Starting phenix.real_space_refine
on Tue Mar  3 19:44:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zz6_15036/03_2026/7zz6_15036.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zz6_15036/03_2026/7zz6_15036.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zz6_15036/03_2026/7zz6_15036.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zz6_15036/03_2026/7zz6_15036.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zz6_15036/03_2026/7zz6_15036.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zz6_15036/03_2026/7zz6_15036.map"
  }
  resolution = 2.15
  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=   0.015
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
     Mn      2      7.51       5
     Mg      2      5.21       5
     S      36      5.16       5
     C    5148      2.51       5
     N    1367      2.21       5
     O    1702      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8257
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "D"
      Number of atoms: 4047
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 509, 4047
          Classifications: {'peptide': 509}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 485}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 4037
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 508, 4037
          Classifications: {'peptide': 508}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 484}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 8
          Unusual residues: {' MG': 1, ' MN': 1, 'PYR': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 8
          Unusual residues: {' MG': 1, ' MN': 1, 'PYR': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 99
          Classifications: {'water': 99}
          Link IDs: {None: 98}
    Chain: "A"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 58
          Classifications: {'water': 58}
          Link IDs: {None: 57}
  Time building chain proxies: 2.23, per 1000 atoms: 0.27
  Number of scatterers: 8257
  At special positions: 0
  Unit cell: (96.46, 71.02, 110.24, 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)
     Mn      2     24.99
     S      36     16.00
     Mg      2     11.99
     O    1702      8.00
     N    1367      7.00
     C    5148      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: 0.72
  Conformation dependent library (CDL) restraints added in 298.7 milliseconds
  

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1894

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 2 sheets defined
      62.1% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'D' and resid 502 through 511
    Processing helix  chain 'D' and resid 511 through 522
    Processing helix  chain 'D' and resid 533 through 540
    Processing helix  chain 'D' and resid 545 through 560
      removed outlier: 3.709A  pdb=" N   GLY D 551 " --> pdb=" O   GLN D 547 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   ILE D 552 " --> pdb=" O   ASP D 548 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   GLN D 554 " --> pdb=" O   LYS D 550 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   ALA D 555 " --> pdb=" O   GLY D 551 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 572 through 580
      removed outlier: 3.712A  pdb=" N   TYR D 578 " --> pdb=" O   PHE D 574 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 584 through 596
    Processing helix  chain 'D' and resid 617 through 631
    Processing helix  chain 'D' and resid 645 through 658
      removed outlier: 4.723A  pdb=" N   LYS D 650 " --> pdb=" O   PRO D 646 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   SER D 651 " --> pdb=" O   GLN D 647 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 681 through 695
    Processing helix  chain 'D' and resid 710 through 725
    Processing helix  chain 'D' and resid 739 through 751
    Processing helix  chain 'D' and resid 759 through 763
    Processing helix  chain 'D' and resid 770 through 778
    Processing helix  chain 'D' and resid 788 through 804
      removed outlier: 3.640A  pdb=" N   HIS D 797 " --> pdb=" O   GLU D 793 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   TYR D 798 " --> pdb=" O   GLN D 794 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LYS D 804 " --> pdb=" O   GLU D 800 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 805 through 810
      Proline residue:  D 808  - end of helix
      No H-bonds generated for 'chain 'D' and resid 805 through 810'
    Processing helix  chain 'D' and resid 817 through 822
      removed outlier: 3.572A  pdb=" N   VAL D 820 " --> pdb=" O   GLN D 817 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 826 through 841
    Processing helix  chain 'D' and resid 842 through 844
      No H-bonds generated for 'chain 'D' and resid 842 through 844'
    Processing helix  chain 'D' and resid 845 through 860
    Processing helix  chain 'D' and resid 868 through 883
      removed outlier: 3.565A  pdb=" N   VAL D 872 " --> pdb=" O   PRO D 868 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 886 through 893
    Processing helix  chain 'D' and resid 894 through 897
    Processing helix  chain 'D' and resid 900 through 908
    Processing helix  chain 'D' and resid 919 through 927
    Processing helix  chain 'D' and resid 936 through 941
    Processing helix  chain 'D' and resid 945 through 957
    Processing helix  chain 'D' and resid 962 through 972
    Processing helix  chain 'D' and resid 972 through 987
    Processing helix  chain 'D' and resid 988 through 992
    Processing helix  chain 'A' and resid 502 through 511
    Processing helix  chain 'A' and resid 511 through 522
    Processing helix  chain 'A' and resid 533 through 540
    Processing helix  chain 'A' and resid 545 through 560
      removed outlier: 3.698A  pdb=" N   GLY A 551 " --> pdb=" O   GLN A 547 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ILE A 552 " --> pdb=" O   ASP A 548 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   GLN A 554 " --> pdb=" O   LYS A 550 " (cutoff:3.500A)
      removed outlier: 5.717A  pdb=" N   ALA A 555 " --> pdb=" O   GLY A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 580
      removed outlier: 3.776A  pdb=" N   TYR A 578 " --> pdb=" O   PHE A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 596
    Processing helix  chain 'A' and resid 617 through 632
    Processing helix  chain 'A' and resid 645 through 658
      removed outlier: 4.628A  pdb=" N   LYS A 650 " --> pdb=" O   PRO A 646 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   SER A 651 " --> pdb=" O   GLN A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 695
    Processing helix  chain 'A' and resid 710 through 723
    Processing helix  chain 'A' and resid 739 through 751
    Processing helix  chain 'A' and resid 759 through 763
    Processing helix  chain 'A' and resid 770 through 778
    Processing helix  chain 'A' and resid 788 through 804
      removed outlier: 3.626A  pdb=" N   HIS A 797 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   TYR A 798 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LYS A 804 " --> pdb=" O   GLU A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 810
      Proline residue:  A 808  - end of helix
      No H-bonds generated for 'chain 'A' and resid 805 through 810'
    Processing helix  chain 'A' and resid 817 through 822
      removed outlier: 3.621A  pdb=" N   VAL A 820 " --> pdb=" O   GLN A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 839
    Processing helix  chain 'A' and resid 840 through 841
      No H-bonds generated for 'chain 'A' and resid 840 through 841'
    Processing helix  chain 'A' and resid 842 through 844
      No H-bonds generated for 'chain 'A' and resid 842 through 844'
    Processing helix  chain 'A' and resid 845 through 861
    Processing helix  chain 'A' and resid 868 through 883
      removed outlier: 3.594A  pdb=" N   VAL A 872 " --> pdb=" O   PRO A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 886 through 893
    Processing helix  chain 'A' and resid 894 through 896
      No H-bonds generated for 'chain 'A' and resid 894 through 896'
    Processing helix  chain 'A' and resid 900 through 908
    Processing helix  chain 'A' and resid 919 through 928
    Processing helix  chain 'A' and resid 936 through 941
    Processing helix  chain 'A' and resid 945 through 957
    Processing helix  chain 'A' and resid 962 through 972
    Processing helix  chain 'A' and resid 972 through 987
    Processing helix  chain 'A' and resid 988 through 992
    Processing sheet with id=AA1, first strand: chain 'D' and resid 526 through 529
      removed outlier: 6.818A  pdb=" N   LEU D 527 " --> pdb=" O   SER D 565 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   GLU D 567 " --> pdb=" O   LEU D 527 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ASP D 529 " --> pdb=" O   GLU D 567 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   TRP D 569 " --> pdb=" O   ASP D 529 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ALA D 566 " --> pdb=" O   GLN D 602 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   LEU D 604 " --> pdb=" O   ALA D 566 " (cutoff:3.500A)
      removed outlier: 8.769A  pdb=" N   MET D 568 " --> pdb=" O   LEU D 604 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   THR D 733 " --> pdb=" O   ASP D 756 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   LEU D 526 " --> pdb=" O   ILE D 755 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   VAL D 757 " --> pdb=" O   LEU D 526 " (cutoff:3.500A)
      removed outlier: 5.668A  pdb=" N   THR D 528 " --> pdb=" O   VAL D 757 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 526 through 529
      removed outlier: 6.835A  pdb=" N   LEU A 527 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   GLU A 567 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ASP A 529 " --> pdb=" O   GLU A 567 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   TRP A 569 " --> pdb=" O   ASP A 529 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   ALA A 566 " --> pdb=" O   GLN A 602 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   LEU A 604 " --> pdb=" O   ALA A 566 " (cutoff:3.500A)
      removed outlier: 8.845A  pdb=" N   MET A 568 " --> pdb=" O   LEU A 604 " (cutoff:3.500A)
      removed outlier: 5.107A  pdb=" N   THR A 733 " --> pdb=" O   ASP A 756 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   LEU A 526 " --> pdb=" O   ILE A 755 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   VAL A 757 " --> pdb=" O   LEU A 526 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   THR A 528 " --> pdb=" O   VAL A 757 " (cutoff:3.500A)

    422 hydrogen bonds defined for protein.
    1191 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: 1.40

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2694
        1.34 -     1.46: 1840
        1.46 -     1.58: 3665
        1.58 -     1.70: 0
        1.70 -     1.82: 70
  Bond restraints: 8269
  Sorted by residual:
  bond pdb=" C1  PYR A1203 "
       pdb=" C2  PYR A1203 "
    ideal  model  delta    sigma   weight residual
    1.558  1.389  0.169 2.00e-02 2.50e+03 7.15e+01
  bond pdb=" C1  PYR D1203 "
       pdb=" C2  PYR D1203 "
    ideal  model  delta    sigma   weight residual
    1.558  1.393  0.165 2.00e-02 2.50e+03 6.84e+01
  bond pdb=" C2  PYR A1203 "
       pdb=" O3  PYR A1203 "
    ideal  model  delta    sigma   weight residual
    1.210  1.309 -0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" C2  PYR D1203 "
       pdb=" O3  PYR D1203 "
    ideal  model  delta    sigma   weight residual
    1.210  1.308 -0.098 2.00e-02 2.50e+03 2.41e+01
  bond pdb=" NZ  KCX A 703 "
       pdb=" CX  KCX A 703 "
    ideal  model  delta    sigma   weight residual
    1.411  1.324  0.087 2.00e-02 2.50e+03 1.91e+01
  ... (remaining 8264 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 11066
        2.51 -     5.03: 109
        5.03 -     7.54: 11
        7.54 -    10.05: 6
       10.05 -    12.57: 1
  Bond angle restraints: 11193
  Sorted by residual:
  angle pdb=" CB  MET D 858 "
        pdb=" CG  MET D 858 "
        pdb=" SD  MET D 858 "
      ideal   model   delta    sigma   weight residual
     112.70  125.27  -12.57 3.00e+00 1.11e-01 1.75e+01
  angle pdb=" CB  MET D 982 "
        pdb=" CG  MET D 982 "
        pdb=" SD  MET D 982 "
      ideal   model   delta    sigma   weight residual
     112.70  122.56   -9.86 3.00e+00 1.11e-01 1.08e+01
  angle pdb=" O1  PYR D1203 "
        pdb=" C1  PYR D1203 "
        pdb=" O2  PYR D1203 "
      ideal   model   delta    sigma   weight residual
     129.19  119.71    9.48 3.00e+00 1.11e-01 9.98e+00
  angle pdb=" O1  PYR A1203 "
        pdb=" C1  PYR A1203 "
        pdb=" O2  PYR A1203 "
      ideal   model   delta    sigma   weight residual
     129.19  120.00    9.19 3.00e+00 1.11e-01 9.39e+00
  angle pdb=" CB  MET A 568 "
        pdb=" CG  MET A 568 "
        pdb=" SD  MET A 568 "
      ideal   model   delta    sigma   weight residual
     112.70  121.75   -9.05 3.00e+00 1.11e-01 9.11e+00
  ... (remaining 11188 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 4355
       17.86 -    35.72: 443
       35.72 -    53.58: 132
       53.58 -    71.44: 32
       71.44 -    89.30: 21
  Dihedral angle restraints: 4983
    sinusoidal: 2026
      harmonic: 2957
  Sorted by residual:
  dihedral pdb=" CA  ASP A 929 "
           pdb=" C   ASP A 929 "
           pdb=" N   LYS A 930 "
           pdb=" CA  LYS A 930 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.71  -23.29     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  LEU D 778 "
           pdb=" C   LEU D 778 "
           pdb=" N   GLU D 779 "
           pdb=" CA  GLU D 779 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.43  -18.57     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  LEU A 778 "
           pdb=" C   LEU A 778 "
           pdb=" N   GLU A 779 "
           pdb=" CA  GLU A 779 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.03  -17.97     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 4980 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 596
       0.029 -    0.057: 385
       0.057 -    0.086: 162
       0.086 -    0.114: 66
       0.114 -    0.143: 12
  Chirality restraints: 1221
  Sorted by residual:
  chirality pdb=" CA  VAL A 866 "
            pdb=" N   VAL A 866 "
            pdb=" C   VAL A 866 "
            pdb=" CB  VAL A 866 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.10e-01
  chirality pdb=" CA  VAL D 866 "
            pdb=" N   VAL D 866 "
            pdb=" C   VAL D 866 "
            pdb=" CB  VAL D 866 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.36e-01
  chirality pdb=" CA  ILE D 666 "
            pdb=" N   ILE D 666 "
            pdb=" C   ILE D 666 "
            pdb=" CB  ILE D 666 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  ... (remaining 1218 not shown)

  Planarity restraints: 1466
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG D 533 "    0.007 2.00e-02 2.50e+03   1.44e-02 2.09e+00
        pdb=" C   ARG D 533 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   ARG D 533 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ASP D 534 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 533 "   -0.007 2.00e-02 2.50e+03   1.42e-02 2.01e+00
        pdb=" C   ARG A 533 "    0.025 2.00e-02 2.50e+03
        pdb=" O   ARG A 533 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASP A 534 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 867 "   -0.021 5.00e-02 4.00e+02   3.15e-02 1.59e+00
        pdb=" N   PRO D 868 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO D 868 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO D 868 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1463 not shown)

  Histogram of nonbonded interaction distances:
        1.38 -     2.09: 3
        2.09 -     2.79: 2245
        2.79 -     3.49: 12466
        3.49 -     4.20: 22577
        4.20 -     4.90: 37839
  Nonbonded interactions: 75130
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 753 "
            pdb="MG    MG A1201 "
     model   vdw
     1.385 2.170
  nonbonded pdb=" NE2 HIS A 732 "
            pdb="MN    MN A1202 "
     model   vdw
     1.835 2.400
  nonbonded pdb=" NE2 HIS D 732 "
            pdb="MN    MN D1202 "
     model   vdw
     1.838 2.400
  nonbonded pdb=" OD1 ASP A 753 "
            pdb=" O   HOH A1301 "
     model   vdw
     2.143 3.040
  nonbonded pdb="MN    MN D1202 "
            pdb=" O   HOH D1335 "
     model   vdw
     2.193 2.320
  ... (remaining 75125 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'D' and resid 487 through 1203)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.260
  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:             0.020
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.110
  Find NCS groups from input model:        0.130
  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:6.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8769
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      :  0.006   0.169   8269  Z= 0.303
  Angle     :  0.682  12.566  11193  Z= 0.359
  Chirality :  0.045   0.143   1221
  Planarity :  0.003   0.032   1466
  Dihedral  : 17.300  89.298   3089
  Min Nonbonded Distance : 1.385

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 15.91 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.64 (0.26), residues: 1007
  helix:  1.07 (0.22), residues: 530
  sheet: -0.96 (0.47), residues: 86
  loop :  0.02 (0.33), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 845 
 TYR   0.011   0.002   TYR D 853 
 PHE   0.013   0.002   PHE D 907 
 TRP   0.007   0.002   TRP D 586 
 HIS   0.005   0.001   HIS D 732 

Details of bonding type rmsd
  covalent geometry    : bond        0.00645 ( 8269)
  covalent geometry    : angle       0.68206 (11193)
  hydrogen bonds       : bond        0.13022 (  422)
  hydrogen bonds       : angle       6.73380 ( 1191)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 48
  time to evaluate  : 0.311 
Fit side-chains
  outliers start: 30
  outliers final: 26
  residues processed: 75
  average time/residue: 0.4645
  time to fit residues: 37.6159
Evaluate side-chains
  73 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 47
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  494 LEU
Chi-restraints excluded: chain D residue  500 LYS
Chi-restraints excluded: chain D residue  569 TRP
Chi-restraints excluded: chain D residue  736 THR
Chi-restraints excluded: chain D residue  757 VAL
Chi-restraints excluded: chain D residue  770 SER
Chi-restraints excluded: chain D residue  814 THR
Chi-restraints excluded: chain D residue  849 ILE
Chi-restraints excluded: chain D residue  883 ASN
Chi-restraints excluded: chain D residue  886 THR
Chi-restraints excluded: chain D residue  928 LYS
Chi-restraints excluded: chain D residue  934 THR
Chi-restraints excluded: chain D residue  948 THR
Chi-restraints excluded: chain D residue  967 ILE
Chi-restraints excluded: chain D residue  982 MET
Chi-restraints excluded: chain A residue  569 TRP
Chi-restraints excluded: chain A residue  609 ASN
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  770 SER
Chi-restraints excluded: chain A residue  849 ILE
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  934 THR
Chi-restraints excluded: chain A residue  948 THR
Chi-restraints excluded: chain A residue  967 ILE
Chi-restraints excluded: chain A residue  993 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3337 r_free = 0.3337 target = 0.061918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.053076 restraints weight = 20646.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 1.30
r_work: 0.2952 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8972
moved from start:          0.0921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8269  Z= 0.136
  Angle     :  0.517   6.355  11193  Z= 0.277
  Chirality :  0.041   0.154   1221
  Planarity :  0.004   0.033   1466
  Dihedral  :  6.946  52.135   1165
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 14.75 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.95 (0.27), residues: 1007
  helix:  1.27 (0.22), residues: 545
  sheet: -0.90 (0.49), residues: 86
  loop :  0.23 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 593 
 TYR   0.008   0.001   TYR A 806 
 PHE   0.013   0.001   PHE D 879 
 TRP   0.004   0.001   TRP D 644 
 HIS   0.005   0.001   HIS D 732 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8269)
  covalent geometry    : angle       0.51698 (11193)
  hydrogen bonds       : bond        0.04507 (  422)
  hydrogen bonds       : angle       5.47407 ( 1191)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 50
  time to evaluate  : 0.314 
Fit side-chains
REVERT: D  929 ASP cc_start: 0.7849 (p0) cc_final: 0.7646 (p0)
  outliers start: 27
  outliers final: 12
  residues processed: 72
  average time/residue: 0.5281
  time to fit residues: 40.7632
Evaluate side-chains
  60 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  569 TRP
Chi-restraints excluded: chain D residue  705 MET
Chi-restraints excluded: chain D residue  736 THR
Chi-restraints excluded: chain D residue  849 ILE
Chi-restraints excluded: chain D residue  967 ILE
Chi-restraints excluded: chain A residue  569 TRP
Chi-restraints excluded: chain A residue  609 ASN
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  849 ILE
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  967 ILE
Chi-restraints excluded: chain A residue  993 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 76 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.1384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.061277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.052240 restraints weight = 20496.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 1.31
r_work: 0.2927 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8993
moved from start:          0.0913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8269  Z= 0.173
  Angle     :  0.541   5.518  11193  Z= 0.289
  Chirality :  0.042   0.153   1221
  Planarity :  0.004   0.038   1466
  Dihedral  :  6.616  51.638   1140
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 14.05 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.96 (0.27), residues: 1007
  helix:  1.34 (0.22), residues: 545
  sheet: -0.95 (0.49), residues: 86
  loop :  0.15 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 593 
 TYR   0.009   0.001   TYR A 685 
 PHE   0.013   0.001   PHE D 879 
 TRP   0.005   0.001   TRP D 799 
 HIS   0.004   0.001   HIS A 536 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 8269)
  covalent geometry    : angle       0.54055 (11193)
  hydrogen bonds       : bond        0.04796 (  422)
  hydrogen bonds       : angle       5.42817 ( 1191)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 48
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  845 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7852 (ptm160)
REVERT: A  893 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7853 (ttt90)
  outliers start: 28
  outliers final: 15
  residues processed: 68
  average time/residue: 0.5111
  time to fit residues: 37.5578
Evaluate side-chains
  62 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 45
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  494 LEU
Chi-restraints excluded: chain D residue  569 TRP
Chi-restraints excluded: chain D residue  609 ASN
Chi-restraints excluded: chain D residue  705 MET
Chi-restraints excluded: chain D residue  736 THR
Chi-restraints excluded: chain D residue  745 SER
Chi-restraints excluded: chain D residue  849 ILE
Chi-restraints excluded: chain D residue  967 ILE
Chi-restraints excluded: chain A residue  569 TRP
Chi-restraints excluded: chain A residue  609 ASN
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  845 ARG
Chi-restraints excluded: chain A residue  849 ILE
Chi-restraints excluded: chain A residue  893 ARG
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  967 ILE
Chi-restraints excluded: chain A residue  993 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 92 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
D 882 GLN
A 829 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.061850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.052807 restraints weight = 20909.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 1.33
r_work: 0.2943 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8979
moved from start:          0.1069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8269  Z= 0.146
  Angle     :  0.517   7.784  11193  Z= 0.274
  Chirality :  0.041   0.152   1221
  Planarity :  0.004   0.039   1466
  Dihedral  :  6.434  51.577   1140
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 13.94 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.05 (0.27), residues: 1007
  helix:  1.41 (0.22), residues: 547
  sheet: -0.94 (0.51), residues: 86
  loop :  0.20 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 593 
 TYR   0.009   0.001   TYR D 685 
 PHE   0.013   0.001   PHE D 879 
 TRP   0.004   0.001   TRP D 799 
 HIS   0.004   0.001   HIS A 536 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8269)
  covalent geometry    : angle       0.51657 (11193)
  hydrogen bonds       : bond        0.04410 (  422)
  hydrogen bonds       : angle       5.26168 ( 1191)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 48
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  845 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7847 (ptm160)
  outliers start: 26
  outliers final: 15
  residues processed: 70
  average time/residue: 0.4892
  time to fit residues: 36.8658
Evaluate side-chains
  62 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 46
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  494 LEU
Chi-restraints excluded: chain D residue  569 TRP
Chi-restraints excluded: chain D residue  609 ASN
Chi-restraints excluded: chain D residue  705 MET
Chi-restraints excluded: chain D residue  736 THR
Chi-restraints excluded: chain D residue  745 SER
Chi-restraints excluded: chain D residue  771 MET
Chi-restraints excluded: chain D residue  849 ILE
Chi-restraints excluded: chain D residue  967 ILE
Chi-restraints excluded: chain A residue  569 TRP
Chi-restraints excluded: chain A residue  609 ASN
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  845 ARG
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  967 ILE
Chi-restraints excluded: chain A residue  993 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 79 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
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 = 0.3308 r_free = 0.3308 target = 0.060649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.051522 restraints weight = 20573.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.31
r_work: 0.2907 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9009
moved from start:          0.0874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8269  Z= 0.223
  Angle     :  0.580   8.002  11193  Z= 0.309
  Chirality :  0.044   0.153   1221
  Planarity :  0.004   0.038   1466
  Dihedral  :  6.705  51.028   1138
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 14.05 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.95 (0.27), residues: 1007
  helix:  1.34 (0.22), residues: 546
  sheet: -1.00 (0.50), residues: 86
  loop :  0.13 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 593 
 TYR   0.012   0.002   TYR A 685 
 PHE   0.014   0.002   PHE D 879 
 TRP   0.006   0.001   TRP D 644 
 HIS   0.006   0.001   HIS A 536 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 8269)
  covalent geometry    : angle       0.58007 (11193)
  hydrogen bonds       : bond        0.05179 (  422)
  hydrogen bonds       : angle       5.46929 ( 1191)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 48
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  845 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7848 (ptm160)
  outliers start: 26
  outliers final: 16
  residues processed: 67
  average time/residue: 0.4919
  time to fit residues: 35.7115
Evaluate side-chains
  63 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 46
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  494 LEU
Chi-restraints excluded: chain D residue  569 TRP
Chi-restraints excluded: chain D residue  600 MET
Chi-restraints excluded: chain D residue  609 ASN
Chi-restraints excluded: chain D residue  705 MET
Chi-restraints excluded: chain D residue  736 THR
Chi-restraints excluded: chain D residue  745 SER
Chi-restraints excluded: chain D residue  849 ILE
Chi-restraints excluded: chain D residue  967 ILE
Chi-restraints excluded: chain A residue  569 TRP
Chi-restraints excluded: chain A residue  609 ASN
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  845 ARG
Chi-restraints excluded: chain A residue  849 ILE
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  967 ILE
Chi-restraints excluded: chain A residue  993 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 99 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3312 r_free = 0.3312 target = 0.060793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.051656 restraints weight = 20268.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 1.31
r_work: 0.2913 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9004
moved from start:          0.0916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8269  Z= 0.210
  Angle     :  0.572   8.032  11193  Z= 0.303
  Chirality :  0.044   0.152   1221
  Planarity :  0.004   0.037   1466
  Dihedral  :  6.677  51.073   1138
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 13.94 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.92 (0.27), residues: 1007
  helix:  1.35 (0.22), residues: 545
  sheet: -1.00 (0.50), residues: 86
  loop :  0.07 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 593 
 TYR   0.011   0.001   TYR A 685 
 PHE   0.014   0.002   PHE D 879 
 TRP   0.005   0.001   TRP D 799 
 HIS   0.005   0.001   HIS A 536 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 8269)
  covalent geometry    : angle       0.57192 (11193)
  hydrogen bonds       : bond        0.05045 (  422)
  hydrogen bonds       : angle       5.42445 ( 1191)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 47
  time to evaluate  : 0.332 
Fit side-chains
  outliers start: 26
  outliers final: 17
  residues processed: 65
  average time/residue: 0.4778
  time to fit residues: 33.5900
Evaluate side-chains
  63 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 46
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  494 LEU
Chi-restraints excluded: chain D residue  569 TRP
Chi-restraints excluded: chain D residue  600 MET
Chi-restraints excluded: chain D residue  609 ASN
Chi-restraints excluded: chain D residue  705 MET
Chi-restraints excluded: chain D residue  736 THR
Chi-restraints excluded: chain D residue  745 SER
Chi-restraints excluded: chain D residue  849 ILE
Chi-restraints excluded: chain D residue  858 MET
Chi-restraints excluded: chain D residue  967 ILE
Chi-restraints excluded: chain A residue  569 TRP
Chi-restraints excluded: chain A residue  609 ASN
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  849 ILE
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  967 ILE
Chi-restraints excluded: chain A residue  993 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 69 optimal weight:    0.4980
   chunk 87 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3332 r_free = 0.3332 target = 0.061597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.052574 restraints weight = 20619.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 1.31
r_work: 0.2938 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8986
moved from start:          0.1058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8269  Z= 0.157
  Angle     :  0.545   9.776  11193  Z= 0.285
  Chirality :  0.042   0.154   1221
  Planarity :  0.004   0.038   1466
  Dihedral  :  6.448  50.794   1138
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 14.52 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.06 (0.27), residues: 1007
  helix:  1.48 (0.22), residues: 545
  sheet: -0.99 (0.50), residues: 86
  loop :  0.12 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 893 
 TYR   0.009   0.001   TYR A 685 
 PHE   0.013   0.001   PHE D 879 
 TRP   0.004   0.001   TRP D 799 
 HIS   0.004   0.001   HIS D 732 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 8269)
  covalent geometry    : angle       0.54513 (11193)
  hydrogen bonds       : bond        0.04523 (  422)
  hydrogen bonds       : angle       5.26306 ( 1191)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 47
  time to evaluate  : 0.396 
Fit side-chains
  outliers start: 23
  outliers final: 17
  residues processed: 62
  average time/residue: 0.4452
  time to fit residues: 30.2276
Evaluate side-chains
  62 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 45
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  494 LEU
Chi-restraints excluded: chain D residue  569 TRP
Chi-restraints excluded: chain D residue  609 ASN
Chi-restraints excluded: chain D residue  705 MET
Chi-restraints excluded: chain D residue  736 THR
Chi-restraints excluded: chain D residue  745 SER
Chi-restraints excluded: chain D residue  771 MET
Chi-restraints excluded: chain D residue  849 ILE
Chi-restraints excluded: chain D residue  858 MET
Chi-restraints excluded: chain D residue  967 ILE
Chi-restraints excluded: chain A residue  569 TRP
Chi-restraints excluded: chain A residue  609 ASN
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  849 ILE
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  967 ILE
Chi-restraints excluded: chain A residue  993 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3332 r_free = 0.3332 target = 0.061580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.052518 restraints weight = 20485.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 1.31
r_work: 0.2939 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8985
moved from start:          0.1071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8269  Z= 0.158
  Angle     :  0.555  10.674  11193  Z= 0.288
  Chirality :  0.042   0.154   1221
  Planarity :  0.004   0.038   1466
  Dihedral  :  6.386  50.649   1138
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.21 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.27), residues: 1007
  helix:  1.48 (0.22), residues: 545
  sheet: -0.98 (0.50), residues: 86
  loop :  0.13 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 893 
 TYR   0.009   0.001   TYR D 685 
 PHE   0.013   0.001   PHE D 879 
 TRP   0.004   0.001   TRP D 799 
 HIS   0.005   0.001   HIS A 536 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8269)
  covalent geometry    : angle       0.55538 (11193)
  hydrogen bonds       : bond        0.04544 (  422)
  hydrogen bonds       : angle       5.26694 ( 1191)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 47
  time to evaluate  : 0.311 
Fit side-chains
  outliers start: 20
  outliers final: 18
  residues processed: 60
  average time/residue: 0.4872
  time to fit residues: 31.7099
Evaluate side-chains
  64 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  494 LEU
Chi-restraints excluded: chain D residue  569 TRP
Chi-restraints excluded: chain D residue  609 ASN
Chi-restraints excluded: chain D residue  705 MET
Chi-restraints excluded: chain D residue  736 THR
Chi-restraints excluded: chain D residue  745 SER
Chi-restraints excluded: chain D residue  771 MET
Chi-restraints excluded: chain D residue  825 MET
Chi-restraints excluded: chain D residue  849 ILE
Chi-restraints excluded: chain D residue  858 MET
Chi-restraints excluded: chain D residue  967 ILE
Chi-restraints excluded: chain A residue  569 TRP
Chi-restraints excluded: chain A residue  609 ASN
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  849 ILE
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  967 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 30 optimal weight:    0.2980
   chunk 3 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0970
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.3359 r_free = 0.3359 target = 0.062583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.053649 restraints weight = 20712.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 1.31
r_work: 0.2974 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8956
moved from start:          0.1306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8269  Z= 0.121
  Angle     :  0.529  11.452  11193  Z= 0.271
  Chirality :  0.041   0.153   1221
  Planarity :  0.004   0.037   1466
  Dihedral  :  6.011  50.407   1136
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.10 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.21 (0.27), residues: 1007
  helix:  1.59 (0.22), residues: 547
  sheet: -0.94 (0.51), residues: 86
  loop :  0.19 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 893 
 TYR   0.008   0.001   TYR D 853 
 PHE   0.013   0.001   PHE D 879 
 TRP   0.004   0.001   TRP D 644 
 HIS   0.005   0.001   HIS D 732 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8269)
  covalent geometry    : angle       0.52889 (11193)
  hydrogen bonds       : bond        0.04006 (  422)
  hydrogen bonds       : angle       5.08761 ( 1191)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 49
  time to evaluate  : 0.331 
Fit side-chains
  outliers start: 19
  outliers final: 10
  residues processed: 62
  average time/residue: 0.4606
  time to fit residues: 30.9906
Evaluate side-chains
  56 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  494 LEU
Chi-restraints excluded: chain D residue  569 TRP
Chi-restraints excluded: chain D residue  609 ASN
Chi-restraints excluded: chain D residue  705 MET
Chi-restraints excluded: chain D residue  736 THR
Chi-restraints excluded: chain D residue  967 ILE
Chi-restraints excluded: chain A residue  569 TRP
Chi-restraints excluded: chain A residue  609 ASN
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  967 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9980
   chunk 94 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
D 882 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.061674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.052798 restraints weight = 20621.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 1.30
r_work: 0.2949 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8975
moved from start:          0.1192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8269  Z= 0.151
  Angle     :  0.563  11.559  11193  Z= 0.288
  Chirality :  0.042   0.154   1221
  Planarity :  0.004   0.038   1466
  Dihedral  :  6.095  50.544   1133
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 15.80 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.21 (0.27), residues: 1007
  helix:  1.61 (0.22), residues: 545
  sheet: -0.95 (0.51), residues: 86
  loop :  0.18 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 593 
 TYR   0.009   0.001   TYR D 685 
 PHE   0.012   0.001   PHE D 879 
 TRP   0.004   0.001   TRP D 799 
 HIS   0.005   0.001   HIS A 536 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8269)
  covalent geometry    : angle       0.56253 (11193)
  hydrogen bonds       : bond        0.04408 (  422)
  hydrogen bonds       : angle       5.19659 ( 1191)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.343 
Fit side-chains
  outliers start: 11
  outliers final: 11
  residues processed: 56
  average time/residue: 0.5091
  time to fit residues: 30.8966
Evaluate side-chains
  57 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  494 LEU
Chi-restraints excluded: chain D residue  569 TRP
Chi-restraints excluded: chain D residue  609 ASN
Chi-restraints excluded: chain D residue  705 MET
Chi-restraints excluded: chain D residue  736 THR
Chi-restraints excluded: chain D residue  967 ILE
Chi-restraints excluded: chain A residue  569 TRP
Chi-restraints excluded: chain A residue  609 ASN
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  849 ILE
Chi-restraints excluded: chain A residue  967 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 83 optimal weight:    0.4980
   chunk 5 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 = 0.3310 r_free = 0.3310 target = 0.060702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.051582 restraints weight = 20607.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 1.31
r_work: 0.2910 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9005
moved from start:          0.0972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8269  Z= 0.229
  Angle     :  0.621  11.532  11193  Z= 0.323
  Chirality :  0.044   0.153   1221
  Planarity :  0.004   0.038   1466
  Dihedral  :  6.466  50.642   1133
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.33 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.05 (0.27), residues: 1007
  helix:  1.49 (0.22), residues: 545
  sheet: -1.00 (0.50), residues: 86
  loop :  0.08 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 593 
 TYR   0.012   0.002   TYR A 853 
 PHE   0.016   0.002   PHE D 879 
 TRP   0.006   0.002   TRP D 799 
 HIS   0.006   0.001   HIS A 536 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 ( 8269)
  covalent geometry    : angle       0.62102 (11193)
  hydrogen bonds       : bond        0.05165 (  422)
  hydrogen bonds       : angle       5.42561 ( 1191)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2757.53 seconds
wall clock time: 47 minutes 44.22 seconds (2864.22 seconds total)