
    Processing helix  chain 'A' and resid 1395 through 1399
      removed outlier: 3.584A  pdb=" N   TRP A1398 " --> pdb=" O   ARG A1395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1420 through 1426
      removed outlier: 3.675A  pdb=" N   ASP A1426 " --> pdb=" O   LYS A1422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1464 through 1477
      removed outlier: 3.563A  pdb=" N   GLY A1469 " --> pdb=" O   GLU A1465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1488 through 1492
    Processing helix  chain 'A' and resid 1518 through 1534
      removed outlier: 3.576A  pdb=" N   TRP A1522 " --> pdb=" O   GLU A1518 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   PHE A1527 " --> pdb=" O   LEU A1523 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ALA A1528 " --> pdb=" O   GLY A1524 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LYS A1529 " --> pdb=" O   LYS A1525 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU A1530 " --> pdb=" O   GLY A1526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1538 through 1548
      removed outlier: 3.583A  pdb=" N   LYS A1545 " --> pdb=" O   ILE A1541A" (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1588 through 1593
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3
      removed outlier: 3.501A  pdb=" N   ILE A 204 " --> pdb=" O   THR A   3 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 11
    Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 55
      removed outlier: 3.965A  pdb=" N   TRP A  42 " --> pdb=" O   THR A  18 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 404
      removed outlier: 4.118A  pdb=" N   ASP A 581 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 531
      removed outlier: 7.615A  pdb=" N   CYS A 407 " --> pdb=" O   ALA A 575 " (cutoff:3.500A)
      removed outlier: 5.406A  pdb=" N   ALA A 575 " --> pdb=" O   CYS A 407 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442
      removed outlier: 3.976A  pdb=" N   ALA A 488 " --> pdb=" O   LEU A 442 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 497 through 504
      removed outlier: 3.597A  pdb=" N   ARG A 503 " --> pdb=" O   ALA A 515 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ALA A 515 " --> pdb=" O   ARG A 503 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 659 through 661
      removed outlier: 7.541A  pdb=" N   CYS A 672 " --> pdb=" O   PHE A 730 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   PHE A 730 " --> pdb=" O   CYS A 672 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 659 through 661
      removed outlier: 7.541A  pdb=" N   CYS A 672 " --> pdb=" O   PHE A 730 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   PHE A 730 " --> pdb=" O   CYS A 672 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ASN A 629 " --> pdb=" O   ILE A 822 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   ILE A 822 " --> pdb=" O   ASN A 629 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   SER A 631 " --> pdb=" O   LEU A 820 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   LEU A 820 " --> pdb=" O   SER A 631 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLU A 633 " --> pdb=" O   LYS A 818 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 655 through 656
    Processing sheet with id=AB2, first strand: chain 'A' and resid 861 through 862
    Processing sheet with id=AB3, first strand: chain 'A' and resid 865 through 868
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1357 through 1358
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1357 through 1358
      removed outlier: 3.622A  pdb=" N   PHE A1460 " --> pdb=" O   GLY A 893 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLY A 893 " --> pdb=" O   PHE A1460 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   LEU A 891 " --> pdb=" O   ASN A1462 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   THR A 892 " --> pdb=" O   LEU A1505 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   LEU A1505 " --> pdb=" O   THR A 892 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   LYS A 894 " --> pdb=" O   VAL A1503 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   VAL A1503 " --> pdb=" O   LYS A 894 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ARG A 896 " --> pdb=" O   GLU A1501 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE A 900 " --> pdb=" O   GLU A1497 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU A1497 " --> pdb=" O   ILE A 900 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 932 through 933
      removed outlier: 6.643A  pdb=" N   LYS A 932 " --> pdb=" O   THR A1444 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 976 through 978
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1227 through 1228
      removed outlier: 3.812A  pdb=" N   TYR A1228 " --> pdb=" O   ILE A1002 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE A1002 " --> pdb=" O   TYR A1228 " (cutoff:3.500A)
      removed outlier: 7.213A  pdb=" N   HIS A1001 " --> pdb=" O   THR A 996 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   THR A 996 " --> pdb=" O   HIS A1001 " (cutoff:3.500A)

    301 hydrogen bonds defined for protein.
    828 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      8 stacking parallelities
  Total time for adding SS restraints: 4.57

  Time building geometry restraints manager: 2.92 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3326
        1.34 -     1.46: 2095
        1.46 -     1.58: 5514
        1.58 -     1.70: 77
        1.70 -     1.82: 70
  Bond restraints: 11082
  Sorted by residual:
  bond pdb=" N   ARG A 147 "
       pdb=" CA  ARG A 147 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.00e-02 1.00e+04 1.10e+01
  bond pdb=" N   ILE A 148 "
       pdb=" CA  ILE A 148 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.84e+00
  bond pdb=" C   THR A1595 "
       pdb=" N   PRO A1596 "
    ideal  model  delta    sigma   weight residual
    1.330  1.362 -0.032 1.22e-02 6.72e+03 7.08e+00
  bond pdb=" N   LYS A1567 "
       pdb=" CA  LYS A1567 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.21e-02 6.83e+03 7.05e+00
  bond pdb=" C   ILE A1230 "
       pdb=" N   PRO A1231 "
    ideal  model  delta    sigma   weight residual
    1.328  1.354 -0.026 1.25e-02 6.40e+03 4.26e+00
  ... (remaining 11077 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 14773
        1.79 -     3.58: 240
        3.58 -     5.36: 93
        5.36 -     7.15: 6
        7.15 -     8.94: 3
  Bond angle restraints: 15115
  Sorted by residual:
  angle pdb=" C4'   U R   1 "
        pdb=" C3'   U R   1 "
        pdb=" O3'   U R   1 "
      ideal   model   delta    sigma   weight residual
     113.00  104.93    8.07 1.50e+00 4.44e-01 2.90e+01
  angle pdb=" CA  ILE A 148 "
        pdb=" C   ILE A 148 "
        pdb=" O   ILE A 148 "
      ideal   model   delta    sigma   weight residual
     120.78  115.43    5.35 1.25e+00 6.40e-01 1.83e+01
  angle pdb=" O3'   U R   0 "
        pdb=" C3'   U R   0 "
        pdb=" C2'   U R   0 "
      ideal   model   delta    sigma   weight residual
     113.70  107.86    5.84 1.50e+00 4.44e-01 1.52e+01
  angle pdb=" CA  LYS A1567 "
        pdb=" C   LYS A1567 "
        pdb=" O   LYS A1567 "
      ideal   model   delta    sigma   weight residual
     120.55  116.80    3.75 1.06e+00 8.90e-01 1.25e+01
  angle pdb=" O3'   G R   2 "
        pdb=" C3'   G R   2 "
        pdb=" C2'   G R   2 "
      ideal   model   delta    sigma   weight residual
     109.50  114.66   -5.16 1.50e+00 4.44e-01 1.19e+01
  ... (remaining 15110 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.80: 6430
       29.80 -    59.61: 299
       59.61 -    89.41: 42
       89.41 -   119.22: 5
      119.22 -   149.02: 1
  Dihedral angle restraints: 6777
    sinusoidal: 3227
      harmonic: 3550
  Sorted by residual:
  dihedral pdb=" O4'   U R   0 "
           pdb=" C1'   U R   0 "
           pdb=" N1    U R   0 "
           pdb=" C2    U R   0 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   50.98  149.02     1      1.50e+01 4.44e-03 7.92e+01
  dihedral pdb=" O4'   U R   0 "
           pdb=" C2'   U R   0 "
           pdb=" C1'   U R   0 "
           pdb=" C3'   U R   0 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -1.70   26.70     1      8.00e+00 1.56e-02 1.60e+01
  dihedral pdb=" C4'   U R   0 "
           pdb=" O4'   U R   0 "
           pdb=" C1'   U R   0 "
           pdb=" C2'   U R   0 "
      ideal   model   delta sinusoidal    sigma   weight residual
       3.00  -23.54   26.54     1      8.00e+00 1.56e-02 1.58e+01
  ... (remaining 6774 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1399
       0.053 -    0.106: 164
       0.106 -    0.158: 58
       0.158 -    0.211: 3
       0.211 -    0.264: 3
  Chirality restraints: 1627
  Sorted by residual:
  chirality pdb=" P     G R   2 "
            pdb=" OP1   G R   2 "
            pdb=" OP2   G R   2 "
            pdb=" O5'   G R   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.67   -0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" C2'   U R   0 "
            pdb=" C3'   U R   0 "
            pdb=" O2'   U R   0 "
            pdb=" C1'   U R   0 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.50   -0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" C2'   U R   1 "
            pdb=" C3'   U R   1 "
            pdb=" O2'   U R   1 "
            pdb=" C1'   U R   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.54   -0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 1624 not shown)

  Planarity restraints: 1821
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A1376 "   -0.073 5.00e-02 4.00e+02   1.11e-01 1.98e+01
        pdb=" N   PRO A1377 "    0.192 5.00e-02 4.00e+02
        pdb=" CA  PRO A1377 "   -0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO A1377 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A1595 "    0.009 2.00e-02 2.50e+03   1.82e-02 3.33e+00
        pdb=" C   THR A1595 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   THR A1595 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PRO A1596 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 147 "   -0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   ARG A 147 "    0.028 2.00e-02 2.50e+03
        pdb=" O   ARG A 147 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE A 148 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1818 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1594
        2.76 -     3.30: 9962
        3.30 -     3.83: 16569
        3.83 -     4.37: 19374
        4.37 -     4.90: 33200
  Nonbonded interactions: 80699
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 417 "
            pdb=" OG  SER A 560 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   ALA A1449 "
            pdb=" ND2 ASN A1452 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" O   GLN A  21 "
            pdb=" NH1 ARG A  26 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" O   GLY A 555 "
            pdb=" NH1 ARG A 569 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   GLU A1437 "
            pdb=" ND2 ASN A1442 "
     model   vdw
     2.265 3.120
  ... (remaining 80694 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:             1.970
  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:          0.490
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     32.750
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.050
  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:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
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      :  0.003   0.037  11097  Z= 0.164
  Angle     :  0.677  12.274  15130  Z= 0.346
  Chirality :  0.042   0.264   1627
  Planarity :  0.005   0.111   1821
  Dihedral  : 16.396 149.022   4487
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.24), residues: 1215
  helix:  0.85 (0.31), residues: 314
  sheet: -0.17 (0.39), residues: 158
  loop : -1.53 (0.22), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 597 
 HIS   0.006   0.001   HIS A 194 
 PHE   0.010   0.001   PHE A 187 
 TYR   0.017   0.001   TYR A 122 
 ARG   0.013   0.000   ARG A1535 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21552 (  293)
  hydrogen bonds       : angle       7.83555 (  828)
  metal coordination   : bond        0.00462 (   15)
  metal coordination   : angle       4.35847 (   15)
  covalent geometry    : bond        0.00349 (11082)
  covalent geometry    : angle       0.66334 (15115)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 1.252 
Fit side-chains
REVERT: A  187 PHE cc_start: 0.7743 (p90) cc_final: 0.7522 (p90)
REVERT: A 1563 MET cc_start: 0.5706 (pmm) cc_final: 0.5466 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.2265
  time to fit residues: 34.5001
Evaluate side-chains
  71 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.7980
   chunk 95 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 114 optimal weight:   10.0000
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.4010 r_free = 0.4010 target = 0.132997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.106022 restraints weight = 21848.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.109012 restraints weight = 12674.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.111058 restraints weight = 8943.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11097  Z= 0.107
  Angle     :  0.521   9.782  15130  Z= 0.260
  Chirality :  0.039   0.149   1627
  Planarity :  0.004   0.083   1821
  Dihedral  : 15.000 143.420   1960
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  6.29 %
    Favored  : 93.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.24), residues: 1215
  helix:  1.09 (0.32), residues: 319
  sheet: -0.14 (0.39), residues: 177
  loop : -1.41 (0.23), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1600 
 HIS   0.003   0.001   HIS A1279 
 PHE   0.014   0.001   PHE A 916 
 TYR   0.012   0.001   TYR A 440 
 ARG   0.002   0.000   ARG A 196 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03782 (  293)
  hydrogen bonds       : angle       5.51323 (  828)
  metal coordination   : bond        0.00489 (   15)
  metal coordination   : angle       3.92077 (   15)
  covalent geometry    : bond        0.00237 (11082)
  covalent geometry    : angle       0.50634 (15115)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 PHE cc_start: 0.7772 (p90) cc_final: 0.7541 (p90)
REVERT: A  355 LEU cc_start: 0.7796 (mt) cc_final: 0.7533 (tt)
REVERT: A 1569 ASP cc_start: 0.4103 (t0) cc_final: 0.3854 (t70)
  outliers start: 6
  outliers final: 4
  residues processed: 76
  average time/residue: 0.2213
  time to fit residues: 25.8265
Evaluate side-chains
  74 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue 1445 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0470
   chunk 108 optimal weight:    0.9980
   chunk 75 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 98 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   chunk 69 optimal weight:   10.0000
   overall best weight:    1.4082

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

Flipped N/Q/H residues before XYZ refinement:
A 505 ASN
A 626 HIS
A 801 ASN
A 963 ASN
A1438 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.131079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.103811 restraints weight = 22238.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.106798 restraints weight = 12887.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.108801 restraints weight = 9133.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11097  Z= 0.115
  Angle     :  0.500   8.609  15130  Z= 0.251
  Chirality :  0.039   0.150   1627
  Planarity :  0.004   0.062   1821
  Dihedral  : 15.137 137.373   1960
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  7.14 %
    Favored  : 91.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.24), residues: 1215
  helix:  1.14 (0.32), residues: 319
  sheet: -0.32 (0.38), residues: 176
  loop : -1.45 (0.22), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1600 
 HIS   0.004   0.001   HIS A 194 
 PHE   0.016   0.001   PHE A1277 
 TYR   0.010   0.001   TYR A 122 
 ARG   0.002   0.000   ARG A 890 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03639 (  293)
  hydrogen bonds       : angle       5.04260 (  828)
  metal coordination   : bond        0.00515 (   15)
  metal coordination   : angle       3.19585 (   15)
  covalent geometry    : bond        0.00263 (11082)
  covalent geometry    : angle       0.49034 (15115)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 1.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 8
  residues processed: 81
  average time/residue: 0.2292
  time to fit residues: 28.2141
Evaluate side-chains
  78 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  687 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 112 optimal weight:    7.9990
   chunk 68 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9980
   chunk 94 optimal weight:    4.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3989 r_free = 0.3989 target = 0.131400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.104247 restraints weight = 21849.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.107233 restraints weight = 12682.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.109169 restraints weight = 8991.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  11097  Z= 0.101
  Angle     :  0.489   8.434  15130  Z= 0.245
  Chirality :  0.038   0.154   1627
  Planarity :  0.004   0.049   1821
  Dihedral  : 15.072 134.565   1960
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  8.36 %
    Favored  : 90.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.24), residues: 1215
  helix:  1.16 (0.32), residues: 320
  sheet: -0.30 (0.37), residues: 183
  loop : -1.40 (0.22), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1600 
 HIS   0.003   0.001   HIS A1001 
 PHE   0.011   0.001   PHE A 776 
 TYR   0.009   0.001   TYR A 122 
 ARG   0.002   0.000   ARG A 890 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03222 (  293)
  hydrogen bonds       : angle       4.83891 (  828)
  metal coordination   : bond        0.00501 (   15)
  metal coordination   : angle       3.07828 (   15)
  covalent geometry    : bond        0.00230 (11082)
  covalent geometry    : angle       0.47983 (15115)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  634 MET cc_start: 0.8604 (mtm) cc_final: 0.8403 (mtp)
REVERT: A 1541 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8204 (tp)
  outliers start: 14
  outliers final: 12
  residues processed: 83
  average time/residue: 0.1987
  time to fit residues: 25.4275
Evaluate side-chains
  86 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  672 CYS
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1445 VAL
Chi-restraints excluded: chain A residue 1541 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 105 optimal weight:    8.9990
   chunk 73 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 125 optimal weight:    2.9990
   chunk 79 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   chunk 86 optimal weight:    5.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 741 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.129230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.102822 restraints weight = 21946.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.105700 restraints weight = 12818.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.107605 restraints weight = 9163.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11097  Z= 0.174
  Angle     :  0.567   7.928  15130  Z= 0.286
  Chirality :  0.040   0.170   1627
  Planarity :  0.004   0.039   1821
  Dihedral  : 15.431 133.353   1960
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  9.48 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.24), residues: 1215
  helix:  0.99 (0.32), residues: 319
  sheet: -0.21 (0.39), residues: 166
  loop : -1.56 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1600 
 HIS   0.005   0.001   HIS A1279 
 PHE   0.022   0.002   PHE A 915 
 TYR   0.011   0.001   TYR A1576 
 ARG   0.004   0.000   ARG A 890 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04123 (  293)
  hydrogen bonds       : angle       5.11404 (  828)
  metal coordination   : bond        0.00539 (   15)
  metal coordination   : angle       3.43277 (   15)
  covalent geometry    : bond        0.00403 (11082)
  covalent geometry    : angle       0.55724 (15115)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 1.577 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 PHE cc_start: 0.7584 (m-80) cc_final: 0.7384 (m-80)
REVERT: A  232 LEU cc_start: 0.7368 (mt) cc_final: 0.6974 (mp)
REVERT: A 1305 MET cc_start: 0.6377 (ptt) cc_final: 0.6139 (ptt)
REVERT: A 1541 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8163 (tp)
  outliers start: 15
  outliers final: 11
  residues processed: 83
  average time/residue: 0.2254
  time to fit residues: 29.8113
Evaluate side-chains
  81 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 1.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  672 CYS
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  914 ASP
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1541 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 107 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 84 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 10 optimal weight:    0.0980
   chunk 58 optimal weight:    0.8980
   chunk 123 optimal weight:    7.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.131956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.105955 restraints weight = 22011.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.108833 restraints weight = 12932.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.110743 restraints weight = 9266.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11097  Z= 0.104
  Angle     :  0.503   8.065  15130  Z= 0.250
  Chirality :  0.038   0.156   1627
  Planarity :  0.004   0.040   1821
  Dihedral  : 15.194 132.260   1960
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  9.86 %
    Favored  : 88.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.24), residues: 1215
  helix:  1.09 (0.31), residues: 318
  sheet: -0.28 (0.38), residues: 174
  loop : -1.44 (0.22), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1600 
 HIS   0.003   0.001   HIS A1279 
 PHE   0.026   0.001   PHE A 915 
 TYR   0.010   0.001   TYR A 122 
 ARG   0.002   0.000   ARG A 890 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03177 (  293)
  hydrogen bonds       : angle       4.83838 (  828)
  metal coordination   : bond        0.00427 (   15)
  metal coordination   : angle       2.72565 (   15)
  covalent geometry    : bond        0.00237 (11082)
  covalent geometry    : angle       0.49537 (15115)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.3970 (OUTLIER) cc_final: 0.3676 (tt)
REVERT: A  197 PHE cc_start: 0.7686 (m-80) cc_final: 0.7470 (m-80)
REVERT: A 1541 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8108 (tp)
  outliers start: 21
  outliers final: 13
  residues processed: 84
  average time/residue: 0.2557
  time to fit residues: 32.0861
Evaluate side-chains
  85 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  672 CYS
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  914 ASP
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1541 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 109 optimal weight:    0.0270
   chunk 39 optimal weight:    0.9990
   chunk 34 optimal weight:    9.9990
   chunk 83 optimal weight:   10.0000
   chunk 75 optimal weight:    3.9990
   overall best weight:    1.4046

-------------------------------------------------------------------------------
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 = 0.3942 r_free = 0.3942 target = 0.130640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.103978 restraints weight = 22148.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.107081 restraints weight = 12658.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.109087 restraints weight = 8925.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11097  Z= 0.116
  Angle     :  0.525  10.075  15130  Z= 0.259
  Chirality :  0.038   0.160   1627
  Planarity :  0.004   0.038   1821
  Dihedral  : 15.204 131.909   1960
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 11.36 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.24), residues: 1215
  helix:  1.08 (0.31), residues: 324
  sheet: -0.39 (0.38), residues: 186
  loop : -1.43 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1600 
 HIS   0.004   0.001   HIS A1279 
 PHE   0.020   0.001   PHE A 187 
 TYR   0.010   0.001   TYR A 122 
 ARG   0.005   0.000   ARG A1443 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03323 (  293)
  hydrogen bonds       : angle       4.73698 (  828)
  metal coordination   : bond        0.00438 (   15)
  metal coordination   : angle       2.71742 (   15)
  covalent geometry    : bond        0.00267 (11082)
  covalent geometry    : angle       0.51775 (15115)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6507 (mmp) cc_final: 0.6255 (mmp)
REVERT: A   60 LEU cc_start: 0.3934 (OUTLIER) cc_final: 0.3648 (tt)
REVERT: A  197 PHE cc_start: 0.7717 (m-80) cc_final: 0.7506 (m-80)
REVERT: A 1541 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8097 (tp)
  outliers start: 19
  outliers final: 15
  residues processed: 82
  average time/residue: 0.3030
  time to fit residues: 38.7666
Evaluate side-chains
  83 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 1.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  672 CYS
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  914 ASP
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue 1274 LEU
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1541 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 50 optimal weight:    0.0470
   chunk 112 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0970
   overall best weight:    0.5076

-------------------------------------------------------------------------------
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 = 0.3976 r_free = 0.3976 target = 0.133353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.106791 restraints weight = 21648.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.110012 restraints weight = 12232.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.112046 restraints weight = 8525.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11097  Z= 0.085
  Angle     :  0.507  10.962  15130  Z= 0.245
  Chirality :  0.037   0.154   1627
  Planarity :  0.003   0.040   1821
  Dihedral  : 15.002 128.848   1960
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 12.30 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.24), residues: 1215
  helix:  1.11 (0.31), residues: 325
  sheet: -0.15 (0.39), residues: 174
  loop : -1.38 (0.22), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1600 
 HIS   0.004   0.000   HIS A 691 
 PHE   0.030   0.001   PHE A 915 
 TYR   0.010   0.001   TYR A 122 
 ARG   0.004   0.000   ARG A1443 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02718 (  293)
  hydrogen bonds       : angle       4.60351 (  828)
  metal coordination   : bond        0.00433 (   15)
  metal coordination   : angle       2.50665 (   15)
  covalent geometry    : bond        0.00188 (11082)
  covalent geometry    : angle       0.50066 (15115)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 1.423 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 PHE cc_start: 0.7691 (m-80) cc_final: 0.7475 (m-80)
REVERT: A 1541 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8039 (tp)
  outliers start: 13
  outliers final: 9
  residues processed: 77
  average time/residue: 0.3261
  time to fit residues: 39.4805
Evaluate side-chains
  79 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  914 ASP
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue 1274 LEU
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1541 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 2 optimal weight:    8.9990
   chunk 90 optimal weight:    0.9990
   chunk 82 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 78 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3914 r_free = 0.3914 target = 0.128009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.101790 restraints weight = 22083.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.104709 restraints weight = 12803.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.106573 restraints weight = 9083.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11097  Z= 0.179
  Angle     :  0.584   9.804  15130  Z= 0.289
  Chirality :  0.040   0.176   1627
  Planarity :  0.004   0.037   1821
  Dihedral  : 15.289 127.558   1960
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.30 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.24), residues: 1215
  helix:  1.00 (0.31), residues: 324
  sheet: -0.16 (0.39), residues: 184
  loop : -1.51 (0.22), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 977 
 HIS   0.004   0.001   HIS A 865 
 PHE   0.024   0.002   PHE A 187 
 TYR   0.010   0.001   TYR A1561 
 ARG   0.005   0.000   ARG A 890 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  293)
  hydrogen bonds       : angle       4.93217 (  828)
  metal coordination   : bond        0.00531 (   15)
  metal coordination   : angle       3.06708 (   15)
  covalent geometry    : bond        0.00414 (11082)
  covalent geometry    : angle       0.57595 (15115)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 1.401 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 TRP cc_start: 0.7131 (t-100) cc_final: 0.5764 (t-100)
REVERT: A   60 LEU cc_start: 0.4088 (OUTLIER) cc_final: 0.3811 (tt)
REVERT: A  197 PHE cc_start: 0.7766 (m-80) cc_final: 0.7555 (m-80)
REVERT: A  232 LEU cc_start: 0.7523 (mt) cc_final: 0.7072 (mt)
REVERT: A 1541 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8038 (tp)
  outliers start: 16
  outliers final: 11
  residues processed: 79
  average time/residue: 0.2710
  time to fit residues: 33.1394
Evaluate side-chains
  80 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 1.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  672 CYS
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  914 ASP
Chi-restraints excluded: chain A residue 1274 LEU
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1431 THR
Chi-restraints excluded: chain A residue 1541 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    8.9990
   chunk 88 optimal weight:    0.7980
   chunk 104 optimal weight:   20.0000
   chunk 108 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   chunk 123 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 59 optimal weight:    2.9990
   chunk 109 optimal weight:    5.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.3918 r_free = 0.3918 target = 0.128891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.102494 restraints weight = 21950.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.105512 restraints weight = 12624.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.107447 restraints weight = 8943.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11097  Z= 0.137
  Angle     :  0.550  10.052  15130  Z= 0.271
  Chirality :  0.039   0.168   1627
  Planarity :  0.004   0.038   1821
  Dihedral  : 15.204 125.668   1960
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.21 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.24), residues: 1215
  helix:  0.99 (0.31), residues: 324
  sheet: -0.06 (0.40), residues: 172
  loop : -1.52 (0.22), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 977 
 HIS   0.003   0.001   HIS A1279 
 PHE   0.029   0.001   PHE A 915 
 TYR   0.011   0.001   TYR A 122 
 ARG   0.004   0.000   ARG A1443 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03498 (  293)
  hydrogen bonds       : angle       4.83281 (  828)
  metal coordination   : bond        0.00452 (   15)
  metal coordination   : angle       2.72229 (   15)
  covalent geometry    : bond        0.00316 (11082)
  covalent geometry    : angle       0.54323 (15115)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 1.125 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 TRP cc_start: 0.7048 (t-100) cc_final: 0.5784 (t-100)
REVERT: A   60 LEU cc_start: 0.3835 (OUTLIER) cc_final: 0.3610 (tt)
REVERT: A 1541 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.7997 (tp)
  outliers start: 16
  outliers final: 13
  residues processed: 82
  average time/residue: 0.2238
  time to fit residues: 29.1473
Evaluate side-chains
  85 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain A residue  626 HIS
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  914 ASP
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue 1274 LEU
Chi-restraints excluded: chain A residue 1290 VAL
Chi-restraints excluded: chain A residue 1431 THR
Chi-restraints excluded: chain A residue 1445 VAL
Chi-restraints excluded: chain A residue 1541 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 95 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0270
   chunk 96 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 93 optimal weight:    8.9990
   chunk 111 optimal weight:    6.9990
   chunk 36 optimal weight:    6.9990
   chunk 12 optimal weight:    9.9990
   chunk 122 optimal weight:    3.9990
   overall best weight:    2.1844

-------------------------------------------------------------------------------
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 = 0.3917 r_free = 0.3917 target = 0.128627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.102341 restraints weight = 21898.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.105367 restraints weight = 12497.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.107358 restraints weight = 8800.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11097  Z= 0.155
  Angle     :  0.567   9.485  15130  Z= 0.280
  Chirality :  0.040   0.172   1627
  Planarity :  0.004   0.038   1821
  Dihedral  : 15.227 125.736   1960
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.49 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.24), residues: 1215
  helix:  0.98 (0.31), residues: 324
  sheet: -0.27 (0.40), residues: 174
  loop : -1.57 (0.22), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 977 
 HIS   0.004   0.001   HIS A1279 
 PHE   0.022   0.001   PHE A 187 
 TYR   0.011   0.001   TYR A 958 
 ARG   0.004   0.000   ARG A1443 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03732 (  293)
  hydrogen bonds       : angle       4.88784 (  828)
  metal coordination   : bond        0.00501 (   15)
  metal coordination   : angle       2.96206 (   15)
  covalent geometry    : bond        0.00358 (11082)
  covalent geometry    : angle       0.55937 (15115)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4041.09 seconds
wall clock time: 75 minutes 42.57 seconds (4542.57 seconds total)