Starting phenix.real_space_refine
on Tue Feb  3 19:05:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9i93_52750/02_2026/9i93_52750_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9i93_52750/02_2026/9i93_52750.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9i93_52750/02_2026/9i93_52750.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9i93_52750/02_2026/9i93_52750.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9i93_52750/02_2026/9i93_52750_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9i93_52750/02_2026/9i93_52750_trim.cif"
  }
  resolution = 2.86
  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=   0.001 sd=   0.010
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: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    3788      2.51       5
     N    1020      2.21       5
     O    1184      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6016
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4590
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 559, 4582
          Classifications: {'peptide': 559}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 538}
      Conformer: "B"
        Number of residues, atoms: 559, 4582
          Classifications: {'peptide': 559}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 538}
          bond proxies already assigned to first conformer: 4698
    Chain: "B"
      Number of atoms: 1181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 150, 1181
          Classifications: {'peptide': 150}
          Link IDs: {'PTRANS': 8, 'TRANS': 141}
    Chain: "C"
      Number of atoms: 130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 130
          Classifications: {'peptide': 16}
          Link IDs: {'TRANS': 15}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 105
          Unusual residues: {'LMT': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'KZ0': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 6
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AASN A 367 " occ=0.63
      ... (14 atoms not shown)
      pdb=" ND2BASN A 367 " occ=0.37
  Time building chain proxies: 2.41, per 1000 atoms: 0.40
  Number of scatterers: 6016
  At special positions: 0
  Unit cell: (85.293, 74.358, 93.312, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O    1184      8.00
     N    1020      7.00
     C    3788      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.58
  Conformation dependent library (CDL) restraints added in 383.2 milliseconds
  

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1370

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 3 sheets defined
      14.1% alpha, 51.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 296 through 302
    Processing helix  chain 'A' and resid 463 through 470
      removed outlier: 3.642A  pdb=" N   ARG A 469 " --> pdb=" O   TRP A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 542
      removed outlier: 3.620A  pdb=" N   PHE A 541 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 667
    Processing helix  chain 'A' and resid 669 through 675
      removed outlier: 3.534A  pdb=" N   SER A 673 " --> pdb=" O   PRO A 669 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 774
    Processing helix  chain 'B' and resid 1010 through 1013
    Processing helix  chain 'B' and resid 1025 through 1038
    Processing helix  chain 'B' and resid 1109 through 1111
      No H-bonds generated for 'chain 'B' and resid 1109 through 1111'
    Processing helix  chain 'B' and resid 1112 through 1138
      removed outlier: 4.301A  pdb=" N   ASP B1129 " --> pdb=" O   LYS B1125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1138 through 1148
      removed outlier: 3.801A  pdb=" N   ARG B1148 " --> pdb=" O   ALA B1144 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 252
      removed outlier: 3.895A  pdb=" N   ILE A 251 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   MET A 255 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   HIS A 745 " --> pdb=" O   TRP A 739 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   TRP A 739 " --> pdb=" O   HIS A 745 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   VAL A 747 " --> pdb=" O   ASN A 737 " (cutoff:3.500A)
      removed outlier: 8.492A  pdb=" N   ALA A 713 " --> pdb=" O   LEU A 736 " (cutoff:3.500A)
      removed outlier: 12.992A  pdb=" N   GLY A 738 " --> pdb=" O   LYS A 711 " (cutoff:3.500A)
      removed outlier: 13.105A  pdb=" N   LYS A 711 " --> pdb=" O   GLY A 738 " (cutoff:3.500A)
      removed outlier: 5.404A  pdb=" N   GLN A 712 " --> pdb=" O   ASP A 706 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   ASP A 706 " --> pdb=" O   GLN A 712 " (cutoff:3.500A)
      removed outlier: 5.482A  pdb=" N   VAL A 635 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ASP A 629 " --> pdb=" O   VAL A 635 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   SER A 605 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   TYR A 584 " --> pdb=" O   SER A 605 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   VAL A 607 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ILE A 566 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ASN A 576 " --> pdb=" O   SER A 564 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   SER A 564 " --> pdb=" O   ASN A 576 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   SER A 578 " --> pdb=" O   VAL A 562 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   VAL A 562 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   GLY A 580 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   THR A 560 " --> pdb=" O   GLY A 580 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   ILE A 582 " --> pdb=" O   VAL A 558 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   VAL A 558 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   TYR A 584 " --> pdb=" O   ASN A 556 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   ASN A 556 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 252
      removed outlier: 3.895A  pdb=" N   ILE A 251 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   MET A 255 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   THR A 356 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 9.169A  pdb=" N   VAL A 334 " --> pdb=" O   TYR A 354 " (cutoff:3.500A)
      removed outlier: 11.270A  pdb=" N   TYR A 354 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   LYS A 375 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   GLU A 391 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 8.170A  pdb=" N   PHE A 377 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   SER A 389 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
      removed outlier: 5.486A  pdb=" N   ALA A 390 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   VAL A 418 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ASP A 402 " --> pdb=" O   PHE A 406 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   PHE A 406 " --> pdb=" O   ASP A 402 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 1041 through 1043
      removed outlier: 3.927A  pdb=" N   LEU B1018 " --> pdb=" O   LEU B1043 " (cutoff:3.500A)
      removed outlier: 8.569A  pdb=" N   LEU B1055 " --> pdb=" O   VAL B1015 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ILE B1017 " --> pdb=" O   LEU B1055 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   LEU B1057 " --> pdb=" O   ILE B1017 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   ASP B1019 " --> pdb=" O   LEU B1057 " (cutoff:3.500A)
      removed outlier: 9.275A  pdb=" N   LYS B1059 " --> pdb=" O   ASP B1019 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   ASN B1085 " --> pdb=" O   GLY B1058 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   VAL B1060 " --> pdb=" O   THR B1083 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   THR B1083 " --> pdb=" O   VAL B1060 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   ILE B1062 " --> pdb=" O   ILE B1081 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ILE B1081 " --> pdb=" O   ILE B1062 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LYS B1064 " --> pdb=" O   GLN B1079 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   GLN B1079 " --> pdb=" O   LYS B1064 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   THR B1066 " --> pdb=" O   GLU B1077 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   GLU B1077 " --> pdb=" O   THR B1066 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   SER B1068 " --> pdb=" O   THR B1075 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   THR B1075 " --> pdb=" O   SER B1068 " (cutoff:3.500A)

    325 hydrogen bonds defined for protein.
    903 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.03

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1969
        1.34 -     1.46: 1494
        1.46 -     1.58: 2659
        1.58 -     1.69: 0
        1.69 -     1.81: 43
  Bond restraints: 6165
  Sorted by residual:
  bond pdb=" N   PHE A 453 "
       pdb=" CA  PHE A 453 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 1.23e-02 6.61e+03 6.30e+00
  bond pdb=" N   ASP C   7 "
       pdb=" CA  ASP C   7 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.029 1.21e-02 6.83e+03 5.92e+00
  bond pdb=" N   ASP A 749 "
       pdb=" CA  ASP A 749 "
    ideal  model  delta    sigma   weight residual
    1.458  1.484 -0.026 1.19e-02 7.06e+03 4.95e+00
  bond pdb=" C3' LMT A 801 "
       pdb=" O3' LMT A 801 "
    ideal  model  delta    sigma   weight residual
    1.404  1.361  0.043 2.00e-02 2.50e+03 4.70e+00
  bond pdb=" C3' LMT A 803 "
       pdb=" O3' LMT A 803 "
    ideal  model  delta    sigma   weight residual
    1.404  1.361  0.043 2.00e-02 2.50e+03 4.66e+00
  ... (remaining 6160 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 8072
        1.70 -     3.41: 239
        3.41 -     5.11: 39
        5.11 -     6.81: 14
        6.81 -     8.51: 9
  Bond angle restraints: 8373
  Sorted by residual:
  angle pdb=" C   CYS C   2 "
        pdb=" CA  CYS C   2 "
        pdb=" CB  CYS C   2 "
      ideal   model   delta    sigma   weight residual
     115.89  110.41    5.48 1.32e+00 5.74e-01 1.72e+01
  angle pdb=" CB  GLU B1046 "
        pdb=" CG  GLU B1046 "
        pdb=" CD  GLU B1046 "
      ideal   model   delta    sigma   weight residual
     112.60  119.08   -6.48 1.70e+00 3.46e-01 1.46e+01
  angle pdb=" N   LYS A 452 "
        pdb=" CA  LYS A 452 "
        pdb=" CB  LYS A 452 "
      ideal   model   delta    sigma   weight residual
     111.37  105.19    6.18 1.82e+00 3.02e-01 1.15e+01
  angle pdb=" CB  LYS A 670 "
        pdb=" CG  LYS A 670 "
        pdb=" CD  LYS A 670 "
      ideal   model   delta    sigma   weight residual
     111.30  119.03   -7.73 2.30e+00 1.89e-01 1.13e+01
  angle pdb=" CA  ASP C   7 "
        pdb=" CB  ASP C   7 "
        pdb=" CG  ASP C   7 "
      ideal   model   delta    sigma   weight residual
     112.60  115.94   -3.34 1.00e+00 1.00e+00 1.11e+01
  ... (remaining 8368 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.35: 3502
       25.35 -    50.70: 181
       50.70 -    76.06: 43
       76.06 -   101.41: 25
      101.41 -   126.76: 10
  Dihedral angle restraints: 3761
    sinusoidal: 1614
      harmonic: 2147
  Sorted by residual:
  dihedral pdb=" C2' LMT A 803 "
           pdb=" C1' LMT A 803 "
           pdb=" O5' LMT A 803 "
           pdb=" C5' LMT A 803 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.86   61.90 -126.76     1      3.00e+01 1.11e-03 1.71e+01
  dihedral pdb=" C2' LMT A 802 "
           pdb=" C1' LMT A 802 "
           pdb=" O5' LMT A 802 "
           pdb=" C5' LMT A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.86   59.82 -124.68     1      3.00e+01 1.11e-03 1.67e+01
  dihedral pdb=" C1' LMT A 801 "
           pdb=" C5' LMT A 801 "
           pdb=" O5' LMT A 801 "
           pdb=" C4' LMT A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.78   61.56 -124.34     1      3.00e+01 1.11e-03 1.67e+01
  ... (remaining 3758 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 776
       0.074 -    0.148: 99
       0.148 -    0.221: 8
       0.221 -    0.295: 1
       0.295 -    0.369: 4
  Chirality restraints: 888
  Sorted by residual:
  chirality pdb=" C5' LMT A 801 "
            pdb=" C4' LMT A 801 "
            pdb=" C6' LMT A 801 "
            pdb=" O5' LMT A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.14   -0.37 2.00e-01 2.50e+01 3.40e+00
  chirality pdb=" C5' LMT A 802 "
            pdb=" C4' LMT A 802 "
            pdb=" C6' LMT A 802 "
            pdb=" O5' LMT A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.19   -0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CA  LYS A 452 "
            pdb=" N   LYS A 452 "
            pdb=" C   LYS A 452 "
            pdb=" CB  LYS A 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.51e+00
  ... (remaining 885 not shown)

  Planarity restraints: 1083
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B1132 "    0.010 2.00e-02 2.50e+03   1.98e-02 3.92e+00
        pdb=" C   ALA B1132 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ALA B1132 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLU B1133 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B1130 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.32e+00
        pdb=" C   ARG B1130 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ARG B1130 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ALA B1131 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B1121 "   -0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" C   ASP B1121 "    0.030 2.00e-02 2.50e+03
        pdb=" O   ASP B1121 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   MET B1122 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1080 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 99
        2.67 -     3.23: 5358
        3.23 -     3.79: 8856
        3.79 -     4.34: 12834
        4.34 -     4.90: 22261
  Nonbonded interactions: 49408
  Sorted by model distance:
  nonbonded pdb=" O   ASP B1005 "
            pdb=" OD1 ASP B1005 "
     model   vdw
     2.115 3.040
  nonbonded pdb=" OE2 GLU A 643 "
            pdb=" OH  TYR A 780 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OG  SER A 683 "
            pdb=" OG1 THR A 707 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OD1 ASP A 647 "
            pdb=" N   GLU A 648 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" N   GLU A 771 "
            pdb=" OE1 GLU A 771 "
     model   vdw
     2.301 3.120
  ... (remaining 49403 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=0.37 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.490
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
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      :  0.005   0.107   6169  Z= 0.288
  Angle     :  0.737   8.513   8373  Z= 0.388
  Chirality :  0.054   0.369    888
  Planarity :  0.005   0.050   1083
  Dihedral  : 19.511 126.760   2391
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 14.44 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.31), residues: 722
  helix:  0.77 (0.54), residues: 91
  sheet:  0.64 (0.27), residues: 365
  loop : -0.73 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C   3 
 TYR   0.013   0.001   TYR A 671 
 PHE   0.015   0.001   PHE A 243 
 TRP   0.012   0.001   TRP A 249 
 HIS   0.009   0.002   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 6165)
  covalent geometry    : angle       0.73666 ( 8373)
  hydrogen bonds       : bond        0.10472 (  315)
  hydrogen bonds       : angle       5.74944 (  903)
  Misc. bond           : bond        0.06109 (    4)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: A  600 ASP cc_start: 0.8489 (m-30) cc_final: 0.8207 (t0)
REVERT: B 1125 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8304 (ttmt)
  outliers start: 7
  outliers final: 5
  residues processed: 77
  average time/residue: 0.6397
  time to fit residues: 51.4370
Evaluate side-chains
  60 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  648 GLU
Chi-restraints excluded: chain A residue  749 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0470
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.1980
   chunk 51 optimal weight:    0.0170
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.3303 r_free = 0.3303 target = 0.084925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.067275 restraints weight = 32731.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 4.64
r_work: 0.2803 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2804
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2804
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6169  Z= 0.120
  Angle     :  0.602   8.892   8373  Z= 0.296
  Chirality :  0.049   0.303    888
  Planarity :  0.004   0.044   1083
  Dihedral  : 11.310  93.336   1018
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.48 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.32), residues: 722
  helix:  1.55 (0.58), residues: 91
  sheet:  0.68 (0.27), residues: 361
  loop : -0.45 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 409 
 TYR   0.013   0.001   TYR A 705 
 PHE   0.009   0.001   PHE B1103 
 TRP   0.011   0.001   TRP A 249 
 HIS   0.002   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6165)
  covalent geometry    : angle       0.60198 ( 8373)
  hydrogen bonds       : bond        0.03294 (  315)
  hydrogen bonds       : angle       4.95441 (  903)
  Misc. bond           : bond        0.00042 (    4)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: A  749 ASP cc_start: 0.8383 (t70) cc_final: 0.8158 (t0)
REVERT: B 1077 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8513 (tp30)
REVERT: C    3 ARG cc_start: 0.7826 (mtm110) cc_final: 0.7616 (mtm110)
  outliers start: 12
  outliers final: 3
  residues processed: 67
  average time/residue: 0.5754
  time to fit residues: 40.4453
Evaluate side-chains
  55 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1077 GLU
Chi-restraints excluded: chain C residue   10 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 37 optimal weight:    0.0050
   chunk 63 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.7596

-------------------------------------------------------------------------------
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 = 0.3295 r_free = 0.3295 target = 0.084645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.067628 restraints weight = 24698.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 4.06
r_work: 0.2827 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2817
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2817
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6169  Z= 0.120
  Angle     :  0.526   5.971   8373  Z= 0.272
  Chirality :  0.046   0.200    888
  Planarity :  0.004   0.045   1083
  Dihedral  :  7.896  58.281   1007
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 16.17 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.32), residues: 722
  helix:  1.67 (0.58), residues: 91
  sheet:  0.71 (0.27), residues: 361
  loop : -0.29 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 409 
 TYR   0.012   0.001   TYR A 705 
 PHE   0.011   0.001   PHE B1103 
 TRP   0.010   0.001   TRP A 249 
 HIS   0.002   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6165)
  covalent geometry    : angle       0.52646 ( 8373)
  hydrogen bonds       : bond        0.03249 (  315)
  hydrogen bonds       : angle       4.86339 (  903)
  Misc. bond           : bond        0.00026 (    4)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A  749 ASP cc_start: 0.8350 (t70) cc_final: 0.8137 (t0)
  outliers start: 17
  outliers final: 3
  residues processed: 65
  average time/residue: 0.5843
  time to fit residues: 40.0311
Evaluate side-chains
  57 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1061 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   chunk 14 optimal weight:    0.3980
   chunk 25 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0870
   chunk 62 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.6964

-------------------------------------------------------------------------------
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 = 0.3249 r_free = 0.3249 target = 0.082173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.064540 restraints weight = 31581.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 4.52
r_work: 0.2745 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2739
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6169  Z= 0.210
  Angle     :  0.566   6.510   8373  Z= 0.297
  Chirality :  0.047   0.236    888
  Planarity :  0.004   0.043   1083
  Dihedral  :  7.647  58.142   1007
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.33 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.32), residues: 722
  helix:  1.64 (0.58), residues: 91
  sheet:  0.67 (0.27), residues: 358
  loop : -0.43 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C   3 
 TYR   0.013   0.001   TYR A 705 
 PHE   0.010   0.001   PHE B1103 
 TRP   0.008   0.001   TRP A 249 
 HIS   0.003   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 6165)
  covalent geometry    : angle       0.56575 ( 8373)
  hydrogen bonds       : bond        0.03627 (  315)
  hydrogen bonds       : angle       5.11377 (  903)
  Misc. bond           : bond        0.00053 (    4)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 10
  residues processed: 65
  average time/residue: 0.5899
  time to fit residues: 40.2321
Evaluate side-chains
  63 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  756 ILE
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1048 THR
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1105 SER
Chi-restraints excluded: chain C residue   15 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3276 r_free = 0.3276 target = 0.083566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.066630 restraints weight = 24929.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 4.06
r_work: 0.2803 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2796
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2796 r_free = 0.2796    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2796 r_free = 0.2796    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2796
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6169  Z= 0.133
  Angle     :  0.530   6.449   8373  Z= 0.280
  Chirality :  0.045   0.199    888
  Planarity :  0.004   0.044   1083
  Dihedral  :  7.025  56.184   1007
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.80 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.32), residues: 722
  helix:  1.87 (0.56), residues: 91
  sheet:  0.66 (0.27), residues: 358
  loop : -0.33 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C   3 
 TYR   0.013   0.001   TYR A 705 
 PHE   0.009   0.001   PHE B1103 
 TRP   0.011   0.001   TRP A 249 
 HIS   0.002   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6165)
  covalent geometry    : angle       0.53036 ( 8373)
  hydrogen bonds       : bond        0.03222 (  315)
  hydrogen bonds       : angle       4.91186 (  903)
  Misc. bond           : bond        0.00027 (    4)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: A  476 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7844 (tm-30)
  outliers start: 12
  outliers final: 5
  residues processed: 66
  average time/residue: 0.6159
  time to fit residues: 42.6168
Evaluate side-chains
  60 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain A residue  756 ILE
Chi-restraints excluded: chain B residue 1007 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.081292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.063853 restraints weight = 31742.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 4.49
r_work: 0.2726 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2719
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2719
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   6169  Z= 0.256
  Angle     :  0.607   8.062   8373  Z= 0.320
  Chirality :  0.047   0.215    888
  Planarity :  0.004   0.044   1083
  Dihedral  :  7.505  58.729   1007
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.95 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.32), residues: 722
  helix:  1.82 (0.56), residues: 91
  sheet:  0.54 (0.27), residues: 358
  loop : -0.54 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C   3 
 TYR   0.014   0.001   TYR A 705 
 PHE   0.009   0.001   PHE A 541 
 TRP   0.007   0.001   TRP A 249 
 HIS   0.003   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 6165)
  covalent geometry    : angle       0.60730 ( 8373)
  hydrogen bonds       : bond        0.03828 (  315)
  hydrogen bonds       : angle       5.18413 (  903)
  Misc. bond           : bond        0.00057 (    4)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: B 1050 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8280 (mmtt)
  outliers start: 16
  outliers final: 8
  residues processed: 67
  average time/residue: 0.5919
  time to fit residues: 41.7437
Evaluate side-chains
  65 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1048 THR
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1105 SER
Chi-restraints excluded: chain C residue   15 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 70 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 712 GLN
B1085 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.081935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.064863 restraints weight = 27241.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.2935 rms_B_bonded: 4.21
r_work: 0.2755 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   6169  Z= 0.200
  Angle     :  0.567   6.784   8373  Z= 0.299
  Chirality :  0.046   0.199    888
  Planarity :  0.004   0.043   1083
  Dihedral  :  7.346  58.013   1007
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.95 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.31), residues: 722
  helix:  1.90 (0.57), residues: 91
  sheet:  0.54 (0.27), residues: 356
  loop : -0.57 (0.37), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C   3 
 TYR   0.013   0.001   TYR A 705 
 PHE   0.010   0.001   PHE A 541 
 TRP   0.010   0.001   TRP A 249 
 HIS   0.002   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 6165)
  covalent geometry    : angle       0.56678 ( 8373)
  hydrogen bonds       : bond        0.03565 (  315)
  hydrogen bonds       : angle       5.10250 (  903)
  Misc. bond           : bond        0.00045 (    4)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: B 1050 LYS cc_start: 0.8546 (mmmt) cc_final: 0.8344 (mmtt)
  outliers start: 13
  outliers final: 8
  residues processed: 67
  average time/residue: 0.5790
  time to fit residues: 40.7563
Evaluate side-chains
  65 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1105 SER
Chi-restraints excluded: chain C residue   15 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 8 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 712 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.083038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.065835 restraints weight = 28576.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 4.31
r_work: 0.2776 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2774
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2774 r_free = 0.2774    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2774 r_free = 0.2774    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2774
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6169  Z= 0.133
  Angle     :  0.542   7.161   8373  Z= 0.286
  Chirality :  0.045   0.190    888
  Planarity :  0.004   0.044   1083
  Dihedral  :  7.013  57.700   1007
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 17.43 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.32), residues: 722
  helix:  2.05 (0.57), residues: 91
  sheet:  0.58 (0.27), residues: 347
  loop : -0.43 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C   3 
 TYR   0.013   0.001   TYR A 705 
 PHE   0.008   0.001   PHE B1103 
 TRP   0.012   0.001   TRP A 249 
 HIS   0.004   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6165)
  covalent geometry    : angle       0.54208 ( 8373)
  hydrogen bonds       : bond        0.03247 (  315)
  hydrogen bonds       : angle       4.95862 (  903)
  Misc. bond           : bond        0.00028 (    4)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: A  476 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7912 (tm-30)
REVERT: B 1077 GLU cc_start: 0.8749 (tp30) cc_final: 0.8512 (mm-30)
  outliers start: 12
  outliers final: 6
  residues processed: 67
  average time/residue: 0.5907
  time to fit residues: 41.5569
Evaluate side-chains
  64 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain C residue   15 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3261 r_free = 0.3261 target = 0.082887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.065594 restraints weight = 29682.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 4.37
r_work: 0.2770 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2762
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2762 r_free = 0.2762    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2762 r_free = 0.2762    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2762
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6169  Z= 0.149
  Angle     :  0.532   6.852   8373  Z= 0.282
  Chirality :  0.045   0.185    888
  Planarity :  0.004   0.043   1083
  Dihedral  :  7.013  59.099   1007
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 18.68 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.32), residues: 722
  helix:  2.12 (0.57), residues: 90
  sheet:  0.58 (0.27), residues: 347
  loop : -0.46 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C   3 
 TYR   0.013   0.001   TYR A 705 
 PHE   0.011   0.001   PHE B1103 
 TRP   0.011   0.001   TRP A 249 
 HIS   0.003   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6165)
  covalent geometry    : angle       0.53216 ( 8373)
  hydrogen bonds       : bond        0.03319 (  315)
  hydrogen bonds       : angle       4.96503 (  903)
  Misc. bond           : bond        0.00033 (    4)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A  476 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7921 (tm-30)
REVERT: B 1077 GLU cc_start: 0.8762 (tp30) cc_final: 0.8550 (mm-30)
  outliers start: 7
  outliers final: 7
  residues processed: 62
  average time/residue: 0.5789
  time to fit residues: 37.7360
Evaluate side-chains
  65 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1105 SER
Chi-restraints excluded: chain C residue   15 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0970
   chunk 24 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.7578

-------------------------------------------------------------------------------
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 = 0.3270 r_free = 0.3270 target = 0.083347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.066407 restraints weight = 25152.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 4.06
r_work: 0.2797 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2799
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2799 r_free = 0.2799    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2799 r_free = 0.2799    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2799
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6169  Z= 0.127
  Angle     :  0.549   9.929   8373  Z= 0.288
  Chirality :  0.044   0.179    888
  Planarity :  0.004   0.044   1083
  Dihedral  :  6.908  59.497   1007
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 17.74 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.32), residues: 722
  helix:  2.15 (0.57), residues: 90
  sheet:  0.59 (0.27), residues: 349
  loop : -0.40 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C   3 
 TYR   0.012   0.001   TYR A 705 
 PHE   0.011   0.001   PHE B1103 
 TRP   0.011   0.001   TRP A 249 
 HIS   0.002   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6165)
  covalent geometry    : angle       0.54933 ( 8373)
  hydrogen bonds       : bond        0.03210 (  315)
  hydrogen bonds       : angle       4.90626 (  903)
  Misc. bond           : bond        0.00025 (    4)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: A  476 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7894 (tm-30)
REVERT: B 1050 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8304 (mmtt)
REVERT: B 1077 GLU cc_start: 0.8751 (tp30) cc_final: 0.8518 (mm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 64
  average time/residue: 0.5573
  time to fit residues: 37.4952
Evaluate side-chains
  65 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain B residue 1007 THR
Chi-restraints excluded: chain B residue 1061 SER
Chi-restraints excluded: chain B residue 1105 SER
Chi-restraints excluded: chain B residue 1117 ASP
Chi-restraints excluded: chain C residue   15 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0980
   chunk 7 optimal weight:    0.3980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 712 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.083914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.067142 restraints weight = 23614.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 3.94
r_work: 0.2817 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2814
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2814
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6169  Z= 0.118
  Angle     :  0.554   9.598   8373  Z= 0.287
  Chirality :  0.044   0.178    888
  Planarity :  0.004   0.044   1083
  Dihedral  :  6.800  59.748   1007
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 18.37 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.32), residues: 722
  helix:  2.17 (0.57), residues: 90
  sheet:  0.60 (0.27), residues: 349
  loop : -0.40 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C   3 
 TYR   0.012   0.001   TYR A 705 
 PHE   0.011   0.001   PHE B1103 
 TRP   0.012   0.001   TRP A 249 
 HIS   0.003   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6165)
  covalent geometry    : angle       0.55362 ( 8373)
  hydrogen bonds       : bond        0.03144 (  315)
  hydrogen bonds       : angle       4.85542 (  903)
  Misc. bond           : bond        0.00023 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2092.73 seconds
wall clock time: 36 minutes 32.12 seconds (2192.12 seconds total)