Starting phenix.real_space_refine
on Mon Jul 28 18:21:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v9x_31829/07_2025/7v9x_31829.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v9x_31829/07_2025/7v9x_31829.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v9x_31829/07_2025/7v9x_31829.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v9x_31829/07_2025/7v9x_31829.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v9x_31829/07_2025/7v9x_31829.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v9x_31829/07_2025/7v9x_31829.cif"
  }
  resolution = 2.82
  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=   0.005 sd=   0.071
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: 5
    Type Number    sf(0)   Gaussians
     P     210      5.49       5
     S      23      5.16       5
     C    5946      2.51       5
     N    1901      2.21       5
     O    2470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10550
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2518
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2518
          Classifications: {'peptide': 314}
          Link IDs: {'PTRANS': 12, 'TRANS': 301}
    Chain: "C"
      Number of atoms: 1096
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1096
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 2, 'TRANS': 129}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 808
          Classifications: {'DNA': 39}
          Link IDs: {'rna3p': 38}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 1225
          Classifications: {'RNA': 58}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 15, 'rna3p': 42}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 176
          Classifications: {'RNA': 8}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 7}
    Chain: "B"
      Number of atoms: 2518
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2518
          Classifications: {'peptide': 314}
          Link IDs: {'PTRANS': 12, 'TRANS': 301}
    Chain: "G"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 808
          Classifications: {'DNA': 39}
          Link IDs: {'rna3p': 38}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 1225
          Classifications: {'RNA': 58}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 15, 'rna3p': 42}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 176
          Classifications: {'RNA': 8}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 7}
  Time building chain proxies: 7.17, per 1000 atoms: 0.68
  Number of scatterers: 10550
  At special positions: 0
  Unit cell: (94.35, 129.2, 155.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     P     210     15.00
     O    2470      8.00
     N    1901      7.00
     C    5946      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.67
  Conformation dependent library (CDL) restraints added in 891.3 milliseconds
  

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1434

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 8 sheets defined
      60.5% alpha, 10.9% beta
      64 base pairs and 116 stacking pairs defined.
    Time for finding SS restraints: 4.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 14
      removed outlier: 3.633A  pdb=" N   LEU A   7 " --> pdb=" O   SER A   3 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ASN A   8 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   PHE A  10 " --> pdb=" O   TYR A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 31
    Processing helix  chain 'A' and resid 33 through 44
      removed outlier: 3.581A  pdb=" N   TYR A  42 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 83
      removed outlier: 3.733A  pdb=" N   LEU A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 87
    Processing helix  chain 'A' and resid 102 through 107
    Processing helix  chain 'A' and resid 108 through 110
      No H-bonds generated for 'chain 'A' and resid 108 through 110'
    Processing helix  chain 'A' and resid 122 through 127
      removed outlier: 3.691A  pdb=" N   LEU A 127 " --> pdb=" O   PHE A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 139
      removed outlier: 3.756A  pdb=" N   VAL A 135 " --> pdb=" O   LYS A 131 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU A 139 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 154
    Processing helix  chain 'A' and resid 165 through 174
    Processing helix  chain 'A' and resid 174 through 188
      removed outlier: 4.625A  pdb=" N   SER A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ARG A 188 " --> pdb=" O   TYR A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 220
      removed outlier: 3.606A  pdb=" N   VAL A 209 " --> pdb=" O   SER A 205 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   SER A 218 " --> pdb=" O   ASP A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 224
    Processing helix  chain 'A' and resid 256 through 272
    Processing helix  chain 'A' and resid 277 through 292
      removed outlier: 3.655A  pdb=" N   VAL A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 311
    Processing helix  chain 'C' and resid 8 through 19
      removed outlier: 3.766A  pdb=" N   GLN C  12 " --> pdb=" O   GLU C   8 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LYS C  19 " --> pdb=" O   GLY C  15 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 213
      Proline residue:  C 208  - end of helix
    Processing helix  chain 'C' and resid 217 through 230
    Processing helix  chain 'C' and resid 236 through 250
    Processing helix  chain 'C' and resid 263 through 274
    Processing helix  chain 'C' and resid 277 through 292
      removed outlier: 3.575A  pdb=" N   ARG C 283 " --> pdb=" O   LEU C 279 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ARG C 292 " --> pdb=" O   ASN C 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 15
      removed outlier: 3.937A  pdb=" N   ASN B   8 " --> pdb=" O   ALA B   4 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE B  10 " --> pdb=" O   TYR B   6 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   LEU B  15 " --> pdb=" O   ARG B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 31
    Processing helix  chain 'B' and resid 33 through 43
    Processing helix  chain 'B' and resid 44 through 46
      No H-bonds generated for 'chain 'B' and resid 44 through 46'
    Processing helix  chain 'B' and resid 69 through 83
      removed outlier: 3.615A  pdb=" N   LEU B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 87
    Processing helix  chain 'B' and resid 102 through 107
    Processing helix  chain 'B' and resid 108 through 110
      No H-bonds generated for 'chain 'B' and resid 108 through 110'
    Processing helix  chain 'B' and resid 123 through 127
    Processing helix  chain 'B' and resid 128 through 139
      removed outlier: 4.060A  pdb=" N   VAL B 132 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LEU B 139 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 154
    Processing helix  chain 'B' and resid 165 through 174
    Processing helix  chain 'B' and resid 175 through 188
      removed outlier: 4.232A  pdb=" N   SER B 187 " --> pdb=" O   GLY B 183 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ARG B 188 " --> pdb=" O   TYR B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 220
      removed outlier: 3.664A  pdb=" N   VAL B 209 " --> pdb=" O   SER B 205 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   SER B 218 " --> pdb=" O   ASP B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 224
    Processing helix  chain 'B' and resid 256 through 273
      removed outlier: 3.619A  pdb=" N   TYR B 260 " --> pdb=" O   GLY B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 292
    Processing helix  chain 'B' and resid 292 through 310
      removed outlier: 3.679A  pdb=" N   LYS B 308 " --> pdb=" O   SER B 304 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LYS B 309 " --> pdb=" O   LYS B 305 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 53
      removed outlier: 3.643A  pdb=" N   ARG A  63 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 195
    Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 243
    Processing sheet with id=AA4, first strand: chain 'C' and resid 253 through 256
    Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 53
      removed outlier: 3.979A  pdb=" N   ARG B  63 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 194
      removed outlier: 3.543A  pdb=" N   PHE B 114 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   VAL B 226 " --> pdb=" O   GLU B 121 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 194
      removed outlier: 3.543A  pdb=" N   PHE B 114 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 243

    332 hydrogen bonds defined for protein.
    948 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      161 hydrogen bonds
      290 hydrogen bond angles
      0 basepair planarities
      64 basepair parallelities
      116 stacking parallelities
  Total time for adding SS restraints: 3.67

  Time building geometry restraints manager: 3.18 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1841
        1.33 -     1.45: 3746
        1.45 -     1.57: 5159
        1.57 -     1.69: 410
        1.69 -     1.81: 34
  Bond restraints: 11190
  Sorted by residual:
  bond pdb=" C3'  DG D  73 "
       pdb=" O3'  DG D  73 "
    ideal  model  delta    sigma   weight residual
    1.422  1.463 -0.041 3.00e-02 1.11e+03 1.86e+00
  bond pdb=" C3'  DC D   3 "
       pdb=" O3'  DC D   3 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.67e+00
  bond pdb=" C3'  DG G  73 "
       pdb=" O3'  DG G  73 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.66e+00
  bond pdb=" C3'   A E  66 "
       pdb=" O3'   A E  66 "
    ideal  model  delta    sigma   weight residual
    1.427  1.444 -0.017 1.50e-02 4.44e+03 1.26e+00
  bond pdb=" CB  TRP B 284 "
       pdb=" CG  TRP B 284 "
    ideal  model  delta    sigma   weight residual
    1.498  1.463  0.035 3.10e-02 1.04e+03 1.24e+00
  ... (remaining 11185 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 15780
        2.10 -     4.20: 241
        4.20 -     6.30: 26
        6.30 -     8.40: 3
        8.40 -    10.50: 1
  Bond angle restraints: 16051
  Sorted by residual:
  angle pdb=" CB  MET C 287 "
        pdb=" CG  MET C 287 "
        pdb=" SD  MET C 287 "
      ideal   model   delta    sigma   weight residual
     112.70  102.20   10.50 3.00e+00 1.11e-01 1.23e+01
  angle pdb=" C3'   A E  66 "
        pdb=" O3'   A E  66 "
        pdb=" P     U E  67 "
      ideal   model   delta    sigma   weight residual
     120.20  125.43   -5.23 1.50e+00 4.44e-01 1.22e+01
  angle pdb=" CA  MET C 287 "
        pdb=" CB  MET C 287 "
        pdb=" CG  MET C 287 "
      ideal   model   delta    sigma   weight residual
     114.10  120.41   -6.31 2.00e+00 2.50e-01 9.95e+00
  angle pdb=" C3'   C E   8 "
        pdb=" O3'   C E   8 "
        pdb=" P     C E   9 "
      ideal   model   delta    sigma   weight residual
     120.20  124.82   -4.62 1.50e+00 4.44e-01 9.50e+00
  angle pdb=" C3'   A H  66 "
        pdb=" O3'   A H  66 "
        pdb=" P     U H  67 "
      ideal   model   delta    sigma   weight residual
     120.20  124.34   -4.14 1.50e+00 4.44e-01 7.61e+00
  ... (remaining 16046 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.67: 6105
       35.67 -    71.33: 642
       71.33 -   107.00: 37
      107.00 -   142.67: 5
      142.67 -   178.33: 17
  Dihedral angle restraints: 6806
    sinusoidal: 4581
      harmonic: 2225
  Sorted by residual:
  dihedral pdb=" O4'   U H  68 "
           pdb=" C1'   U H  68 "
           pdb=" N1    U H  68 "
           pdb=" C2    U H  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   23.34  176.66     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U E  68 "
           pdb=" C1'   U E  68 "
           pdb=" N1    U E  68 "
           pdb=" C2    U E  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   43.99  156.01     1      1.50e+01 4.44e-03 8.16e+01
  dihedral pdb=" O4'   C H  65 "
           pdb=" C1'   C H  65 "
           pdb=" N1    C H  65 "
           pdb=" C2    C H  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   71.06  128.94     1      1.50e+01 4.44e-03 6.95e+01
  ... (remaining 6803 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1466
       0.040 -    0.079: 342
       0.079 -    0.119: 87
       0.119 -    0.159: 17
       0.159 -    0.198: 4
  Chirality restraints: 1916
  Sorted by residual:
  chirality pdb=" C3'   A E  66 "
            pdb=" C4'   A E  66 "
            pdb=" O3'   A E  66 "
            pdb=" C2'   A E  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.55   -0.20 2.00e-01 2.50e+01 9.85e-01
  chirality pdb=" C1'   C H  65 "
            pdb=" O4'   C H  65 "
            pdb=" C2'   C H  65 "
            pdb=" N1    C H  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.27    0.19 2.00e-01 2.50e+01 9.29e-01
  chirality pdb=" C1'   C E  65 "
            pdb=" O4'   C E  65 "
            pdb=" C2'   C E  65 "
            pdb=" N1    C E  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.30    0.17 2.00e-01 2.50e+01 7.11e-01
  ... (remaining 1913 not shown)

  Planarity restraints: 1259
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A E  17 "   -0.023 2.00e-02 2.50e+03   1.08e-02 3.19e+00
        pdb=" N9    A E  17 "    0.026 2.00e-02 2.50e+03
        pdb=" C8    A E  17 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A E  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    A E  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A E  17 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A E  17 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A E  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    A E  17 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A E  17 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A E  17 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  80 "    0.008 2.00e-02 2.50e+03   1.62e-02 2.62e+00
        pdb=" C   LEU B  80 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   LEU B  80 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ARG B  81 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA D   6 "   -0.018 2.00e-02 2.50e+03   8.09e-03 1.80e+00
        pdb=" N9   DA D   6 "    0.018 2.00e-02 2.50e+03
        pdb=" C8   DA D   6 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7   DA D   6 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DA D   6 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA D   6 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6   DA D   6 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1   DA D   6 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA D   6 "    0.000 2.00e-02 2.50e+03
        pdb=" N3   DA D   6 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA D   6 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1256 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1933
        2.77 -     3.30: 8918
        3.30 -     3.84: 18963
        3.84 -     4.37: 23081
        4.37 -     4.90: 35214
  Nonbonded interactions: 88109
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B   8 "
            pdb=" NH2 ARG B  11 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   TYR C 211 "
            pdb=" NH2 ARG B  31 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" O   LEU A  39 "
            pdb=" OG1 THR A  43 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" NZ  LYS B  60 "
            pdb=" OE2 GLU B 121 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" O   PHE B 287 "
            pdb=" OG  SER B 290 "
     model   vdw
     2.276 3.040
  ... (remaining 88104 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'I'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     29.330
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:44.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   76.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  11190  Z= 0.197
  Angle     :  0.626  10.501  16051  Z= 0.335
  Chirality :  0.039   0.198   1916
  Planarity :  0.004   0.045   1259
  Dihedral  : 24.075 178.334   5372
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.30), residues: 750
  helix:  0.89 (0.27), residues: 394
  sheet:  1.50 (0.64), residues: 62
  loop : -1.26 (0.33), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 284 
 HIS   0.005   0.001   HIS B 280 
 PHE   0.013   0.002   PHE B  92 
 TYR   0.013   0.001   TYR B 179 
 ARG   0.005   0.000   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12453 (  484)
  hydrogen bonds       : angle       4.54192 ( 1238)
  covalent geometry    : bond        0.00452 (11190)
  covalent geometry    : angle       0.62634 (16051)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.935 
Fit side-chains
REVERT: A   45 ASP cc_start: 0.7618 (m-30) cc_final: 0.7343 (m-30)
REVERT: A  231 LYS cc_start: 0.6377 (mptt) cc_final: 0.6075 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 1.2871
  time to fit residues: 123.0777
Evaluate side-chains
  63 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0040
   chunk 38 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 71 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 82 optimal weight:    8.9990
   overall best weight:    2.1798

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

Flipped N/Q/H residues before XYZ refinement:
A 228 ASN
B 104 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.146606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.098398 restraints weight = 14580.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.74
r_work: 0.3142 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.0649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  11190  Z= 0.198
  Angle     :  0.626   8.919  16051  Z= 0.333
  Chirality :  0.039   0.196   1916
  Planarity :  0.005   0.037   1259
  Dihedral  : 26.279 179.704   3825
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  8.65 %
    Favored  : 89.88 %
  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:  0.21 (0.30), residues: 750
  helix:  0.97 (0.26), residues: 402
  sheet:  2.00 (0.62), residues: 58
  loop : -1.46 (0.33), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 284 
 HIS   0.005   0.001   HIS A 280 
 PHE   0.013   0.002   PHE B  92 
 TYR   0.014   0.001   TYR B 179 
 ARG   0.007   0.000   ARG C 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05343 (  484)
  hydrogen bonds       : angle       3.72258 ( 1238)
  covalent geometry    : bond        0.00452 (11190)
  covalent geometry    : angle       0.62576 (16051)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.8048 (m-30) cc_final: 0.7649 (m-30)
REVERT: A   62 MET cc_start: 0.7378 (pmm) cc_final: 0.6609 (ppp)
REVERT: A  119 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8421 (m-30)
REVERT: A  231 LYS cc_start: 0.6107 (mptt) cc_final: 0.5831 (mptt)
REVERT: B  251 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7657 (mm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 70
  average time/residue: 1.2520
  time to fit residues: 95.3645
Evaluate side-chains
  72 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 90 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
B 296 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.145590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.097598 restraints weight = 14723.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.74
r_work: 0.3127 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.0876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  11190  Z= 0.209
  Angle     :  0.628   9.781  16051  Z= 0.335
  Chirality :  0.040   0.197   1916
  Planarity :  0.004   0.039   1259
  Dihedral  : 26.235 179.321   3825
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 10.56 %
    Favored  : 87.54 %
  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:  0.14 (0.30), residues: 750
  helix:  0.97 (0.26), residues: 402
  sheet:  1.93 (0.61), residues: 58
  loop : -1.58 (0.33), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B 284 
 HIS   0.005   0.001   HIS A 280 
 PHE   0.013   0.002   PHE B  92 
 TYR   0.014   0.001   TYR B 179 
 ARG   0.005   0.000   ARG C 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05377 (  484)
  hydrogen bonds       : angle       3.65717 ( 1238)
  covalent geometry    : bond        0.00479 (11190)
  covalent geometry    : angle       0.62843 (16051)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 1.905 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7970 (m-30) cc_final: 0.7653 (m-30)
REVERT: A   62 MET cc_start: 0.7371 (pmm) cc_final: 0.6691 (ppp)
REVERT: A  119 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8430 (m-30)
REVERT: A  231 LYS cc_start: 0.6068 (mptt) cc_final: 0.5775 (mptt)
REVERT: C  241 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7283 (tpm-80)
REVERT: C  249 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7695 (m-40)
REVERT: B  251 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7688 (mm-30)
REVERT: B  282 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7917 (ttp-170)
  outliers start: 13
  outliers final: 5
  residues processed: 69
  average time/residue: 1.7586
  time to fit residues: 132.4356
Evaluate side-chains
  72 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  241 ARG
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain C residue  249 ASN
Chi-restraints excluded: chain C residue  296 THR
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 85 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 21 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    1.7186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.146695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.098569 restraints weight = 14719.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.74
r_work: 0.3149 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.0913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11190  Z= 0.170
  Angle     :  0.602   9.036  16051  Z= 0.321
  Chirality :  0.038   0.194   1916
  Planarity :  0.004   0.037   1259
  Dihedral  : 26.216 179.439   3825
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.58 %
    Favored  : 86.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.30), residues: 750
  helix:  1.08 (0.26), residues: 400
  sheet:  1.95 (0.61), residues: 58
  loop : -1.53 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A 280 
 PHE   0.014   0.001   PHE B  92 
 TYR   0.012   0.001   TYR B 179 
 ARG   0.005   0.000   ARG C 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04940 (  484)
  hydrogen bonds       : angle       3.57615 ( 1238)
  covalent geometry    : bond        0.00379 (11190)
  covalent geometry    : angle       0.60204 (16051)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7945 (m-30) cc_final: 0.7636 (m-30)
REVERT: A   62 MET cc_start: 0.7386 (pmm) cc_final: 0.6698 (ppp)
REVERT: A  119 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8400 (m-30)
REVERT: A  231 LYS cc_start: 0.6118 (mptt) cc_final: 0.5811 (mptt)
REVERT: B  251 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7686 (mm-30)
REVERT: B  282 ARG cc_start: 0.8210 (ttm110) cc_final: 0.7891 (ttp-170)
  outliers start: 12
  outliers final: 6
  residues processed: 70
  average time/residue: 1.5940
  time to fit residues: 120.8247
Evaluate side-chains
  70 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 40 optimal weight:   10.0000
   chunk 68 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0050
   overall best weight:    1.9398

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

Flipped N/Q/H residues before XYZ refinement:
C 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.146256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.098357 restraints weight = 14661.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.75
r_work: 0.3138 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.0992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11190  Z= 0.181
  Angle     :  0.603   9.528  16051  Z= 0.320
  Chirality :  0.038   0.194   1916
  Planarity :  0.004   0.037   1259
  Dihedral  : 26.184 179.568   3825
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.32 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.30), residues: 750
  helix:  1.13 (0.26), residues: 400
  sheet:  1.92 (0.61), residues: 58
  loop : -1.51 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A 280 
 PHE   0.013   0.001   PHE B  92 
 TYR   0.013   0.001   TYR B 179 
 ARG   0.004   0.000   ARG C 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04981 (  484)
  hydrogen bonds       : angle       3.53300 ( 1238)
  covalent geometry    : bond        0.00410 (11190)
  covalent geometry    : angle       0.60286 (16051)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7907 (m-30) cc_final: 0.7603 (m-30)
REVERT: A  119 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8395 (m-30)
REVERT: A  231 LYS cc_start: 0.6133 (mptt) cc_final: 0.5829 (mptt)
REVERT: C  241 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7282 (tpm-80)
REVERT: B  251 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7697 (mm-30)
REVERT: B  282 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7910 (ttp-170)
  outliers start: 12
  outliers final: 6
  residues processed: 71
  average time/residue: 1.5619
  time to fit residues: 119.7797
Evaluate side-chains
  71 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  241 ARG
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain C residue  296 THR
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0270
   chunk 38 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 75 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 56 optimal weight:    0.8980
   chunk 57 optimal weight:    0.4980
   chunk 33 optimal weight:    7.9990
   overall best weight:    0.8640

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.147621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.100185 restraints weight = 14693.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 1.69
r_work: 0.3170 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.1068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11190  Z= 0.133
  Angle     :  0.584   9.753  16051  Z= 0.310
  Chirality :  0.037   0.190   1916
  Planarity :  0.004   0.033   1259
  Dihedral  : 26.170 179.971   3825
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.61 %
    Favored  : 85.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.30), residues: 750
  helix:  1.25 (0.27), residues: 400
  sheet:  2.02 (0.62), residues: 58
  loop : -1.44 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.013   0.001   PHE B  92 
 TYR   0.011   0.001   TYR B 179 
 ARG   0.003   0.000   ARG C 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04450 (  484)
  hydrogen bonds       : angle       3.45447 ( 1238)
  covalent geometry    : bond        0.00282 (11190)
  covalent geometry    : angle       0.58440 (16051)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7866 (m-30) cc_final: 0.7568 (m-30)
REVERT: A  119 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8369 (m-30)
REVERT: A  207 LYS cc_start: 0.8251 (ptmm) cc_final: 0.7945 (pttp)
REVERT: A  231 LYS cc_start: 0.6064 (mptt) cc_final: 0.5761 (mptt)
REVERT: C  241 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7273 (tpm-80)
REVERT: B  251 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7721 (mm-30)
REVERT: B  282 ARG cc_start: 0.8234 (ttm110) cc_final: 0.7923 (ttp-170)
  outliers start: 13
  outliers final: 4
  residues processed: 69
  average time/residue: 1.3512
  time to fit residues: 100.5646
Evaluate side-chains
  70 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  241 ARG
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 64 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0770
   chunk 0 optimal weight:    6.9990
   chunk 73 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 45 optimal weight:    8.9990
   overall best weight:    1.0942

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.147772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.100253 restraints weight = 14790.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.67
r_work: 0.3170 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11190  Z= 0.139
  Angle     :  0.576   9.269  16051  Z= 0.306
  Chirality :  0.037   0.190   1916
  Planarity :  0.004   0.033   1259
  Dihedral  : 26.141 179.713   3825
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.05 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.30), residues: 750
  helix:  1.24 (0.27), residues: 398
  sheet:  2.04 (0.62), residues: 58
  loop : -1.45 (0.33), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.012   0.001   PHE B  92 
 TYR   0.010   0.001   TYR B 179 
 ARG   0.003   0.000   ARG C 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04464 (  484)
  hydrogen bonds       : angle       3.41378 ( 1238)
  covalent geometry    : bond        0.00303 (11190)
  covalent geometry    : angle       0.57587 (16051)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7863 (m-30) cc_final: 0.7591 (m-30)
REVERT: A  119 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8376 (m-30)
REVERT: A  207 LYS cc_start: 0.8234 (ptmm) cc_final: 0.7938 (pttp)
REVERT: A  231 LYS cc_start: 0.6062 (mptt) cc_final: 0.5749 (mptt)
REVERT: C  241 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7275 (tpm-80)
REVERT: B  251 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7730 (mm-30)
REVERT: B  282 ARG cc_start: 0.8227 (ttm110) cc_final: 0.7911 (ttp-170)
  outliers start: 12
  outliers final: 7
  residues processed: 70
  average time/residue: 1.3273
  time to fit residues: 100.5818
Evaluate side-chains
  73 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  241 ARG
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain C residue  257 THR
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 31 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.147177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.099375 restraints weight = 14673.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.74
r_work: 0.3150 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3026 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11190  Z= 0.159
  Angle     :  0.587   9.919  16051  Z= 0.311
  Chirality :  0.037   0.193   1916
  Planarity :  0.004   0.034   1259
  Dihedral  : 26.109 179.652   3825
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.05 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.30), residues: 750
  helix:  1.29 (0.27), residues: 400
  sheet:  1.31 (0.59), residues: 68
  loop : -1.37 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A 280 
 PHE   0.012   0.001   PHE B  92 
 TYR   0.012   0.001   TYR B 179 
 ARG   0.003   0.000   ARG C 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04664 (  484)
  hydrogen bonds       : angle       3.41786 ( 1238)
  covalent geometry    : bond        0.00354 (11190)
  covalent geometry    : angle       0.58677 (16051)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7866 (m-30) cc_final: 0.7610 (m-30)
REVERT: A  119 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8380 (m-30)
REVERT: A  207 LYS cc_start: 0.8251 (ptmm) cc_final: 0.7921 (pttp)
REVERT: A  231 LYS cc_start: 0.6056 (mptt) cc_final: 0.5745 (mptt)
REVERT: C  241 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7279 (tpm-80)
REVERT: B  251 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7684 (mm-30)
REVERT: B  282 ARG cc_start: 0.8226 (ttm110) cc_final: 0.7900 (ttp-170)
  outliers start: 14
  outliers final: 6
  residues processed: 71
  average time/residue: 1.2998
  time to fit residues: 99.4158
Evaluate side-chains
  72 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  241 ARG
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain C residue  257 THR
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.148092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.100082 restraints weight = 14846.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.74
r_work: 0.3154 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3029 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11190  Z= 0.134
  Angle     :  0.585  10.074  16051  Z= 0.310
  Chirality :  0.037   0.191   1916
  Planarity :  0.004   0.033   1259
  Dihedral  : 26.105 179.903   3825
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.05 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.31), residues: 750
  helix:  1.36 (0.27), residues: 400
  sheet:  1.33 (0.59), residues: 68
  loop : -1.34 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.012   0.001   PHE B  92 
 TYR   0.011   0.001   TYR B 179 
 ARG   0.003   0.000   ARG C 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04443 (  484)
  hydrogen bonds       : angle       3.37940 ( 1238)
  covalent geometry    : bond        0.00287 (11190)
  covalent geometry    : angle       0.58541 (16051)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7854 (m-30) cc_final: 0.7603 (m-30)
REVERT: A  119 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8361 (m-30)
REVERT: A  207 LYS cc_start: 0.8234 (ptmm) cc_final: 0.7907 (pttp)
REVERT: A  231 LYS cc_start: 0.6068 (mptt) cc_final: 0.5636 (mptt)
REVERT: C  241 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7278 (tpm-80)
REVERT: B   54 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6267 (tt0)
REVERT: B  251 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7704 (mm-30)
REVERT: B  282 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7898 (ttp-170)
  outliers start: 14
  outliers final: 6
  residues processed: 70
  average time/residue: 1.2825
  time to fit residues: 96.9988
Evaluate side-chains
  73 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  241 ARG
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain C residue  257 THR
Chi-restraints excluded: chain B residue   54 GLU
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 79 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 68 optimal weight:    0.4980
   chunk 88 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 82 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    2.0986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.146596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.098239 restraints weight = 14761.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.77
r_work: 0.3127 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.1135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11190  Z= 0.189
  Angle     :  0.613  10.783  16051  Z= 0.325
  Chirality :  0.039   0.196   1916
  Planarity :  0.004   0.035   1259
  Dihedral  : 26.123 179.877   3825
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.05 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.30), residues: 750
  helix:  1.24 (0.27), residues: 400
  sheet:  1.25 (0.58), residues: 68
  loop : -1.40 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A 280 
 PHE   0.013   0.002   PHE B  92 
 TYR   0.013   0.001   TYR B 179 
 ARG   0.003   0.000   ARG C 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05062 (  484)
  hydrogen bonds       : angle       3.49263 ( 1238)
  covalent geometry    : bond        0.00430 (11190)
  covalent geometry    : angle       0.61320 (16051)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.7900 (m-30) cc_final: 0.7618 (m-30)
REVERT: A  119 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8392 (m-30)
REVERT: A  231 LYS cc_start: 0.6102 (mptt) cc_final: 0.5789 (mptt)
REVERT: C  241 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7249 (tpm-80)
REVERT: B   54 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6316 (tt0)
REVERT: B  251 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7717 (mm-30)
REVERT: B  282 ARG cc_start: 0.8206 (ttm110) cc_final: 0.7886 (ttp-170)
  outliers start: 14
  outliers final: 8
  residues processed: 72
  average time/residue: 1.2402
  time to fit residues: 96.4641
Evaluate side-chains
  75 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  241 ARG
Chi-restraints excluded: chain C residue  242 SER
Chi-restraints excluded: chain C residue  257 THR
Chi-restraints excluded: chain B residue   54 GLU
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 85 optimal weight:    7.9990
   chunk 21 optimal weight:    0.7980
   chunk 74 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0270
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.3644

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.147080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.098886 restraints weight = 14733.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.75
r_work: 0.3137 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11190  Z= 0.155
  Angle     :  0.603  11.327  16051  Z= 0.320
  Chirality :  0.037   0.194   1916
  Planarity :  0.004   0.034   1259
  Dihedral  : 26.121 179.586   3825
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.05 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.30), residues: 750
  helix:  1.27 (0.27), residues: 400
  sheet:  1.28 (0.58), residues: 68
  loop : -1.39 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.012   0.001   PHE B  92 
 TYR   0.013   0.001   TYR B 179 
 ARG   0.002   0.000   ARG C 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04781 (  484)
  hydrogen bonds       : angle       3.47361 ( 1238)
  covalent geometry    : bond        0.00343 (11190)
  covalent geometry    : angle       0.60303 (16051)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8262.70 seconds
wall clock time: 146 minutes 56.06 seconds (8816.06 seconds total)