Starting phenix.real_space_refine
on Thu Mar  6 04:02:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7z4z_14511/03_2025/7z4z_14511.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7z4z_14511/03_2025/7z4z_14511.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7z4z_14511/03_2025/7z4z_14511.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7z4z_14511/03_2025/7z4z_14511.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7z4z_14511/03_2025/7z4z_14511.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7z4z_14511/03_2025/7z4z_14511.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      11      5.16       5
     C    3082      2.51       5
     N     838      2.21       5
     O     886      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4817
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1096
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 1096
          Classifications: {'peptide': 149}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 7, 'TRANS': 141}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 147
          Unresolved non-hydrogen dihedrals: 93
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 72
    Chain: "B"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1317
          Classifications: {'peptide': 188}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 13, 'TRANS': 174}
          Unresolved non-hydrogen bonds: 193
          Unresolved non-hydrogen angles: 237
          Unresolved non-hydrogen dihedrals: 162
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 10, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 114
    Chain: "C"
      Number of atoms: 1111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1111
          Classifications: {'peptide': 152}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 7, 'TRANS': 144}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 129
          Unresolved non-hydrogen angles: 158
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 89
    Chain: "D"
      Number of atoms: 1293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1293
          Classifications: {'peptide': 184}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 13, 'TRANS': 170}
          Unresolved non-hydrogen bonds: 187
          Unresolved non-hydrogen angles: 229
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 101
  Time building chain proxies: 3.38, per 1000 atoms: 0.70
  Number of scatterers: 4817
  At special positions: 0
  Unit cell: (67.828, 74.392, 110.494, 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      11     16.00
     O     886      8.00
     N     838      7.00
     C    3082      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: 1.07
  Conformation dependent library (CDL) restraints added in 586.6 milliseconds
  

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1282

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 3 sheets defined
      29.1% alpha, 9.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 74
      removed outlier: 4.007A  pdb=" N   ASN A  67 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   ARG A  72 " --> pdb=" O   GLN A  68 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   LYS A  73 " --> pdb=" O   GLU A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 124
      removed outlier: 3.664A  pdb=" N   GLU A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 645
      removed outlier: 3.799A  pdb=" N   TYR B 643 " --> pdb=" O   GLU B 639 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 650 through 654
    Processing helix  chain 'B' and resid 703 through 710
      removed outlier: 3.698A  pdb=" N   ASN B 709 " --> pdb=" O   GLU B 705 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 755 through 767
      removed outlier: 3.517A  pdb=" N   GLN B 767 " --> pdb=" O   ILE B 763 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 789 through 807
    Processing helix  chain 'C' and resid 62 through 74
      removed outlier: 3.853A  pdb=" N   GLN C  68 " --> pdb=" O   ARG C  64 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLU C  69 " --> pdb=" O   ALA C  65 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   LYS C  71 " --> pdb=" O   ASN C  67 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ARG C  72 " --> pdb=" O   GLN C  68 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LYS C  73 " --> pdb=" O   GLU C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 107
      removed outlier: 3.716A  pdb=" N   GLN C 107 " --> pdb=" O   ILE C 104 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 126
      removed outlier: 4.070A  pdb=" N   VAL C 120 " --> pdb=" O   VAL C 116 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   LYS C 121 " --> pdb=" O   SER C 117 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 625 through 641
      removed outlier: 3.915A  pdb=" N   GLU D 641 " --> pdb=" O   GLY D 637 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 703 through 709
      removed outlier: 4.299A  pdb=" N   ASN D 709 " --> pdb=" O   GLU D 705 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 734 through 736
      No H-bonds generated for 'chain 'D' and resid 734 through 736'
    Processing helix  chain 'D' and resid 754 through 770
      removed outlier: 3.641A  pdb=" N   SER D 758 " --> pdb=" O   ASP D 754 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   VAL D 759 " --> pdb=" O   ASN D 755 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   LEU D 760 " --> pdb=" O   ARG D 756 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LYS D 768 " --> pdb=" O   GLN D 764 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 788 through 805
      removed outlier: 3.617A  pdb=" N   TYR D 805 " --> pdb=" O   GLU D 801 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 182
      removed outlier: 3.800A  pdb=" N   SER A 171 " --> pdb=" O   LYS A 182 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE C  97 " --> pdb=" O   VAL A 172 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   TYR A 174 " --> pdb=" O   LEU C  95 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   LEU C  95 " --> pdb=" O   TYR A 174 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY C 170 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 725 through 732
      removed outlier: 6.856A  pdb=" N   VAL B 695 " --> pdb=" O   PHE B 677 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   PHE B 677 " --> pdb=" O   VAL B 695 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   GLU B 697 " --> pdb=" O   VAL B 675 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL B 673 " --> pdb=" O   LEU B 699 " (cutoff:3.500A)
      removed outlier: 5.741A  pdb=" N   ARG B 701 " --> pdb=" O   TRP B 671 " (cutoff:3.500A)
      removed outlier: 8.393A  pdb=" N   TRP B 671 " --> pdb=" O   ARG B 701 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLY B 672 " --> pdb=" O   VAL B 660 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   LYS B 661 " --> pdb=" O   SER B 737 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 727 through 732
      removed outlier: 3.701A  pdb=" N   VAL D 673 " --> pdb=" O   LEU D 699 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ASP D 668 " --> pdb=" O   ASN D 664 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ASN D 664 " --> pdb=" O   ASP D 668 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   GLY D 670 " --> pdb=" O   VAL D 662 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   VAL D 662 " --> pdb=" O   GLY D 670 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   ARG D 658 " --> pdb=" O   VAL D 674 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   VAL D 742 " --> pdb=" O   LEU D 659 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   LYS D 661 " --> pdb=" O   SER D 740 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   SER D 740 " --> pdb=" O   LYS D 661 " (cutoff:3.500A)

    146 hydrogen bonds defined for protein.
    420 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: 1.29 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 827
        1.29 -     1.42: 1136
        1.42 -     1.55: 2927
        1.55 -     1.68: 0
        1.68 -     1.81: 16
  Bond restraints: 4906
  Sorted by residual:
  bond pdb=" C   PHE C 207 "
       pdb=" O   PHE C 207 "
    ideal  model  delta    sigma   weight residual
    1.230  1.164  0.066 1.74e-02 3.30e+03 1.44e+01
  bond pdb=" CG  ASP B 754 "
       pdb=" OD1 ASP B 754 "
    ideal  model  delta    sigma   weight residual
    1.249  1.185  0.064 1.90e-02 2.77e+03 1.15e+01
  bond pdb=" N   ARG B 751 "
       pdb=" CA  ARG B 751 "
    ideal  model  delta    sigma   weight residual
    1.457  1.504 -0.047 1.41e-02 5.03e+03 1.11e+01
  bond pdb=" CA  PHE C 207 "
       pdb=" C   PHE C 207 "
    ideal  model  delta    sigma   weight residual
    1.532  1.490  0.042 1.41e-02 5.03e+03 9.05e+00
  bond pdb=" N   VAL B 753 "
       pdb=" CA  VAL B 753 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.90e+00
  ... (remaining 4901 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.59: 6586
        2.59 -     5.19: 93
        5.19 -     7.78: 14
        7.78 -    10.38: 2
       10.38 -    12.97: 1
  Bond angle restraints: 6696
  Sorted by residual:
  angle pdb=" N   ASN B 755 "
        pdb=" CA  ASN B 755 "
        pdb=" C   ASN B 755 "
      ideal   model   delta    sigma   weight residual
     112.23   99.26   12.97 1.26e+00 6.30e-01 1.06e+02
  angle pdb=" CA  ASP B 754 "
        pdb=" CB  ASP B 754 "
        pdb=" CG  ASP B 754 "
      ideal   model   delta    sigma   weight residual
     112.60  105.68    6.92 1.00e+00 1.00e+00 4.78e+01
  angle pdb=" N   ASP B 754 "
        pdb=" CA  ASP B 754 "
        pdb=" C   ASP B 754 "
      ideal   model   delta    sigma   weight residual
     114.75  107.82    6.93 1.26e+00 6.30e-01 3.03e+01
  angle pdb=" C   VAL C 206 "
        pdb=" N   PHE C 207 "
        pdb=" CA  PHE C 207 "
      ideal   model   delta    sigma   weight residual
     123.04  115.84    7.20 1.59e+00 3.96e-01 2.05e+01
  angle pdb=" CA  ASP B 754 "
        pdb=" C   ASP B 754 "
        pdb=" N   ASN B 755 "
      ideal   model   delta    sigma   weight residual
     119.80  114.03    5.77 1.34e+00 5.57e-01 1.85e+01
  ... (remaining 6691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 2712
       17.69 -    35.37: 220
       35.37 -    53.06: 42
       53.06 -    70.74: 8
       70.74 -    88.43: 4
  Dihedral angle restraints: 2986
    sinusoidal: 1024
      harmonic: 1962
  Sorted by residual:
  dihedral pdb=" C   ARG B 751 "
           pdb=" N   ARG B 751 "
           pdb=" CA  ARG B 751 "
           pdb=" CB  ARG B 751 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.03   14.43     0      2.50e+00 1.60e-01 3.33e+01
  dihedral pdb=" N   ARG B 751 "
           pdb=" C   ARG B 751 "
           pdb=" CA  ARG B 751 "
           pdb=" CB  ARG B 751 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  136.97  -14.17     0      2.50e+00 1.60e-01 3.21e+01
  dihedral pdb=" CA  ALA A 165 "
           pdb=" C   ALA A 165 "
           pdb=" N   PHE A 166 "
           pdb=" CA  PHE A 166 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.43  -27.57     0      5.00e+00 4.00e-02 3.04e+01
  ... (remaining 2983 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 756
       0.100 -    0.200: 41
       0.200 -    0.299: 1
       0.299 -    0.399: 0
       0.399 -    0.499: 1
  Chirality restraints: 799
  Sorted by residual:
  chirality pdb=" CA  ARG B 751 "
            pdb=" N   ARG B 751 "
            pdb=" C   ARG B 751 "
            pdb=" CB  ARG B 751 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.22e+00
  chirality pdb=" CA  HIS C 209 "
            pdb=" N   HIS C 209 "
            pdb=" C   HIS C 209 "
            pdb=" CB  HIS C 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CA  ASN B 755 "
            pdb=" N   ASN B 755 "
            pdb=" C   ASN B 755 "
            pdb=" CB  ASN B 755 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.47e-01
  ... (remaining 796 not shown)

  Planarity restraints: 881
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 754 "    0.019 2.00e-02 2.50e+03   3.93e-02 1.54e+01
        pdb=" C   ASP B 754 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   ASP B 754 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ASN B 755 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 207 "   -0.013 2.00e-02 2.50e+03   2.68e-02 7.19e+00
        pdb=" C   PHE C 207 "    0.046 2.00e-02 2.50e+03
        pdb=" O   PHE C 207 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   SER C 208 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D 719 "    0.043 5.00e-02 4.00e+02   6.50e-02 6.77e+00
        pdb=" N   PRO D 720 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO D 720 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO D 720 "    0.036 5.00e-02 4.00e+02
  ... (remaining 878 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.82: 1476
        2.82 -     3.34: 4438
        3.34 -     3.86: 7059
        3.86 -     4.38: 7728
        4.38 -     4.90: 13370
  Nonbonded interactions: 34071
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  77 "
            pdb=" OG1 THR A  78 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OD1 ASN A 189 "
            pdb=" N   GLU A 190 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" O   GLU B 641 "
            pdb=" ND1 HIS B 645 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" OD2 ASP A 181 "
            pdb=" NH1 ARG B 743 "
     model   vdw
     2.391 3.120
  nonbonded pdb=" N   ASN B 755 "
            pdb=" N   ARG B 756 "
     model   vdw
     2.402 2.560
  ... (remaining 34066 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' and (resid 61 through 78 or (resid 79 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 80 through 89 or (resid 90 through 91 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 92 through 100 or (re \ 
sid 101 through 103 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 104 through 120 or (resid 121 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 122 through 123 or (resid 124 through 125 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 126 through 131 or (resid 132  \ 
through 136 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 
7 through 148 or (resid 149 through 165 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 166 through 195 or (resid 196 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 197 through 198 or (resid 199 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 200 through 208 or (re \ 
sid 209 and (name N or name CA or name C or name O or name CB )) or resid 210 th \ 
rough 218))
  selection = (chain 'C' and ((resid 61 through 66 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 67 through 68 or (resid 69 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 70 through 84 or (resid 85 through 91 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 92 through 130 or (r \ 
esid 131 through 136 and (name N or name CA or name C or name O or name CB )) or \ 
 resid 137 through 147 or (resid 148 through 165 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 166 through 168 or (resid 169 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 170 through 211 or (resid 212 \ 
 through 214 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 
15 through 218))
}
ncs_group {
  reference = (chain 'B' and (resid 624 through 637 or (resid 638 through 639 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 640 through 703 or (resid 704  \ 
and (name N or name CA or name C or name O or name CB )) or resid 705 through 72 \ 
4 or (resid 725 through 726 and (name N or name CA or name C or name O or name C \ 
B )) or resid 727 through 744 or (resid 745 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 746 through 773 or (resid 774 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 775 through 792 or (resid 793 thro \ 
ugh 794 and (name N or name CA or name C or name O or name CB )) or resid 795 or \ 
 (resid 796 through 807 and (name N or name CA or name C or name O or name CB )) \ 
))
  selection = (chain 'D' and (resid 624 through 641 or (resid 642 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 643 through 663 or (resid 664 through 665  \ 
and (name N or name CA or name C or name O or name CB )) or resid 666 or (resid  \ 
667 and (name N or name CA or name C or name O or name CB )) or resid 668 throug \ 
h 677 or (resid 678 through 684 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 685 through 718 or (resid 719 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 720 or (resid 721 through 723 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 724 through 730 or (resid 731  \ 
and (name N or name CA or name C or name O or name CB )) or resid 732 through 76 \ 
3 or (resid 764 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 765 through 779 or (resid 780 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 781 through 801 or (resid 802 through 807 and (name N or name  \ 
CA or name C or name O or name CB ))))
}

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=0.00 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.810
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   4906  Z= 0.232
  Angle     :  0.751  12.974   6696  Z= 0.431
  Chirality :  0.050   0.499    799
  Planarity :  0.006   0.065    881
  Dihedral  : 14.175  88.428   1704
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  2.12 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.82 (0.25), residues: 661
  helix: -2.09 (0.32), residues: 184
  sheet: -1.39 (1.44), residues: 16
  loop : -4.10 (0.22), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 198 
 HIS   0.002   0.000   HIS B 645 
 PHE   0.039   0.001   PHE C 207 
 TYR   0.008   0.001   TYR D 649 
 ARG   0.002   0.000   ARG D 701 

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  658 ARG cc_start: 0.8583 (mmm160) cc_final: 0.8160 (mmm160)
REVERT: B  708 LYS cc_start: 0.9000 (tppt) cc_final: 0.8467 (mtmm)
REVERT: B  761 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7627 (mptt)
REVERT: C  173 LEU cc_start: 0.9141 (tp) cc_final: 0.8753 (tp)
REVERT: C  191 ASN cc_start: 0.9025 (t0) cc_final: 0.8719 (t0)
REVERT: D  642 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6767 (mp0)
REVERT: D  655 GLN cc_start: 0.8109 (mt0) cc_final: 0.7851 (mt0)
REVERT: D  768 LYS cc_start: 0.8696 (pttm) cc_final: 0.7556 (tppt)
REVERT: D  788 GLN cc_start: 0.7973 (mp10) cc_final: 0.7748 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1693
  time to fit residues: 46.8706
Evaluate side-chains
  181 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0470
   chunk 16 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.9884

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

Flipped N/Q/H residues before XYZ refinement:
B 757 GLN
C  67 ASN
C 118 ASN
** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 764 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.153728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.121550 restraints weight = 7985.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.125013 restraints weight = 4787.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.126955 restraints weight = 3378.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   4906  Z= 0.222
  Angle     :  0.702   9.468   6696  Z= 0.350
  Chirality :  0.047   0.187    799
  Planarity :  0.005   0.063    881
  Dihedral  :  4.718  20.961    697
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  : 11.04 %
    Favored  : 88.50 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 16.30 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.53 (0.29), residues: 661
  helix: -0.36 (0.36), residues: 195
  sheet: -1.28 (1.15), residues: 21
  loop : -3.63 (0.24), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 198 
 HIS   0.004   0.001   HIS C 109 
 PHE   0.008   0.001   PHE A 178 
 TYR   0.008   0.001   TYR A 203 
 ARG   0.006   0.001   ARG D 751 

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 210
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7634 (mt-10)
REVERT: B  708 LYS cc_start: 0.9128 (tppt) cc_final: 0.8400 (mtmm)
REVERT: B  725 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7064 (tm-30)
REVERT: B  761 LYS cc_start: 0.8422 (mtpp) cc_final: 0.7565 (mmtm)
REVERT: C  108 TYR cc_start: 0.8557 (m-80) cc_final: 0.8140 (m-80)
REVERT: C  114 GLU cc_start: 0.8121 (tp30) cc_final: 0.7634 (tp30)
REVERT: C  173 LEU cc_start: 0.8901 (tp) cc_final: 0.8517 (tp)
REVERT: C  191 ASN cc_start: 0.9332 (t0) cc_final: 0.8852 (t0)
REVERT: D  641 GLU cc_start: 0.8705 (mp0) cc_final: 0.8013 (pm20)
REVERT: D  642 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6992 (mp0)
REVERT: D  675 VAL cc_start: 0.9221 (t) cc_final: 0.8932 (p)
REVERT: D  768 LYS cc_start: 0.9120 (pttm) cc_final: 0.8135 (tppt)
  outliers start: 21
  outliers final: 11
  residues processed: 216
  average time/residue: 0.1668
  time to fit residues: 45.1190
Evaluate side-chains
  209 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 198
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  660 VAL
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  710 SER
Chi-restraints excluded: chain D residue  733 VAL
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
B 767 GLN
C  67 ASN
** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 764 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.147517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.115783 restraints weight = 8124.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.118925 restraints weight = 4912.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.120641 restraints weight = 3531.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.3422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4906  Z= 0.250
  Angle     :  0.687   9.923   6696  Z= 0.345
  Chirality :  0.046   0.176    799
  Planarity :  0.005   0.067    881
  Dihedral  :  4.896  21.742    697
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 12.86 %
    Favored  : 86.84 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 21.81 %
    Favored  : 72.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.30), residues: 661
  helix:  0.41 (0.38), residues: 191
  sheet: -0.15 (1.74), residues: 11
  loop : -3.34 (0.25), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 671 
 HIS   0.004   0.001   HIS C 109 
 PHE   0.009   0.001   PHE C 115 
 TYR   0.006   0.001   TYR D 694 
 ARG   0.009   0.000   ARG D 751 

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 202
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
REVERT: B  661 LYS cc_start: 0.6160 (OUTLIER) cc_final: 0.5559 (tttp)
REVERT: B  708 LYS cc_start: 0.9151 (tppt) cc_final: 0.8474 (mttp)
REVERT: B  725 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7054 (tm-30)
REVERT: B  761 LYS cc_start: 0.8460 (mtpp) cc_final: 0.7584 (mmtm)
REVERT: C  173 LEU cc_start: 0.8966 (tp) cc_final: 0.8551 (tp)
REVERT: C  191 ASN cc_start: 0.9379 (t0) cc_final: 0.8894 (t0)
REVERT: C  203 TYR cc_start: 0.8273 (p90) cc_final: 0.7950 (p90)
REVERT: D  641 GLU cc_start: 0.8663 (mp0) cc_final: 0.8174 (mp0)
REVERT: D  642 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7020 (mp0)
REVERT: D  768 LYS cc_start: 0.9162 (pttm) cc_final: 0.8098 (tppp)
REVERT: D  782 ASP cc_start: 0.8724 (m-30) cc_final: 0.8273 (m-30)
  outliers start: 28
  outliers final: 20
  residues processed: 210
  average time/residue: 0.1646
  time to fit residues: 43.5583
Evaluate side-chains
  211 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 190
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue  643 TYR
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  661 LYS
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  767 GLN
Chi-restraints excluded: chain B residue  785 ILE
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain D residue  646 LYS
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  659 LEU
Chi-restraints excluded: chain D residue  709 ASN
Chi-restraints excluded: chain D residue  731 VAL
Chi-restraints excluded: chain D residue  733 VAL
Chi-restraints excluded: chain D residue  741 SER
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** B 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 ASN
C 118 ASN
** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.143604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.111824 restraints weight = 8357.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.114962 restraints weight = 5010.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.117179 restraints weight = 3576.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.4049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4906  Z= 0.289
  Angle     :  0.709  10.325   6696  Z= 0.356
  Chirality :  0.047   0.177    799
  Planarity :  0.005   0.070    881
  Dihedral  :  5.091  23.427    697
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 14.98 %
    Favored  : 84.87 %
  Rotamer:
    Outliers :  7.27 %
    Allowed  : 26.21 %
    Favored  : 66.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.66 (0.31), residues: 661
  helix:  0.79 (0.38), residues: 192
  sheet:  0.11 (1.61), residues: 11
  loop : -3.25 (0.26), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 109 
 PHE   0.010   0.002   PHE A 178 
 TYR   0.007   0.001   TYR A 203 
 ARG   0.006   0.001   ARG D 751 

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 200
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 TYR cc_start: 0.9052 (m-80) cc_final: 0.8162 (m-80)
REVERT: A  111 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7619 (mt-10)
REVERT: B  661 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.5777 (tttp)
REVERT: B  708 LYS cc_start: 0.9164 (tppt) cc_final: 0.8462 (mtmm)
REVERT: B  725 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7059 (tm-30)
REVERT: B  761 LYS cc_start: 0.8507 (mtpp) cc_final: 0.7631 (mmtm)
REVERT: C  108 TYR cc_start: 0.8499 (m-80) cc_final: 0.8252 (m-80)
REVERT: C  111 GLU cc_start: 0.8874 (mp0) cc_final: 0.8649 (pm20)
REVERT: C  191 ASN cc_start: 0.9396 (t0) cc_final: 0.8967 (t0)
REVERT: C  203 TYR cc_start: 0.8256 (p90) cc_final: 0.8000 (p90)
REVERT: D  641 GLU cc_start: 0.8635 (mp0) cc_final: 0.7994 (mp0)
REVERT: D  642 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6886 (mp0)
REVERT: D  768 LYS cc_start: 0.9091 (pttm) cc_final: 0.8207 (tppt)
REVERT: D  782 ASP cc_start: 0.8662 (m-30) cc_final: 0.8453 (m-30)
REVERT: D  788 GLN cc_start: 0.8330 (mp10) cc_final: 0.7913 (mp10)
  outliers start: 33
  outliers final: 27
  residues processed: 209
  average time/residue: 0.1939
  time to fit residues: 50.7880
Evaluate side-chains
  216 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 188
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue  643 TYR
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  660 VAL
Chi-restraints excluded: chain B residue  661 LYS
Chi-restraints excluded: chain B residue  669 PHE
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  726 MET
Chi-restraints excluded: chain B residue  785 ILE
Chi-restraints excluded: chain C residue   67 ASN
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain D residue  646 LYS
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  659 LEU
Chi-restraints excluded: chain D residue  709 ASN
Chi-restraints excluded: chain D residue  710 SER
Chi-restraints excluded: chain D residue  731 VAL
Chi-restraints excluded: chain D residue  733 VAL
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  741 SER
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 50 optimal weight:    0.6980
   chunk 32 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 14 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 20 optimal weight:    0.1980
   chunk 12 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 118 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.147942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.116648 restraints weight = 8225.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.120078 restraints weight = 4864.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.122475 restraints weight = 3406.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.4193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4906  Z= 0.188
  Angle     :  0.695  11.120   6696  Z= 0.337
  Chirality :  0.046   0.173    799
  Planarity :  0.005   0.065    881
  Dihedral  :  4.791  22.926    697
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 12.10 %
    Favored  : 87.59 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 26.65 %
    Favored  : 66.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.30 (0.32), residues: 661
  helix:  1.24 (0.39), residues: 192
  sheet:  0.60 (1.51), residues: 11
  loop : -3.10 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 671 
 HIS   0.002   0.001   HIS B 645 
 PHE   0.008   0.001   PHE D 677 
 TYR   0.005   0.001   TYR D 649 
 ARG   0.006   0.000   ARG D 751 

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 196
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7717 (mt-10)
REVERT: A  166 PHE cc_start: 0.7831 (m-10) cc_final: 0.7586 (m-10)
REVERT: B  661 LYS cc_start: 0.6211 (OUTLIER) cc_final: 0.5435 (tttp)
REVERT: B  725 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7060 (tm-30)
REVERT: B  727 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8478 (mm-40)
REVERT: B  761 LYS cc_start: 0.8456 (mtpp) cc_final: 0.7587 (mmtm)
REVERT: C  108 TYR cc_start: 0.8635 (m-80) cc_final: 0.8360 (m-80)
REVERT: C  111 GLU cc_start: 0.8878 (mp0) cc_final: 0.8592 (pm20)
REVERT: C  173 LEU cc_start: 0.8905 (tp) cc_final: 0.8702 (tp)
REVERT: C  191 ASN cc_start: 0.9355 (t0) cc_final: 0.8995 (t0)
REVERT: C  203 TYR cc_start: 0.7935 (p90) cc_final: 0.7729 (p90)
REVERT: C  207 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7392 (m-80)
REVERT: D  641 GLU cc_start: 0.8718 (mp0) cc_final: 0.8140 (mp0)
REVERT: D  642 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6814 (mp0)
REVERT: D  648 LYS cc_start: 0.7992 (ttpt) cc_final: 0.7782 (ttpt)
REVERT: D  655 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8410 (mm-40)
REVERT: D  667 ASP cc_start: 0.8477 (m-30) cc_final: 0.8275 (m-30)
REVERT: D  675 VAL cc_start: 0.9212 (t) cc_final: 0.8818 (p)
REVERT: D  768 LYS cc_start: 0.8888 (pttm) cc_final: 0.8001 (tppp)
REVERT: D  782 ASP cc_start: 0.8762 (m-30) cc_final: 0.8271 (m-30)
  outliers start: 29
  outliers final: 20
  residues processed: 208
  average time/residue: 0.1682
  time to fit residues: 43.7224
Evaluate side-chains
  210 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 188
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  646 LYS
Chi-restraints excluded: chain B residue  661 LYS
Chi-restraints excluded: chain B residue  669 PHE
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  726 MET
Chi-restraints excluded: chain C residue  118 ASN
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  207 PHE
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  651 LEU
Chi-restraints excluded: chain D residue  663 LYS
Chi-restraints excluded: chain D residue  696 VAL
Chi-restraints excluded: chain D residue  709 ASN
Chi-restraints excluded: chain D residue  710 SER
Chi-restraints excluded: chain D residue  741 SER
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 23 optimal weight:    8.9990
   chunk 57 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 26 optimal weight:    0.4980
   chunk 28 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A  75 ASN
** B 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 757 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.142060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.110434 restraints weight = 8499.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.113626 restraints weight = 5124.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.115913 restraints weight = 3663.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.4561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4906  Z= 0.252
  Angle     :  0.704  11.368   6696  Z= 0.346
  Chirality :  0.046   0.175    799
  Planarity :  0.005   0.063    881
  Dihedral  :  4.890  23.348    697
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 14.52 %
    Favored  : 85.17 %
  Rotamer:
    Outliers :  7.05 %
    Allowed  : 27.75 %
    Favored  : 65.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.32), residues: 661
  helix:  1.34 (0.39), residues: 189
  sheet:  0.81 (1.47), residues: 11
  loop : -3.02 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D 671 
 HIS   0.004   0.001   HIS A 109 
 PHE   0.008   0.001   PHE A 178 
 TYR   0.006   0.001   TYR C 108 
 ARG   0.006   0.000   ARG D 751 

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 194
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7794 (mt-10)
REVERT: B  725 GLU cc_start: 0.7506 (tm-30) cc_final: 0.6973 (tm-30)
REVERT: B  761 LYS cc_start: 0.8489 (mtpp) cc_final: 0.7641 (mmtm)
REVERT: C  108 TYR cc_start: 0.8563 (m-80) cc_final: 0.8318 (m-80)
REVERT: C  111 GLU cc_start: 0.8915 (mp0) cc_final: 0.8646 (pm20)
REVERT: C  173 LEU cc_start: 0.8862 (tp) cc_final: 0.8595 (tp)
REVERT: C  191 ASN cc_start: 0.9244 (t0) cc_final: 0.8940 (t0)
REVERT: D  641 GLU cc_start: 0.8781 (mp0) cc_final: 0.8122 (mp0)
REVERT: D  642 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6858 (mp0)
REVERT: D  768 LYS cc_start: 0.9067 (pttm) cc_final: 0.8096 (tppp)
REVERT: D  782 ASP cc_start: 0.8664 (m-30) cc_final: 0.8387 (m-30)
  outliers start: 32
  outliers final: 23
  residues processed: 207
  average time/residue: 0.1668
  time to fit residues: 43.1250
Evaluate side-chains
  214 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 191
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  646 LYS
Chi-restraints excluded: chain B residue  669 PHE
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  726 MET
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  659 LEU
Chi-restraints excluded: chain D residue  663 LYS
Chi-restraints excluded: chain D residue  696 VAL
Chi-restraints excluded: chain D residue  707 LEU
Chi-restraints excluded: chain D residue  710 SER
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  781 ASP
Chi-restraints excluded: chain D residue  790 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0020
   chunk 64 optimal weight:   10.0000
   chunk 26 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0030
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.5000

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

Flipped N/Q/H residues before XYZ refinement:
** B 655 GLN ** 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 = 0.3707 r_free = 0.3707 target = 0.147352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.117743 restraints weight = 8202.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.121181 restraints weight = 4838.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.123612 restraints weight = 3356.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.4639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4906  Z= 0.182
  Angle     :  0.705  12.017   6696  Z= 0.337
  Chirality :  0.047   0.168    799
  Planarity :  0.005   0.063    881
  Dihedral  :  4.553  20.910    697
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 12.25 %
    Favored  : 87.44 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 29.96 %
    Favored  : 65.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.32), residues: 661
  helix:  1.48 (0.38), residues: 192
  sheet:  1.06 (1.51), residues: 11
  loop : -3.03 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 671 
 HIS   0.002   0.001   HIS B 645 
 PHE   0.009   0.001   PHE C 115 
 TYR   0.005   0.001   TYR A 108 
 ARG   0.007   0.000   ARG D 751 

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 198
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 TYR cc_start: 0.9004 (m-80) cc_final: 0.8228 (m-80)
REVERT: A  111 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7720 (mt-10)
REVERT: B  661 LYS cc_start: 0.6640 (tttt) cc_final: 0.5945 (tttp)
REVERT: B  725 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6985 (tm-30)
REVERT: B  727 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8549 (mm-40)
REVERT: B  761 LYS cc_start: 0.8463 (mtpp) cc_final: 0.7604 (mmtm)
REVERT: C  108 TYR cc_start: 0.8531 (m-80) cc_final: 0.8303 (m-80)
REVERT: C  173 LEU cc_start: 0.8863 (tp) cc_final: 0.8630 (tp)
REVERT: C  191 ASN cc_start: 0.9267 (t0) cc_final: 0.8953 (t0)
REVERT: D  641 GLU cc_start: 0.8780 (mp0) cc_final: 0.8135 (mp0)
REVERT: D  642 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6698 (mp0)
REVERT: D  768 LYS cc_start: 0.8800 (pttm) cc_final: 0.7872 (tppp)
REVERT: D  782 ASP cc_start: 0.8490 (m-30) cc_final: 0.8234 (m-30)
  outliers start: 21
  outliers final: 15
  residues processed: 206
  average time/residue: 0.1665
  time to fit residues: 42.8448
Evaluate side-chains
  203 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 188
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  669 PHE
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  763 ILE
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  663 LYS
Chi-restraints excluded: chain D residue  696 VAL
Chi-restraints excluded: chain D residue  731 VAL
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 64 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0670
   chunk 25 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    1.5724

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

Flipped N/Q/H residues before XYZ refinement:
** B 655 GLN ** 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 = 0.3649 r_free = 0.3649 target = 0.142620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.113717 restraints weight = 8394.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.117157 restraints weight = 4878.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.119533 restraints weight = 3355.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.4863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4906  Z= 0.244
  Angle     :  0.721  11.994   6696  Z= 0.348
  Chirality :  0.047   0.173    799
  Planarity :  0.005   0.062    881
  Dihedral  :  4.757  23.048    697
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 14.37 %
    Favored  : 85.33 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 30.18 %
    Favored  : 65.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.33), residues: 661
  helix:  1.63 (0.39), residues: 192
  sheet:  1.11 (1.50), residues: 11
  loop : -3.03 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 671 
 HIS   0.003   0.001   HIS C 109 
 PHE   0.009   0.001   PHE A 166 
 TYR   0.006   0.001   TYR A 203 
 ARG   0.006   0.000   ARG D 751 

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 191
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7746 (mt-10)
REVERT: B  661 LYS cc_start: 0.6569 (tttt) cc_final: 0.6112 (tttp)
REVERT: B  725 GLU cc_start: 0.7504 (tm-30) cc_final: 0.6966 (tm-30)
REVERT: B  761 LYS cc_start: 0.8493 (mtpp) cc_final: 0.7665 (mmtm)
REVERT: C  108 TYR cc_start: 0.8489 (m-80) cc_final: 0.8255 (m-80)
REVERT: C  173 LEU cc_start: 0.8854 (tp) cc_final: 0.8580 (tp)
REVERT: C  190 GLU cc_start: 0.8860 (pm20) cc_final: 0.8648 (pm20)
REVERT: C  191 ASN cc_start: 0.9225 (t0) cc_final: 0.8946 (t0)
REVERT: D  641 GLU cc_start: 0.8811 (mp0) cc_final: 0.8255 (mp0)
REVERT: D  642 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6826 (mp0)
REVERT: D  768 LYS cc_start: 0.8909 (pttm) cc_final: 0.7967 (tppp)
REVERT: D  782 ASP cc_start: 0.8606 (m-30) cc_final: 0.8339 (m-30)
  outliers start: 21
  outliers final: 18
  residues processed: 197
  average time/residue: 0.1732
  time to fit residues: 42.6660
Evaluate side-chains
  207 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 189
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  669 PHE
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  726 MET
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  659 LEU
Chi-restraints excluded: chain D residue  663 LYS
Chi-restraints excluded: chain D residue  696 VAL
Chi-restraints excluded: chain D residue  707 LEU
Chi-restraints excluded: chain D residue  731 VAL
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0470
   chunk 33 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 64 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    2.0086

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

Flipped N/Q/H residues before XYZ refinement:
** B 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 655 GLN ** 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 = 0.3610 r_free = 0.3610 target = 0.139162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.109359 restraints weight = 8504.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.112578 restraints weight = 5048.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.114594 restraints weight = 3548.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.5334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4906  Z= 0.289
  Angle     :  0.785  11.962   6696  Z= 0.386
  Chirality :  0.048   0.182    799
  Planarity :  0.006   0.065    881
  Dihedral  :  5.216  24.298    697
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.28 %
    Favored  : 84.42 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 30.18 %
    Favored  : 64.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.32), residues: 661
  helix:  1.56 (0.39), residues: 187
  sheet:  1.06 (1.49), residues: 11
  loop : -2.99 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 671 
 HIS   0.004   0.001   HIS C 109 
 PHE   0.029   0.002   PHE C 115 
 TYR   0.009   0.001   TYR D 694 
 ARG   0.007   0.001   ARG D 751 

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 195
  time to evaluate  : 0.557 
Fit side-chains
REVERT: A  111 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7780 (mt-10)
REVERT: B  661 LYS cc_start: 0.6674 (tttt) cc_final: 0.6319 (tttp)
REVERT: B  725 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7018 (tm-30)
REVERT: B  761 LYS cc_start: 0.8544 (mtpp) cc_final: 0.7731 (mmtm)
REVERT: B  790 LEU cc_start: 0.9030 (mm) cc_final: 0.8815 (mm)
REVERT: C  173 LEU cc_start: 0.8855 (tp) cc_final: 0.8608 (tp)
REVERT: C  191 ASN cc_start: 0.9141 (t0) cc_final: 0.8875 (t0)
REVERT: D  641 GLU cc_start: 0.8858 (mp0) cc_final: 0.8195 (mp0)
REVERT: D  642 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6817 (mp0)
REVERT: D  648 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7704 (ttpt)
REVERT: D  768 LYS cc_start: 0.8930 (pttm) cc_final: 0.8089 (tppp)
REVERT: D  782 ASP cc_start: 0.8668 (m-30) cc_final: 0.8446 (m-30)
  outliers start: 25
  outliers final: 18
  residues processed: 203
  average time/residue: 0.1672
  time to fit residues: 42.4417
Evaluate side-chains
  206 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 188
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  669 PHE
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  785 ILE
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  659 LEU
Chi-restraints excluded: chain D residue  663 LYS
Chi-restraints excluded: chain D residue  696 VAL
Chi-restraints excluded: chain D residue  712 THR
Chi-restraints excluded: chain D residue  731 VAL
Chi-restraints excluded: chain D residue  735 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
C 118 ASN
** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.138320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.108834 restraints weight = 8494.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.111998 restraints weight = 4935.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.114114 restraints weight = 3451.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.5507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   4906  Z= 0.326
  Angle     :  0.829  12.366   6696  Z= 0.408
  Chirality :  0.049   0.180    799
  Planarity :  0.006   0.062    881
  Dihedral  :  5.392  24.496    697
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.58 %
    Favored  : 84.11 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 31.06 %
    Favored  : 63.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.32), residues: 661
  helix:  1.54 (0.39), residues: 187
  sheet:  1.31 (1.55), residues: 11
  loop : -3.03 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 198 
 HIS   0.004   0.001   HIS B 645 
 PHE   0.025   0.002   PHE C 115 
 TYR   0.012   0.001   TYR C 108 
 ARG   0.006   0.001   ARG D 751 

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 190
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7825 (mt-10)
REVERT: A  196 GLU cc_start: 0.7905 (mp0) cc_final: 0.7698 (mp0)
REVERT: B  661 LYS cc_start: 0.6613 (tttt) cc_final: 0.6156 (tttp)
REVERT: B  725 GLU cc_start: 0.7533 (tm-30) cc_final: 0.6964 (tm-30)
REVERT: B  761 LYS cc_start: 0.8550 (mtpp) cc_final: 0.7710 (mmtm)
REVERT: B  790 LEU cc_start: 0.9059 (mm) cc_final: 0.8847 (mm)
REVERT: C  110 GLN cc_start: 0.7884 (tp40) cc_final: 0.7478 (tm-30)
REVERT: C  111 GLU cc_start: 0.8957 (pm20) cc_final: 0.8710 (pm20)
REVERT: C  113 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7951 (mt-10)
REVERT: C  173 LEU cc_start: 0.8846 (tp) cc_final: 0.8588 (tp)
REVERT: C  190 GLU cc_start: 0.8959 (pm20) cc_final: 0.8739 (pm20)
REVERT: C  191 ASN cc_start: 0.9177 (t0) cc_final: 0.8951 (t0)
REVERT: D  641 GLU cc_start: 0.8870 (mp0) cc_final: 0.8217 (mp0)
REVERT: D  642 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6827 (mp0)
REVERT: D  648 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7753 (ttpt)
REVERT: D  768 LYS cc_start: 0.8922 (pttm) cc_final: 0.8083 (tppp)
  outliers start: 23
  outliers final: 19
  residues processed: 198
  average time/residue: 0.1699
  time to fit residues: 42.3038
Evaluate side-chains
  204 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  669 PHE
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  785 ILE
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  659 LEU
Chi-restraints excluded: chain D residue  663 LYS
Chi-restraints excluded: chain D residue  696 VAL
Chi-restraints excluded: chain D residue  712 THR
Chi-restraints excluded: chain D residue  731 VAL
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 63 optimal weight:    7.9990
   chunk 59 optimal weight:    0.0870
   chunk 42 optimal weight:    0.9980
   chunk 21 optimal weight:    5.9990
   chunk 2 optimal weight:    0.4980
   chunk 61 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.0760

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

Flipped N/Q/H residues before XYZ refinement:
** D 655 GLN ** 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 = 0.3652 r_free = 0.3652 target = 0.142812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.112206 restraints weight = 8360.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.115500 restraints weight = 4906.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.117843 restraints weight = 3441.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.5603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4906  Z= 0.224
  Angle     :  0.805  13.041   6696  Z= 0.389
  Chirality :  0.048   0.170    799
  Planarity :  0.005   0.062    881
  Dihedral  :  5.083  23.256    697
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 12.71 %
    Favored  : 86.99 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 31.94 %
    Favored  : 64.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.33), residues: 661
  helix:  1.70 (0.39), residues: 187
  sheet:  1.56 (1.60), residues: 11
  loop : -2.95 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 198 
 HIS   0.003   0.001   HIS B 645 
 PHE   0.025   0.001   PHE C 115 
 TYR   0.007   0.001   TYR D 694 
 ARG   0.007   0.000   ARG D 751 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1899.89 seconds
wall clock time: 33 minutes 30.18 seconds (2010.18 seconds total)