Starting phenix.real_space_refine
on Wed Mar  4 04:30:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x7r_33046/03_2026/7x7r_33046.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x7r_33046/03_2026/7x7r_33046.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x7r_33046/03_2026/7x7r_33046.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x7r_33046/03_2026/7x7r_33046.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x7r_33046/03_2026/7x7r_33046.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x7r_33046/03_2026/7x7r_33046.map"
  }
  resolution = 3.5
  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=   1.000
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      56      5.49       5
     S      31      5.16       5
     C    6510      2.51       5
     N    1854      2.21       5
     O    2074      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10529
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 758
          Classifications: {'RNA': 36}
          Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 4, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 20, 'rna3p': 15}
    Chain: "J"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 436
          Classifications: {'RNA': 20}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 5}
          Link IDs: {'rna2p': 4, 'rna3p': 15}
    Chain: "A"
      Number of atoms: 9331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1237, 9331
          Classifications: {'peptide': 1237}
          Incomplete info: {'truncation_to_alanine': 178}
          Link IDs: {'PTRANS': 59, 'TRANS': 1177}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 662
          Unresolved non-hydrogen angles: 806
          Unresolved non-hydrogen dihedrals: 535
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'GLU:plan': 42, 'ASN:plan1': 19, 'GLN:plan1': 9, 'ASP:plan': 25, 'HIS:plan': 3, 'ARG:plan': 9, 'PHE:plan': 4, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 427
    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   4549  SG  CYS A 491      21.330  25.347 102.757  1.00 39.67           S
  ATOM   4631  SG  CYS A 503      21.864  25.027 104.149  1.00 40.30           S
  ATOM   4653  SG  CYS A 506      24.237  26.584 103.898  1.00 34.60           S
  ATOM   1852  SG  CYS A  88      28.779  35.019 134.217  1.00 54.56           S
  ATOM   2090  SG  CYS A 121      27.754  36.202 137.716  1.00 80.87           S
  ATOM   2121  SG  CYS A 127      31.434  36.295 136.707  1.00 63.26           S
  ATOM   2145  SG  CYS A 130      28.979  38.632 135.016  1.00 57.48           S
  ATOM   6514  SG  CYS A 750      12.128  24.187  73.080  1.00 80.94           S
  ATOM   6527  SG  CYS A 752      15.322  22.825  71.640  1.00 66.35           S
  ATOM   6549  SG  CYS A 755      15.557  24.790  74.873  1.00 52.19           S
  ATOM   8530  SG  CYS A1406      19.111  40.825  43.697  1.00 53.55           S
  ATOM   8581  SG  CYS A1414      18.032  40.581  41.695  1.00 43.81           S
  ATOM   8598  SG  CYS A1417      21.390  39.108  43.424  1.00 39.10           S

  Time building chain proxies: 2.65, per 1000 atoms: 0.25
  Number of scatterers: 10529
  At special positions: 0
  Unit cell: (73.1499, 84.5499, 152, 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      31     16.00
     P      56     15.00
     O    2074      8.00
     N    1854      7.00
     C    6510      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: 0.84
  Conformation dependent library (CDL) restraints added in 431.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1801 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A 491 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A 503 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A 506 "
      pdb="  ZN A1802 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A 130 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A  88 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A 127 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A 121 "
      pdb="  ZN A1803 "
        pdb="ZN    ZN A1803 " - pdb=" ND1 HIS A 747 "
        pdb="ZN    ZN A1803 " - pdb=" SG  CYS A 752 "
        pdb="ZN    ZN A1803 " - pdb=" SG  CYS A 750 "
        pdb="ZN    ZN A1803 " - pdb=" SG  CYS A 755 "
      pdb="  ZN A1804 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1406 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1414 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1417 "
      Number of angles added : 9


  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2260

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 14 sheets defined
      29.0% alpha, 15.0% beta
      5 base pairs and 12 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 30
      removed outlier: 4.282A  pdb=" N   LYS A  30 " --> pdb=" O   TRP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 38
      removed outlier: 4.011A  pdb=" N   MET A  36 " --> pdb=" O   SER A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 78
      removed outlier: 3.516A  pdb=" N   VAL A  63 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 134
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 3.648A  pdb=" N   ILE A 172 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 227
    Processing helix  chain 'A' and resid 271 through 287
    Processing helix  chain 'A' and resid 290 through 293
      removed outlier: 3.677A  pdb=" N   ILE A 293 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 290 through 293'
    Processing helix  chain 'A' and resid 294 through 303
    Processing helix  chain 'A' and resid 308 through 313
    Processing helix  chain 'A' and resid 338 through 350
      removed outlier: 4.276A  pdb=" N   LYS A 344 " --> pdb=" O   ARG A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 372
    Processing helix  chain 'A' and resid 471 through 488
    Processing helix  chain 'A' and resid 505 through 510
      removed outlier: 3.761A  pdb=" N   ARG A 510 " --> pdb=" O   CYS A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 580
      removed outlier: 3.795A  pdb=" N   ARG A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 625
      removed outlier: 3.577A  pdb=" N   TYR A 621 " --> pdb=" O   LYS A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 626 through 628
      No H-bonds generated for 'chain 'A' and resid 626 through 628'
    Processing helix  chain 'A' and resid 630 through 637
      removed outlier: 3.999A  pdb=" N   GLU A 636 " --> pdb=" O   LYS A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 642
      removed outlier: 3.820A  pdb=" N   LEU A 642 " --> pdb=" O   GLU A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 657
      removed outlier: 3.567A  pdb=" N   CYS A 657 " --> pdb=" O   GLU A 654 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 654 through 657'
    Processing helix  chain 'A' and resid 658 through 665
      removed outlier: 3.791A  pdb=" N   LYS A 662 " --> pdb=" O   LEU A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 691
      removed outlier: 3.527A  pdb=" N   LEU A 691 " --> pdb=" O   THR A 687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 740
    Processing helix  chain 'A' and resid 754 through 759
    Processing helix  chain 'A' and resid 831 through 847
      removed outlier: 3.508A  pdb=" N   ILE A 845 " --> pdb=" O   ALA A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 859
      removed outlier: 3.515A  pdb=" N   VAL A 858 " --> pdb=" O   LYS A 855 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 878
      removed outlier: 3.824A  pdb=" N   GLU A 878 " --> pdb=" O   ASP A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1016
      removed outlier: 3.741A  pdb=" N   LEU A1003 " --> pdb=" O   PRO A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1394 through 1399
      removed outlier: 3.823A  pdb=" N   LEU A1399 " --> pdb=" O   LEU A1395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1414 through 1421
      removed outlier: 3.500A  pdb=" N   LEU A1419 " --> pdb=" O   PRO A1415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1463 through 1468
      removed outlier: 4.341A  pdb=" N   SER A1467 " --> pdb=" O   ARG A1463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1486 through 1493
      removed outlier: 3.801A  pdb=" N   ILE A1490 " --> pdb=" O   GLY A1486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1494 through 1499
    Processing helix  chain 'A' and resid 1528 through 1540
      removed outlier: 3.847A  pdb=" N   GLY A1533 " --> pdb=" O   GLU A1529 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   LEU A1534 " --> pdb=" O   TRP A1530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1590 through 1599
      removed outlier: 4.103A  pdb=" N   GLY A1594 " --> pdb=" O   TYR A1590 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ILE A1599 " --> pdb=" O   TYR A1595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1615 through 1618
      removed outlier: 3.602A  pdb=" N   VAL A1618 " --> pdb=" O   GLN A1615 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1615 through 1618'
    Processing helix  chain 'A' and resid 1619 through 1629
      removed outlier: 3.815A  pdb=" N   LYS A1624 " --> pdb=" O   PRO A1620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1673 through 1683
      removed outlier: 3.661A  pdb=" N   VAL A1678 " --> pdb=" O   TYR A1674 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   LYS A1679 " --> pdb=" O   LYS A1675 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 158
      removed outlier: 5.527A  pdb=" N   PHE A 153 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   THR A 210 " --> pdb=" O   PHE A 153 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   ASN A 155 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ARG A 208 " --> pdb=" O   ASN A 155 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLU A 238 " --> pdb=" O   GLU A  11 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22
    Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111
      removed outlier: 6.012A  pdb=" N   THR A 110 " --> pdb=" O   VAL A 405 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 181
      removed outlier: 3.889A  pdb=" N   ASP A 190 " --> pdb=" O   ARG A 180 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 512 through 513
      removed outlier: 6.732A  pdb=" N   GLU A 415 " --> pdb=" O   GLU A 611 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   GLU A 611 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   ILE A 417 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
      removed outlier: 5.060A  pdb=" N   ILE A 609 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   VAL A 419 " --> pdb=" O   ILE A 607 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   ILE A 607 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 469 through 470
    Processing sheet with id=AA7, first strand: chain 'A' and resid 528 through 534
      removed outlier: 5.884A  pdb=" N   SER A 544 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
      removed outlier: 8.897A  pdb=" N   ASN A 534 " --> pdb=" O   ASP A 542 " (cutoff:3.500A)
      removed outlier: 10.447A  pdb=" N   ASP A 542 " --> pdb=" O   ASN A 534 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 721 through 722
      removed outlier: 3.823A  pdb=" N   ARG A 768 " --> pdb=" O   TRP A 825 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 721 through 722
      removed outlier: 3.627A  pdb=" N   GLU A 677 " --> pdb=" O   GLY A 865 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   GLY A 865 " --> pdb=" O   GLU A 677 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 925 through 927
    Processing sheet with id=AB2, first strand: chain 'A' and resid 950 through 952
      removed outlier: 7.224A  pdb=" N   GLY A 952 " --> pdb=" O   GLU A1525 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   GLU A1525 " --> pdb=" O   GLY A 952 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ASN A 955 " --> pdb=" O   ASP A1565 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1430 through 1431
      removed outlier: 6.773A  pdb=" N   ASN A 955 " --> pdb=" O   ASP A1565 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 985 through 986
      removed outlier: 6.201A  pdb=" N   LYS A 985 " --> pdb=" O   THR A1508 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'A' and resid 991 through 992

    277 hydrogen bonds defined for protein.
    768 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      14 hydrogen bonds
      28 hydrogen bond angles
      0 basepair planarities
      5 basepair parallelities
      12 stacking parallelities
  Total time for adding SS restraints: 1.99

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2879
        1.33 -     1.45: 2252
        1.45 -     1.57: 5606
        1.57 -     1.69: 110
        1.69 -     1.81: 42
  Bond restraints: 10889
  Sorted by residual:
  bond pdb=" N1    C J  23 "
       pdb=" C2    C J  23 "
    ideal  model  delta    sigma   weight residual
    1.397  1.419 -0.022 2.00e-02 2.50e+03 1.25e+00
  bond pdb=" C3'   A J  19 "
       pdb=" O3'   A J  19 "
    ideal  model  delta    sigma   weight residual
    1.427  1.443 -0.016 1.50e-02 4.44e+03 1.19e+00
  bond pdb=" N   PHE A  24 "
       pdb=" CA  PHE A  24 "
    ideal  model  delta    sigma   weight residual
    1.457  1.467 -0.010 1.29e-02 6.01e+03 5.88e-01
  bond pdb=" O3'   A J  19 "
       pdb=" P     G J  20 "
    ideal  model  delta    sigma   weight residual
    1.607  1.618 -0.011 1.50e-02 4.44e+03 5.51e-01
  bond pdb=" N   ASP A 400 "
       pdb=" CA  ASP A 400 "
    ideal  model  delta    sigma   weight residual
    1.460  1.471 -0.011 1.54e-02 4.22e+03 5.40e-01
  ... (remaining 10884 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 14689
        1.66 -     3.33: 277
        3.33 -     4.99: 54
        4.99 -     6.65: 11
        6.65 -     8.32: 5
  Bond angle restraints: 15036
  Sorted by residual:
  angle pdb=" C3'   A J  19 "
        pdb=" O3'   A J  19 "
        pdb=" P     G J  20 "
      ideal   model   delta    sigma   weight residual
     120.20  125.16   -4.96 1.50e+00 4.44e-01 1.09e+01
  angle pdb=" N   VAL A1618 "
        pdb=" CA  VAL A1618 "
        pdb=" C   VAL A1618 "
      ideal   model   delta    sigma   weight residual
     112.29  109.52    2.77 9.40e-01 1.13e+00 8.68e+00
  angle pdb=" C1'   C J  23 "
        pdb=" N1    C J  23 "
        pdb=" C2    C J  23 "
      ideal   model   delta    sigma   weight residual
     118.80  127.12   -8.32 3.00e+00 1.11e-01 7.68e+00
  angle pdb=" C   PHE A 780 "
        pdb=" N   GLU A 781 "
        pdb=" CA  GLU A 781 "
      ideal   model   delta    sigma   weight residual
     121.54  126.82   -5.28 1.91e+00 2.74e-01 7.63e+00
  angle pdb=" C   PHE A  24 "
        pdb=" CA  PHE A  24 "
        pdb=" CB  PHE A  24 "
      ideal   model   delta    sigma   weight residual
     110.42  115.78   -5.36 1.99e+00 2.53e-01 7.26e+00
  ... (remaining 15031 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.18: 6210
       35.18 -    70.36: 249
       70.36 -   105.53: 32
      105.53 -   140.71: 0
      140.71 -   175.89: 5
  Dihedral angle restraints: 6496
    sinusoidal: 2968
      harmonic: 3528
  Sorted by residual:
  dihedral pdb=" O4'   U C -14 "
           pdb=" C1'   U C -14 "
           pdb=" N1    U C -14 "
           pdb=" C2    U C -14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   58.81  141.19     1      1.50e+01 4.44e-03 7.59e+01
  dihedral pdb=" O4'   U J  36 "
           pdb=" C1'   U J  36 "
           pdb=" N1    U J  36 "
           pdb=" C2    U J  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   56.11  175.89     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U C  -9 "
           pdb=" C1'   U C  -9 "
           pdb=" N1    U C  -9 "
           pdb=" C2    U C  -9 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   47.38 -175.38     1      1.70e+01 3.46e-03 6.63e+01
  ... (remaining 6493 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1363
       0.046 -    0.091: 262
       0.091 -    0.137: 70
       0.137 -    0.182: 5
       0.182 -    0.228: 1
  Chirality restraints: 1701
  Sorted by residual:
  chirality pdb=" CB  ILE A1468 "
            pdb=" CA  ILE A1468 "
            pdb=" CG1 ILE A1468 "
            pdb=" CG2 ILE A1468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" C3'   A J  19 "
            pdb=" C4'   A J  19 "
            pdb=" O3'   A J  19 "
            pdb=" C2'   A J  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.58   -0.16 2.00e-01 2.50e+01 6.67e-01
  chirality pdb=" C1'   U C -14 "
            pdb=" O4'   U C -14 "
            pdb=" C2'   U C -14 "
            pdb=" N1    U C -14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.31    0.16 2.00e-01 2.50e+01 6.40e-01
  ... (remaining 1698 not shown)

  Planarity restraints: 1726
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1475 "   -0.028 5.00e-02 4.00e+02   4.25e-02 2.89e+00
        pdb=" N   PRO A1476 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A1476 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A1476 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 316 "    0.025 5.00e-02 4.00e+02   3.76e-02 2.26e+00
        pdb=" N   PRO A 317 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 317 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 317 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C C   1 "    0.017 2.00e-02 2.50e+03   9.94e-03 2.22e+00
        pdb=" N1    C C   1 "   -0.024 2.00e-02 2.50e+03
        pdb=" C2    C C   1 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    C C   1 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    C C   1 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    C C   1 "    0.002 2.00e-02 2.50e+03
        pdb=" N4    C C   1 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    C C   1 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    C C   1 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1723 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 154
        2.63 -     3.19: 9366
        3.19 -     3.76: 16766
        3.76 -     4.33: 22090
        4.33 -     4.90: 35754
  Nonbonded interactions: 84130
  Sorted by model distance:
  nonbonded pdb=" O2'   U C   5 "
            pdb=" O   ALA A 685 "
     model   vdw
     2.058 3.040
  nonbonded pdb=" O   LEU A1648 "
            pdb=" OG1 THR A1662 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OG  SER A 680 "
            pdb=" O   GLY A 859 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O2'   G J  20 "
            pdb=" O4'   U J  21 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" NH2 ARG A 737 "
            pdb=" OE1 GLU A1525 "
     model   vdw
     2.264 3.120
  ... (remaining 84125 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:             1.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     13.120
  Find NCS groups from input model:        0.040
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6626
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      :  0.002   0.035  10903  Z= 0.100
  Angle     :  0.587   8.316  15045  Z= 0.291
  Chirality :  0.040   0.228   1701
  Planarity :  0.003   0.043   1726
  Dihedral  : 18.553 175.890   4236
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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: -1.19 (0.25), residues: 1217
  helix:  0.20 (0.32), residues: 292
  sheet: -0.80 (0.42), residues: 170
  loop : -1.22 (0.24), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  19 
 TYR   0.018   0.001   TYR A 649 
 PHE   0.023   0.001   PHE A 546 
 TRP   0.015   0.001   TRP A 862 
 HIS   0.004   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 (10889)
  covalent geometry    : angle       0.58426 (15036)
  hydrogen bonds       : bond        0.19878 (  278)
  hydrogen bonds       : angle       8.62184 (  796)
  metal coordination   : bond        0.00317 (   14)
  metal coordination   : angle       2.35710 (    9)

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

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

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 MET cc_start: 0.6243 (tmm) cc_final: 0.5741 (tmm)
REVERT: A  191 TYR cc_start: 0.6919 (p90) cc_final: 0.6715 (p90)
REVERT: A  627 MET cc_start: 0.7202 (mtt) cc_final: 0.6970 (mtt)
REVERT: A  760 ASN cc_start: 0.7368 (p0) cc_final: 0.7139 (p0)
REVERT: A 1004 ARG cc_start: 0.7627 (tpt170) cc_final: 0.7185 (tpp-160)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1125
  time to fit residues: 25.4896
Evaluate side-chains
  114 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 924 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.191431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.152081 restraints weight = 14588.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.158454 restraints weight = 7704.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.162720 restraints weight = 5175.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.165527 restraints weight = 3984.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.167402 restraints weight = 3343.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6190
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10903  Z= 0.129
  Angle     :  0.591   8.312  15045  Z= 0.297
  Chirality :  0.042   0.308   1701
  Planarity :  0.004   0.043   1726
  Dihedral  : 19.395 176.173   2200
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.11 %
    Favored  : 88.56 %
  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: -1.37 (0.24), residues: 1217
  helix:  0.04 (0.30), residues: 308
  sheet: -0.96 (0.40), residues: 176
  loop : -1.34 (0.24), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 356 
 TYR   0.021   0.002   TYR A 199 
 PHE   0.021   0.001   PHE A 824 
 TRP   0.008   0.001   TRP A  44 
 HIS   0.005   0.001   HIS A 924 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10889)
  covalent geometry    : angle       0.58502 (15036)
  hydrogen bonds       : bond        0.03834 (  278)
  hydrogen bonds       : angle       6.05408 (  796)
  metal coordination   : bond        0.00549 (   14)
  metal coordination   : angle       3.55687 (    9)

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

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

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 137
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A  507 ILE cc_start: 0.7889 (mt) cc_final: 0.7257 (pt)
REVERT: A  526 GLU cc_start: 0.7530 (pt0) cc_final: 0.7124 (pt0)
REVERT: A  624 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7846 (tt0)
REVERT: A  760 ASN cc_start: 0.7872 (p0) cc_final: 0.7391 (p0)
REVERT: A 1004 ARG cc_start: 0.7742 (tpt170) cc_final: 0.7273 (tpp-160)
  outliers start: 12
  outliers final: 7
  residues processed: 144
  average time/residue: 0.1117
  time to fit residues: 22.5922
Evaluate side-chains
  123 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  547 ASP
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  815 LYS
Chi-restraints excluded: chain A residue  924 HIS
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  961 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 113 optimal weight:    0.7980
   chunk 126 optimal weight:    0.7980
   chunk 91 optimal weight:    4.9990
   chunk 122 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 63 optimal weight:    7.9990
   chunk 78 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4392 r_free = 0.4392 target = 0.188535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.148065 restraints weight = 15001.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.154469 restraints weight = 7982.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.158672 restraints weight = 5394.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.161370 restraints weight = 4193.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.163254 restraints weight = 3558.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6190
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10903  Z= 0.128
  Angle     :  0.572  11.205  15045  Z= 0.286
  Chirality :  0.042   0.315   1701
  Planarity :  0.004   0.058   1726
  Dihedral  : 19.384 176.328   2200
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 15.67 %
    Favored  : 83.00 %
  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: -1.31 (0.24), residues: 1217
  helix:  0.07 (0.30), residues: 314
  sheet: -0.76 (0.41), residues: 176
  loop : -1.35 (0.24), residues: 727

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 564 
 TYR   0.017   0.001   TYR A 199 
 PHE   0.020   0.001   PHE A 824 
 TRP   0.017   0.001   TRP A1530 
 HIS   0.003   0.001   HIS A1418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (10889)
  covalent geometry    : angle       0.56661 (15036)
  hydrogen bonds       : bond        0.03448 (  278)
  hydrogen bonds       : angle       5.55680 (  796)
  metal coordination   : bond        0.00457 (   14)
  metal coordination   : angle       3.24023 (    9)

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

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

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.8304 (mpp) cc_final: 0.8086 (mpp)
REVERT: A  507 ILE cc_start: 0.7871 (mt) cc_final: 0.7249 (pt)
REVERT: A  624 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7891 (tt0)
REVERT: A  627 MET cc_start: 0.7818 (mtt) cc_final: 0.7539 (mtt)
REVERT: A  760 ASN cc_start: 0.7875 (p0) cc_final: 0.7386 (p0)
  outliers start: 12
  outliers final: 10
  residues processed: 142
  average time/residue: 0.1136
  time to fit residues: 22.8959
Evaluate side-chains
  133 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  547 ASP
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  924 HIS
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  965 ILE
Chi-restraints excluded: chain A residue 1562 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 120 optimal weight:    4.9990
   chunk 86 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 95 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 106 optimal weight:    0.0030
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
A 924 HIS
** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1544 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.189520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.148855 restraints weight = 15180.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.155222 restraints weight = 8099.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.159331 restraints weight = 5493.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.162073 restraints weight = 4301.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.163649 restraints weight = 3651.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6268
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   0.031  10903  Z= 0.121
  Angle     :  0.566  11.959  15045  Z= 0.281
  Chirality :  0.041   0.301   1701
  Planarity :  0.004   0.055   1726
  Dihedral  : 19.323 176.631   2200
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.11 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.25), residues: 1217
  helix:  0.14 (0.30), residues: 308
  sheet: -0.72 (0.42), residues: 169
  loop : -1.34 (0.23), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 356 
 TYR   0.016   0.001   TYR A 199 
 PHE   0.036   0.001   PHE A 226 
 TRP   0.019   0.001   TRP A1530 
 HIS   0.002   0.001   HIS A1483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (10889)
  covalent geometry    : angle       0.56179 (15036)
  hydrogen bonds       : bond        0.03185 (  278)
  hydrogen bonds       : angle       5.24059 (  796)
  metal coordination   : bond        0.00401 (   14)
  metal coordination   : angle       3.00052 (    9)

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

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

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.8333 (mpp) cc_final: 0.8085 (mpp)
REVERT: A  507 ILE cc_start: 0.7932 (mt) cc_final: 0.7257 (pt)
REVERT: A  514 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6279 (pp)
REVERT: A  624 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7903 (tt0)
REVERT: A  627 MET cc_start: 0.7880 (mtt) cc_final: 0.7645 (mtt)
REVERT: A  760 ASN cc_start: 0.8016 (p0) cc_final: 0.7464 (p0)
REVERT: A 1016 LYS cc_start: 0.8275 (pptt) cc_final: 0.6994 (tptt)
REVERT: A 1418 HIS cc_start: 0.5849 (m-70) cc_final: 0.5518 (m-70)
  outliers start: 27
  outliers final: 13
  residues processed: 151
  average time/residue: 0.1063
  time to fit residues: 22.6375
Evaluate side-chains
  137 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  924 HIS
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  965 ILE
Chi-restraints excluded: chain A residue 1562 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 455 HIS
A 776 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.184508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.143802 restraints weight = 15066.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.149887 restraints weight = 8189.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.153902 restraints weight = 5616.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.156525 restraints weight = 4413.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.158270 restraints weight = 3766.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.4110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6325
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10903  Z= 0.187
  Angle     :  0.625  12.913  15045  Z= 0.314
  Chirality :  0.043   0.322   1701
  Planarity :  0.005   0.068   1726
  Dihedral  : 19.463 178.368   2200
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 19.11 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.25), residues: 1217
  helix:  0.13 (0.30), residues: 295
  sheet: -0.76 (0.43), residues: 169
  loop : -1.37 (0.24), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 472 
 TYR   0.017   0.002   TYR A 199 
 PHE   0.027   0.002   PHE A 824 
 TRP   0.022   0.001   TRP A1530 
 HIS   0.009   0.001   HIS A 924 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (10889)
  covalent geometry    : angle       0.61919 (15036)
  hydrogen bonds       : bond        0.03516 (  278)
  hydrogen bonds       : angle       5.35833 (  796)
  metal coordination   : bond        0.00695 (   14)
  metal coordination   : angle       3.57568 (    9)

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

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

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 121
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.8337 (mpp) cc_final: 0.8047 (mpp)
REVERT: A  514 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6401 (pp)
REVERT: A  624 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7941 (tt0)
REVERT: A  627 MET cc_start: 0.7934 (mtt) cc_final: 0.7668 (mtt)
REVERT: A  776 ASN cc_start: 0.7459 (OUTLIER) cc_final: 0.6205 (p0)
REVERT: A 1016 LYS cc_start: 0.8364 (pptt) cc_final: 0.7106 (tptt)
  outliers start: 31
  outliers final: 18
  residues processed: 137
  average time/residue: 0.1057
  time to fit residues: 20.3522
Evaluate side-chains
  141 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  547 ASP
Chi-restraints excluded: chain A residue  606 ASP
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  776 ASN
Chi-restraints excluded: chain A residue  863 VAL
Chi-restraints excluded: chain A residue  924 HIS
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  964 LEU
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1467 SER
Chi-restraints excluded: chain A residue 1531 GLU
Chi-restraints excluded: chain A residue 1562 ILE
Chi-restraints excluded: chain A residue 1617 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 90 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 95 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 119 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 455 HIS
A 466 ASN
** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.186941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.146365 restraints weight = 15010.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.152556 restraints weight = 8126.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.156695 restraints weight = 5555.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.159404 restraints weight = 4346.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.161152 restraints weight = 3687.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6306
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10903  Z= 0.129
  Angle     :  0.592  13.347  15045  Z= 0.293
  Chirality :  0.042   0.310   1701
  Planarity :  0.004   0.061   1726
  Dihedral  : 19.391 178.215   2200
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 20.89 %
    Favored  : 76.11 %
  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: -1.32 (0.25), residues: 1217
  helix:  0.21 (0.31), residues: 289
  sheet: -0.79 (0.42), residues: 169
  loop : -1.37 (0.23), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 356 
 TYR   0.016   0.002   TYR A 199 
 PHE   0.021   0.001   PHE A 824 
 TRP   0.025   0.001   TRP A1530 
 HIS   0.005   0.001   HIS A 455 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10889)
  covalent geometry    : angle       0.58727 (15036)
  hydrogen bonds       : bond        0.03166 (  278)
  hydrogen bonds       : angle       5.18621 (  796)
  metal coordination   : bond        0.00369 (   14)
  metal coordination   : angle       3.10358 (    9)

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

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

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A   36 MET cc_start: 0.8322 (mpp) cc_final: 0.8026 (mpp)
REVERT: A  514 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6267 (pp)
REVERT: A  624 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7930 (tt0)
REVERT: A  627 MET cc_start: 0.7982 (mtt) cc_final: 0.7650 (mtt)
REVERT: A 1004 ARG cc_start: 0.7838 (tpt170) cc_final: 0.7465 (tpt90)
REVERT: A 1016 LYS cc_start: 0.8352 (pptt) cc_final: 0.7158 (tptt)
REVERT: A 1512 MET cc_start: 0.6962 (mmm) cc_final: 0.6704 (mmm)
REVERT: A 1525 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6517 (pt0)
  outliers start: 27
  outliers final: 23
  residues processed: 146
  average time/residue: 0.1107
  time to fit residues: 22.6261
Evaluate side-chains
  145 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  547 ASP
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  675 THR
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  924 HIS
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  964 LEU
Chi-restraints excluded: chain A residue  965 ILE
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1467 SER
Chi-restraints excluded: chain A residue 1531 GLU
Chi-restraints excluded: chain A residue 1562 ILE
Chi-restraints excluded: chain A residue 1591 ILE
Chi-restraints excluded: chain A residue 1617 HIS
Chi-restraints excluded: chain A residue 1629 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 127 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 111 optimal weight:    4.9990
   chunk 123 optimal weight:    0.0980
   chunk 47 optimal weight:    0.0980
   chunk 22 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 80 optimal weight:    6.9990
   chunk 110 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 455 HIS
A 924 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.189333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.149535 restraints weight = 14889.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.155659 restraints weight = 8130.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.159719 restraints weight = 5592.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.162366 restraints weight = 4378.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.164157 restraints weight = 3724.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6278
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10903  Z= 0.111
  Angle     :  0.580  13.952  15045  Z= 0.285
  Chirality :  0.041   0.334   1701
  Planarity :  0.004   0.057   1726
  Dihedral  : 19.320 178.179   2200
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 21.78 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.25), residues: 1217
  helix:  0.23 (0.31), residues: 289
  sheet: -0.73 (0.42), residues: 169
  loop : -1.35 (0.23), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 564 
 TYR   0.029   0.002   TYR A 621 
 PHE   0.019   0.001   PHE A 824 
 TRP   0.028   0.001   TRP A1530 
 HIS   0.004   0.001   HIS A 455 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (10889)
  covalent geometry    : angle       0.57462 (15036)
  hydrogen bonds       : bond        0.03027 (  278)
  hydrogen bonds       : angle       5.01948 (  796)
  metal coordination   : bond        0.00371 (   14)
  metal coordination   : angle       3.19304 (    9)

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

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

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 0.443 
Fit side-chains
REVERT: A   36 MET cc_start: 0.8310 (mpp) cc_final: 0.8002 (mpp)
REVERT: A  167 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.5036 (pp)
REVERT: A  514 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6077 (pp)
REVERT: A  624 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7923 (tt0)
REVERT: A  627 MET cc_start: 0.8038 (mtt) cc_final: 0.7642 (mtt)
REVERT: A 1004 ARG cc_start: 0.7853 (tpt170) cc_final: 0.7548 (tpt90)
REVERT: A 1016 LYS cc_start: 0.8323 (pptt) cc_final: 0.7159 (tptt)
REVERT: A 1525 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6605 (pt0)
REVERT: A 1531 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7470 (tm-30)
  outliers start: 30
  outliers final: 22
  residues processed: 148
  average time/residue: 0.1105
  time to fit residues: 23.0255
Evaluate side-chains
  143 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  182 ASP
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  547 ASP
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  675 THR
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  924 HIS
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  964 LEU
Chi-restraints excluded: chain A residue  965 ILE
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1467 SER
Chi-restraints excluded: chain A residue 1531 GLU
Chi-restraints excluded: chain A residue 1562 ILE
Chi-restraints excluded: chain A residue 1617 HIS
Chi-restraints excluded: chain A residue 1629 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 27 optimal weight:    0.2980
   chunk 65 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 30 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 101 optimal weight:    0.0670
   chunk 37 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0770
   overall best weight:    0.4276

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

Flipped N/Q/H residues before XYZ refinement:
A 455 HIS
A 466 ASN
** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.190140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.150104 restraints weight = 14809.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.156420 restraints weight = 7982.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.160550 restraints weight = 5425.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.163318 restraints weight = 4238.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.165102 restraints weight = 3583.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.4178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6248
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  10903  Z= 0.106
  Angle     :  0.586  14.243  15045  Z= 0.287
  Chirality :  0.041   0.324   1701
  Planarity :  0.004   0.065   1726
  Dihedral  : 19.269 178.113   2200
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 22.11 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.24), residues: 1217
  helix:  0.22 (0.30), residues: 296
  sheet: -0.63 (0.42), residues: 169
  loop : -1.37 (0.23), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 564 
 TYR   0.021   0.002   TYR A 621 
 PHE   0.019   0.001   PHE A 824 
 TRP   0.031   0.001   TRP A1530 
 HIS   0.004   0.001   HIS A 455 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (10889)
  covalent geometry    : angle       0.58255 (15036)
  hydrogen bonds       : bond        0.02917 (  278)
  hydrogen bonds       : angle       4.92207 (  796)
  metal coordination   : bond        0.00304 (   14)
  metal coordination   : angle       2.83057 (    9)

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

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

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A   36 MET cc_start: 0.8316 (mpp) cc_final: 0.8040 (mpp)
REVERT: A  167 LEU cc_start: 0.5436 (OUTLIER) cc_final: 0.5007 (pp)
REVERT: A  514 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.5951 (pp)
REVERT: A  624 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7937 (tt0)
REVERT: A  627 MET cc_start: 0.8044 (mtt) cc_final: 0.7595 (mtt)
REVERT: A 1004 ARG cc_start: 0.7792 (tpt170) cc_final: 0.7528 (tpt90)
REVERT: A 1016 LYS cc_start: 0.8310 (pptt) cc_final: 0.7201 (tptt)
REVERT: A 1525 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6578 (pt0)
  outliers start: 28
  outliers final: 24
  residues processed: 142
  average time/residue: 0.1035
  time to fit residues: 21.0789
Evaluate side-chains
  147 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  182 ASP
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  547 ASP
Chi-restraints excluded: chain A residue  675 THR
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  924 HIS
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  964 LEU
Chi-restraints excluded: chain A residue  965 ILE
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1467 SER
Chi-restraints excluded: chain A residue 1531 GLU
Chi-restraints excluded: chain A residue 1562 ILE
Chi-restraints excluded: chain A residue 1617 HIS
Chi-restraints excluded: chain A residue 1629 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 40 optimal weight:    7.9990
   chunk 84 optimal weight:    0.0000
   chunk 39 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 124 optimal weight:    5.9990
   chunk 105 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0000
   overall best weight:    0.9392

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

Flipped N/Q/H residues before XYZ refinement:
A 455 HIS
A 924 HIS
** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.187382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.147062 restraints weight = 15007.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.153220 restraints weight = 8168.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.157309 restraints weight = 5592.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.159987 restraints weight = 4377.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.161748 restraints weight = 3716.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6323
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10903  Z= 0.139
  Angle     :  0.607  13.936  15045  Z= 0.298
  Chirality :  0.042   0.314   1701
  Planarity :  0.004   0.068   1726
  Dihedral  : 19.337 178.732   2200
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 23.33 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.25), residues: 1217
  helix:  0.19 (0.30), residues: 296
  sheet: -0.68 (0.42), residues: 169
  loop : -1.37 (0.24), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 564 
 TYR   0.021   0.002   TYR A 199 
 PHE   0.024   0.001   PHE A 824 
 TRP   0.032   0.001   TRP A1530 
 HIS   0.004   0.001   HIS A 455 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (10889)
  covalent geometry    : angle       0.60210 (15036)
  hydrogen bonds       : bond        0.03125 (  278)
  hydrogen bonds       : angle       4.97739 (  796)
  metal coordination   : bond        0.00401 (   14)
  metal coordination   : angle       3.13125 (    9)

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

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

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   36 MET cc_start: 0.8321 (mpp) cc_final: 0.8044 (mpp)
REVERT: A  167 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.5141 (pp)
REVERT: A  514 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6179 (pp)
REVERT: A  624 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7989 (tt0)
REVERT: A  627 MET cc_start: 0.8067 (mtt) cc_final: 0.7627 (mtt)
REVERT: A 1004 ARG cc_start: 0.7879 (tpt170) cc_final: 0.7587 (tpt90)
REVERT: A 1016 LYS cc_start: 0.8323 (pptt) cc_final: 0.7216 (tptt)
REVERT: A 1418 HIS cc_start: 0.6063 (m-70) cc_final: 0.5695 (m90)
REVERT: A 1525 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6653 (pt0)
  outliers start: 26
  outliers final: 23
  residues processed: 138
  average time/residue: 0.1052
  time to fit residues: 20.7703
Evaluate side-chains
  146 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  182 ASP
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  547 ASP
Chi-restraints excluded: chain A residue  675 THR
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  863 VAL
Chi-restraints excluded: chain A residue  924 HIS
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  964 LEU
Chi-restraints excluded: chain A residue  965 ILE
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1467 SER
Chi-restraints excluded: chain A residue 1531 GLU
Chi-restraints excluded: chain A residue 1617 HIS
Chi-restraints excluded: chain A residue 1629 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 14 optimal weight:    0.0050
   chunk 46 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 111 optimal weight:    0.6980
   chunk 117 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
A 455 HIS
** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.190479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.151094 restraints weight = 14913.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.157256 restraints weight = 8123.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.161327 restraints weight = 5557.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.164023 restraints weight = 4348.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.165787 restraints weight = 3676.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6280
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10903  Z= 0.123
  Angle     :  0.602  14.245  15045  Z= 0.296
  Chirality :  0.042   0.318   1701
  Planarity :  0.004   0.065   1726
  Dihedral  : 19.331 178.544   2200
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 23.11 %
    Favored  : 73.89 %
  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: -1.26 (0.24), residues: 1217
  helix:  0.22 (0.30), residues: 296
  sheet: -0.60 (0.42), residues: 169
  loop : -1.37 (0.23), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 564 
 TYR   0.021   0.002   TYR A 199 
 PHE   0.022   0.001   PHE A 824 
 TRP   0.034   0.001   TRP A1530 
 HIS   0.004   0.001   HIS A 924 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10889)
  covalent geometry    : angle       0.59807 (15036)
  hydrogen bonds       : bond        0.03020 (  278)
  hydrogen bonds       : angle       4.93858 (  796)
  metal coordination   : bond        0.00334 (   14)
  metal coordination   : angle       2.95643 (    9)

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

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

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2434 Ramachandran restraints generated.
    1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A   36 MET cc_start: 0.8318 (mpp) cc_final: 0.8040 (mpp)
REVERT: A  167 LEU cc_start: 0.5546 (OUTLIER) cc_final: 0.5110 (pp)
REVERT: A  514 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6159 (pp)
REVERT: A  624 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7992 (tt0)
REVERT: A  627 MET cc_start: 0.8061 (mtt) cc_final: 0.7606 (mtt)
REVERT: A 1004 ARG cc_start: 0.7854 (tpt170) cc_final: 0.7576 (tpt90)
REVERT: A 1016 LYS cc_start: 0.8320 (pptt) cc_final: 0.8083 (ptmt)
REVERT: A 1418 HIS cc_start: 0.6051 (m-70) cc_final: 0.5692 (m90)
REVERT: A 1525 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6649 (pt0)
  outliers start: 27
  outliers final: 23
  residues processed: 135
  average time/residue: 0.1034
  time to fit residues: 19.9375
Evaluate side-chains
  145 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  182 ASP
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  547 ASP
Chi-restraints excluded: chain A residue  675 THR
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  924 HIS
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  964 LEU
Chi-restraints excluded: chain A residue  965 ILE
Chi-restraints excluded: chain A residue 1399 LEU
Chi-restraints excluded: chain A residue 1467 SER
Chi-restraints excluded: chain A residue 1531 GLU
Chi-restraints excluded: chain A residue 1562 ILE
Chi-restraints excluded: chain A residue 1617 HIS
Chi-restraints excluded: chain A residue 1629 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 81 optimal weight:    0.4980
   chunk 110 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 74 optimal weight:    0.0670
   chunk 11 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
A 455 HIS
A 924 HIS
** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.189003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.148857 restraints weight = 14943.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.155108 restraints weight = 8082.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.159310 restraints weight = 5496.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.162020 restraints weight = 4275.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.163601 restraints weight = 3619.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6257
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10903  Z= 0.113
  Angle     :  0.593  14.326  15045  Z= 0.290
  Chirality :  0.041   0.331   1701
  Planarity :  0.004   0.067   1726
  Dihedral  : 19.296 178.429   2200
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 23.44 %
    Favored  : 73.67 %
  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: -1.20 (0.24), residues: 1217
  helix:  0.33 (0.31), residues: 290
  sheet: -0.58 (0.42), residues: 169
  loop : -1.35 (0.23), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 564 
 TYR   0.020   0.002   TYR A 199 
 PHE   0.021   0.001   PHE A 824 
 TRP   0.034   0.001   TRP A1530 
 HIS   0.004   0.001   HIS A 455 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (10889)
  covalent geometry    : angle       0.58964 (15036)
  hydrogen bonds       : bond        0.02940 (  278)
  hydrogen bonds       : angle       4.87124 (  796)
  metal coordination   : bond        0.00306 (   14)
  metal coordination   : angle       2.77212 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1914.14 seconds
wall clock time: 33 minutes 54.40 seconds (2034.40 seconds total)