Starting phenix.real_space_refine
on Fri Jan 17 00:45:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yju_39350/01_2025/8yju_39350.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yju_39350/01_2025/8yju_39350.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yju_39350/01_2025/8yju_39350.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yju_39350/01_2025/8yju_39350.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yju_39350/01_2025/8yju_39350.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yju_39350/01_2025/8yju_39350.cif"
  }
  resolution = 3.78
  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
  Anisotropic ADP refinement not supported. Converting 361 atoms to isotropic.
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      64      5.49       5
     S      61      5.16       5
     C    6060      2.51       5
     N    1669      2.21       5
     O    2085      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 9939
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1955
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 7, 'TRANS': 246}
    Chain: "A"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1947
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 7, 'TRANS': 245}
    Chain: "C"
      Number of atoms: 1940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1940
          Classifications: {'peptide': 253}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 7, 'TRANS': 245}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "D"
      Number of atoms: 2769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2769
          Classifications: {'peptide': 351}
          Link IDs: {'PTRANS': 15, 'TRANS': 335}
    Chain: "J"
      Number of atoms: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 406
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "E"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 638
          Classifications: {'DNA': 31}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 30}
    Chain: "F"
      Number of atoms: 224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 224
          Classifications: {'DNA': 11}
          Link IDs: {'rna3p': 10}
    Chain: "H"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 60
          Classifications: {'DNA': 3}
          Link IDs: {'rna3p': 2}
  Time building chain proxies: 6.34, per 1000 atoms: 0.64
  Number of scatterers: 9939
  At special positions: 0
  Unit cell: (111.22, 101.26, 108.73, 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      61     16.00
     P      64     15.00
     O    2085      8.00
     N    1669      7.00
     C    6060      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: 2.81
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2098

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 11 sheets defined
      31.2% alpha, 25.0% beta
      16 base pairs and 53 stacking pairs defined.
    Time for finding SS restraints: 3.81
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 20
      removed outlier: 4.325A  pdb=" N   LEU B  12 " --> pdb=" O   GLN B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 80
    Processing helix  chain 'B' and resid 141 through 152
    Processing helix  chain 'B' and resid 209 through 216
    Processing helix  chain 'B' and resid 217 through 219
      No H-bonds generated for 'chain 'B' and resid 217 through 219'
    Processing helix  chain 'A' and resid 8 through 20
      removed outlier: 4.274A  pdb=" N   LEU A  12 " --> pdb=" O   GLN A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 82
    Processing helix  chain 'A' and resid 141 through 155
      removed outlier: 3.538A  pdb=" N   HIS A 153 " --> pdb=" O   ARG A 149 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ILE A 154 " --> pdb=" O   ASP A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 216
    Processing helix  chain 'A' and resid 217 through 219
      No H-bonds generated for 'chain 'A' and resid 217 through 219'
    Processing helix  chain 'C' and resid 9 through 20
    Processing helix  chain 'C' and resid 72 through 80
    Processing helix  chain 'C' and resid 140 through 155
      removed outlier: 3.995A  pdb=" N   HIS C 153 " --> pdb=" O   ARG C 149 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   ILE C 154 " --> pdb=" O   ASP C 150 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY C 155 " --> pdb=" O   LEU C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 216
    Processing helix  chain 'D' and resid 5 through 14
    Processing helix  chain 'D' and resid 22 through 26
      removed outlier: 4.142A  pdb=" N   TYR D  26 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 46
      removed outlier: 3.611A  pdb=" N   ALA D  45 " --> pdb=" O   GLN D  41 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   VAL D  46 " --> pdb=" O   PHE D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 77
    Processing helix  chain 'D' and resid 90 through 118
      removed outlier: 3.984A  pdb=" N   GLU D  96 " --> pdb=" O   LEU D  92 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   GLN D 113 " --> pdb=" O   LYS D 109 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 130
    Processing helix  chain 'D' and resid 134 through 149
    Processing helix  chain 'D' and resid 158 through 169
    Processing helix  chain 'D' and resid 180 through 186
      removed outlier: 3.661A  pdb=" N   THR D 184 " --> pdb=" O   MET D 180 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 217
    Processing helix  chain 'D' and resid 219 through 230
    Processing helix  chain 'D' and resid 242 through 254
      removed outlier: 3.649A  pdb=" N   ALA D 246 " --> pdb=" O   GLY D 242 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 262
    Processing helix  chain 'D' and resid 275 through 285
    Processing helix  chain 'D' and resid 302 through 311
      removed outlier: 3.601A  pdb=" N   LEU D 306 " --> pdb=" O   ASN D 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 318 through 334
      removed outlier: 3.740A  pdb=" N   GLY D 334 " --> pdb=" O   LYS D 330 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 339 through 344
      removed outlier: 4.006A  pdb=" N   PHE D 343 " --> pdb=" O   ARG D 339 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 61
      removed outlier: 3.502A  pdb=" N   LEU B  99 " --> pdb=" O   MET B 116 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU A 205 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 71
      removed outlier: 3.697A  pdb=" N   MET B  68 " --> pdb=" O   TRP B  28 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   GLU B  25 " --> pdb=" O   MET B  40 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   MET B  40 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   CYS B  27 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN B  38 " --> pdb=" O   CYS B  27 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLY B  34 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU B  50 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   SER B  39 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLY B 245 " --> pdb=" O   ILE B 241 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   LYS B 240 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   THR B 224 " --> pdb=" O   LYS B 240 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 206 through 208
      removed outlier: 5.167A  pdb=" N   ALA B 157 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   SER B 172 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   SER C 112 " --> pdb=" O   PHE C 103 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   THR C  59 " --> pdb=" O   ARG C   5 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 4 through 5
    Processing sheet with id=AA5, first strand: chain 'A' and resid 66 through 71
      removed outlier: 3.704A  pdb=" N   MET A  68 " --> pdb=" O   TRP A  28 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   GLU A  25 " --> pdb=" O   MET A  40 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   MET A  40 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   CYS A  27 " --> pdb=" O   GLN A  38 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   GLN A  38 " --> pdb=" O   CYS A  27 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   GLY A 245 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   SER A 230 " --> pdb=" O   PRO A 234 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   LYS A 240 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   THR A 224 " --> pdb=" O   LYS A 240 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 92
      removed outlier: 3.645A  pdb=" N   MET A 116 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   SER C 172 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   ALA C 157 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 25 through 27
    Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 30
      removed outlier: 5.447A  pdb=" N   SER C 230 " --> pdb=" O   PRO C 234 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 124 through 127
      removed outlier: 7.206A  pdb=" N   GLN C 125 " --> pdb=" O   THR D 347 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   LYS D 345 " --> pdb=" O   GLY C 127 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 18 through 19
    Processing sheet with id=AB2, first strand: chain 'D' and resid 152 through 154
      removed outlier: 3.605A  pdb=" N   ASP D  34 " --> pdb=" O   ALA D 176 " (cutoff:3.500A)

    442 hydrogen bonds defined for protein.
    1242 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      32 hydrogen bonds
      64 hydrogen bond angles
      0 basepair planarities
      16 basepair parallelities
      53 stacking parallelities
  Total time for adding SS restraints: 3.70

  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 -     1.34: 2791
        1.34 -     1.46: 2255
        1.46 -     1.58: 4952
        1.58 -     1.70: 125
        1.70 -     1.82: 98
  Bond restraints: 10221
  Sorted by residual:
  bond pdb=" CG1 ILE D  72 "
       pdb=" CD1 ILE D  72 "
    ideal  model  delta    sigma   weight residual
    1.513  1.426  0.087 3.90e-02 6.57e+02 4.99e+00
  bond pdb=" C   VAL A 233 "
       pdb=" N   PRO A 234 "
    ideal  model  delta    sigma   weight residual
    1.331  1.358 -0.026 1.20e-02 6.94e+03 4.86e+00
  bond pdb=" CA  ILE D  72 "
       pdb=" CB  ILE D  72 "
    ideal  model  delta    sigma   weight residual
    1.540  1.565 -0.024 1.25e-02 6.40e+03 3.82e+00
  bond pdb=" CB  ASP D  34 "
       pdb=" CG  ASP D  34 "
    ideal  model  delta    sigma   weight residual
    1.516  1.561 -0.045 2.50e-02 1.60e+03 3.20e+00
  bond pdb=" CG  ARG B 149 "
       pdb=" CD  ARG B 149 "
    ideal  model  delta    sigma   weight residual
    1.520  1.573 -0.053 3.00e-02 1.11e+03 3.09e+00
  ... (remaining 10216 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.64: 13668
        2.64 -     5.28: 310
        5.28 -     7.91: 66
        7.91 -    10.55: 19
       10.55 -    13.19: 4
  Bond angle restraints: 14067
  Sorted by residual:
  angle pdb=" N   THR A 219 "
        pdb=" CA  THR A 219 "
        pdb=" C   THR A 219 "
      ideal   model   delta    sigma   weight residual
     109.81  120.98  -11.17 2.21e+00 2.05e-01 2.55e+01
  angle pdb=" C   ALA A 242 "
        pdb=" N   ASP A 243 "
        pdb=" CA  ASP A 243 "
      ideal   model   delta    sigma   weight residual
     121.54  130.81   -9.27 1.91e+00 2.74e-01 2.35e+01
  angle pdb=" C   ALA C 231 "
        pdb=" N   ASP C 232 "
        pdb=" CA  ASP C 232 "
      ideal   model   delta    sigma   weight residual
     121.54  130.46   -8.92 1.91e+00 2.74e-01 2.18e+01
  angle pdb=" N   THR C 219 "
        pdb=" CA  THR C 219 "
        pdb=" C   THR C 219 "
      ideal   model   delta    sigma   weight residual
     109.81  119.55   -9.74 2.21e+00 2.05e-01 1.94e+01
  angle pdb=" CG1 VAL D  52 "
        pdb=" CB  VAL D  52 "
        pdb=" CG2 VAL D  52 "
      ideal   model   delta    sigma   weight residual
     110.80  101.11    9.69 2.20e+00 2.07e-01 1.94e+01
  ... (remaining 14062 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.90: 5533
       27.90 -    55.81: 574
       55.81 -    83.71: 51
       83.71 -   111.61: 5
      111.61 -   139.51: 1
  Dihedral angle restraints: 6164
    sinusoidal: 2930
      harmonic: 3234
  Sorted by residual:
  dihedral pdb=" CA  VAL C   7 "
           pdb=" C   VAL C   7 "
           pdb=" N   GLN C   8 "
           pdb=" CA  GLN C   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.88   21.12     0      5.00e+00 4.00e-02 1.78e+01
  dihedral pdb=" CA  ASP D  51 "
           pdb=" C   ASP D  51 "
           pdb=" N   VAL D  52 "
           pdb=" CA  VAL D  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.91  -21.09     0      5.00e+00 4.00e-02 1.78e+01
  dihedral pdb=" CA  THR C 216 "
           pdb=" C   THR C 216 "
           pdb=" N   LYS C 217 "
           pdb=" CA  LYS C 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.20   20.80     0      5.00e+00 4.00e-02 1.73e+01
  ... (remaining 6161 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1292
       0.063 -    0.125: 269
       0.125 -    0.188: 48
       0.188 -    0.251: 7
       0.251 -    0.314: 3
  Chirality restraints: 1619
  Sorted by residual:
  chirality pdb=" CA  THR C 219 "
            pdb=" N   THR C 219 "
            pdb=" C   THR C 219 "
            pdb=" CB  THR C 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.21    0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" CB  VAL D  52 "
            pdb=" CA  VAL D  52 "
            pdb=" CG1 VAL D  52 "
            pdb=" CG2 VAL D  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.90    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" CA  THR A 219 "
            pdb=" N   THR A 219 "
            pdb=" C   THR A 219 "
            pdb=" CB  THR A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.27    0.26 2.00e-01 2.50e+01 1.64e+00
  ... (remaining 1616 not shown)

  Planarity restraints: 1589
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 128 "    0.063 5.00e-02 4.00e+02   9.58e-02 1.47e+01
        pdb=" N   PRO A 129 "   -0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO A 129 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO A 129 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 219 "    0.051 5.00e-02 4.00e+02   7.51e-02 9.02e+00
        pdb=" N   PRO A 220 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO A 220 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 220 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 139 "   -0.048 5.00e-02 4.00e+02   7.29e-02 8.51e+00
        pdb=" N   PRO B 140 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO B 140 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 140 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 1586 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 2882
        2.84 -     3.35: 8185
        3.35 -     3.87: 17588
        3.87 -     4.38: 19465
        4.38 -     4.90: 32681
  Nonbonded interactions: 80801
  Sorted by model distance:
  nonbonded pdb=" O   VAL D 123 "
            pdb=" OG1 THR D 127 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" OG1 THR D 177 "
            pdb=" OD1 ASP D 179 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" O   CYS B 148 "
            pdb=" OG  SER B 152 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" O   ASN B  71 "
            pdb=" OG  SER B  74 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" OG  SER B  43 "
            pdb=" OH  TYR B 211 "
     model   vdw
     2.368 3.040
  ... (remaining 80796 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 2 through 108 or (resid 109 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 110 through 188 or (resid 189 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 190 through 254))
  selection = (chain 'B' and (resid 2 through 108 or (resid 109 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 110 through 188 or (resid 189 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 190 through 254))
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     28.990
  Find NCS groups from input model:        0.260
  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:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
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   0.087  10221  Z= 0.336
  Angle     :  1.025  13.187  14067  Z= 0.527
  Chirality :  0.056   0.314   1619
  Planarity :  0.008   0.096   1589
  Dihedral  : 19.788 139.515   4066
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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: -3.41 (0.21), residues: 1103
  helix: -2.68 (0.20), residues: 318
  sheet: -1.41 (0.30), residues: 280
  loop : -2.39 (0.22), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 274 
 HIS   0.008   0.002   HIS D  63 
 PHE   0.024   0.003   PHE D  42 
 TYR   0.030   0.003   TYR B 249 
 ARG   0.015   0.001   ARG B 149 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.270 
Fit side-chains
   revert: symmetry clash
REVERT: B  150 ASP cc_start: 0.7795 (p0) cc_final: 0.7540 (p0)
REVERT: A   16 LEU cc_start: 0.8678 (mm) cc_final: 0.8426 (mm)
REVERT: D  234 TYR cc_start: 0.8518 (m-80) cc_final: 0.8114 (m-10)
REVERT: D  269 PRO cc_start: 0.8443 (Cg_endo) cc_final: 0.8189 (Cg_exo)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1968
  time to fit residues: 42.8724
Evaluate side-chains
  115 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 46 optimal weight:    0.3980
   chunk 90 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B  49 GLN
A 204 GLN
C  24 ASN
C 200 ASN
** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.139419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.108126 restraints weight = 16256.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.108575 restraints weight = 14501.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.109631 restraints weight = 13695.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10221  Z= 0.291
  Angle     :  0.647   6.095  14067  Z= 0.356
  Chirality :  0.045   0.156   1619
  Planarity :  0.005   0.063   1589
  Dihedral  : 20.931 148.987   1939
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  9.87 %
    Favored  : 89.41 %
  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: -2.22 (0.22), residues: 1103
  helix: -0.71 (0.26), residues: 324
  sheet: -1.27 (0.30), residues: 288
  loop : -2.06 (0.23), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 274 
 HIS   0.003   0.001   HIS D 253 
 PHE   0.013   0.002   PHE A 144 
 TYR   0.012   0.002   TYR B 239 
 ARG   0.006   0.001   ARG C  53 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 128
  time to evaluate  : 1.197 
Fit side-chains
REVERT: D   37 MET cc_start: 0.7858 (ttp) cc_final: 0.7584 (ttt)
REVERT: D  269 PRO cc_start: 0.8583 (Cg_endo) cc_final: 0.8375 (Cg_exo)
  outliers start: 7
  outliers final: 4
  residues processed: 130
  average time/residue: 0.2017
  time to fit residues: 39.9378
Evaluate side-chains
  108 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain D residue  275 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 45 optimal weight:    0.3980
   chunk 47 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 105 optimal weight:    3.9990
   chunk 98 optimal weight:    0.0170
   chunk 71 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
B  49 GLN
C  24 ASN
** C  38 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 = 0.3990 r_free = 0.3990 target = 0.139883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.109034 restraints weight = 16443.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.109025 restraints weight = 14498.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.110415 restraints weight = 13746.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10221  Z= 0.207
  Angle     :  0.581   6.021  14067  Z= 0.320
  Chirality :  0.043   0.148   1619
  Planarity :  0.004   0.051   1589
  Dihedral  : 20.672 145.217   1939
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.77 %
    Favored  : 86.19 %
  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: -1.64 (0.23), residues: 1103
  helix:  0.28 (0.28), residues: 331
  sheet: -1.36 (0.29), residues: 293
  loop : -1.83 (0.25), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D  63 
 PHE   0.009   0.001   PHE D  42 
 TYR   0.008   0.001   TYR B 239 
 ARG   0.003   0.000   ARG C  53 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 1.087 
Fit side-chains
REVERT: A   75 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7738 (tmm)
REVERT: C   11 ILE cc_start: 0.7849 (mt) cc_final: 0.7630 (mt)
REVERT: D   37 MET cc_start: 0.7763 (ttp) cc_final: 0.7549 (ttt)
REVERT: D   65 MET cc_start: 0.6920 (mmp) cc_final: 0.6650 (mmp)
  outliers start: 10
  outliers final: 7
  residues processed: 122
  average time/residue: 0.1757
  time to fit residues: 33.0478
Evaluate side-chains
  114 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  296 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B  49 GLN
** B 131 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 = 0.3930 r_free = 0.3930 target = 0.135582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.104033 restraints weight = 16229.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.104356 restraints weight = 14375.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.105899 restraints weight = 12898.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10221  Z= 0.316
  Angle     :  0.628   6.455  14067  Z= 0.341
  Chirality :  0.044   0.169   1619
  Planarity :  0.004   0.068   1589
  Dihedral  : 20.829 144.285   1939
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.89 %
    Favored  : 82.24 %
  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: -1.45 (0.24), residues: 1103
  helix:  0.53 (0.28), residues: 334
  sheet: -1.45 (0.29), residues: 287
  loop : -1.66 (0.26), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 274 
 HIS   0.005   0.001   HIS D  63 
 PHE   0.014   0.002   PHE D  42 
 TYR   0.011   0.002   TYR C 239 
 ARG   0.004   0.000   ARG C  61 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 1.035 
Fit side-chains
REVERT: A   75 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7538 (tmm)
REVERT: A  108 GLN cc_start: 0.8210 (mp10) cc_final: 0.7825 (mp10)
REVERT: D   37 MET cc_start: 0.7924 (ttp) cc_final: 0.7646 (ttt)
  outliers start: 18
  outliers final: 10
  residues processed: 120
  average time/residue: 0.1960
  time to fit residues: 35.2438
Evaluate side-chains
  106 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  296 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 105 optimal weight:    0.3980
   chunk 29 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   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  49 GLN
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  48 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 = 0.4094 r_free = 0.4094 target = 0.145920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.116662 restraints weight = 16095.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.115996 restraints weight = 17904.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.117456 restraints weight = 18381.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10221  Z= 0.226
  Angle     :  0.588   8.307  14067  Z= 0.320
  Chirality :  0.043   0.237   1619
  Planarity :  0.004   0.069   1589
  Dihedral  : 20.692 144.720   1939
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.72 %
    Favored  : 81.31 %
  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: -1.24 (0.24), residues: 1103
  helix:  0.82 (0.29), residues: 333
  sheet: -1.30 (0.30), residues: 273
  loop : -1.64 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 274 
 HIS   0.005   0.001   HIS D  63 
 PHE   0.020   0.001   PHE D  68 
 TYR   0.011   0.002   TYR C 239 
 ARG   0.006   0.000   ARG B 149 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 1.121 
Fit side-chains
REVERT: B   37 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8281 (tt)
REVERT: A   75 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7483 (tmm)
REVERT: A  108 GLN cc_start: 0.7984 (mp10) cc_final: 0.7637 (mp10)
REVERT: A  131 GLN cc_start: 0.8219 (pm20) cc_final: 0.7634 (pm20)
REVERT: C   11 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7609 (mt)
REVERT: C  205 LEU cc_start: 0.8733 (mp) cc_final: 0.8452 (mt)
  outliers start: 19
  outliers final: 11
  residues processed: 123
  average time/residue: 0.1797
  time to fit residues: 33.5159
Evaluate side-chains
  114 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  296 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 59 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B  49 GLN
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 137 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.145437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.115998 restraints weight = 16275.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.115299 restraints weight = 18154.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.116511 restraints weight = 18788.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.3232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10221  Z= 0.252
  Angle     :  0.609   8.229  14067  Z= 0.328
  Chirality :  0.044   0.221   1619
  Planarity :  0.004   0.066   1589
  Dihedral  : 20.685 144.576   1939
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.13 %
    Favored  : 80.27 %
  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: -1.20 (0.24), residues: 1103
  helix:  0.94 (0.29), residues: 333
  sheet: -1.40 (0.29), residues: 278
  loop : -1.61 (0.26), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 274 
 HIS   0.004   0.001   HIS D  63 
 PHE   0.022   0.002   PHE D  68 
 TYR   0.011   0.002   TYR C 239 
 ARG   0.003   0.000   ARG B 149 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 1.060 
Fit side-chains
REVERT: B   37 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8170 (tt)
REVERT: A   25 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6749 (mt-10)
REVERT: A   75 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7496 (tmm)
REVERT: A  131 GLN cc_start: 0.8226 (pm20) cc_final: 0.7721 (pm20)
REVERT: C   25 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7372 (mm-30)
REVERT: D  160 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5905 (mt-10)
  outliers start: 25
  outliers final: 15
  residues processed: 131
  average time/residue: 0.1783
  time to fit residues: 35.6186
Evaluate side-chains
  121 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  244 MET
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  296 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 112 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0970
   chunk 56 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0470
   chunk 16 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.4876

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

Flipped N/Q/H residues before XYZ refinement:
B  49 GLN
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 193 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.147193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.117602 restraints weight = 16407.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.117131 restraints weight = 17537.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.118452 restraints weight = 18156.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.3357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  10221  Z= 0.207
  Angle     :  0.599   7.612  14067  Z= 0.324
  Chirality :  0.043   0.218   1619
  Planarity :  0.004   0.066   1589
  Dihedral  : 20.677 144.933   1939
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.90 %
    Favored  : 79.13 %
  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: -1.12 (0.24), residues: 1103
  helix:  1.04 (0.29), residues: 334
  sheet: -1.38 (0.28), residues: 283
  loop : -1.57 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  28 
 HIS   0.004   0.001   HIS B  44 
 PHE   0.019   0.001   PHE D  68 
 TYR   0.009   0.001   TYR D  40 
 ARG   0.002   0.000   ARG B 149 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 1.138 
Fit side-chains
REVERT: B   37 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8294 (tt)
REVERT: B   90 LEU cc_start: 0.8967 (mm) cc_final: 0.8660 (mp)
REVERT: A   75 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7385 (tmm)
REVERT: A  131 GLN cc_start: 0.8054 (pm20) cc_final: 0.7533 (pm20)
REVERT: C   11 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7672 (mt)
REVERT: C   25 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7345 (mm-30)
REVERT: C   68 MET cc_start: 0.8518 (pmm) cc_final: 0.8132 (pmm)
REVERT: C  205 LEU cc_start: 0.8765 (mp) cc_final: 0.8503 (mt)
REVERT: D   40 TYR cc_start: 0.7760 (m-10) cc_final: 0.7253 (m-10)
REVERT: D  160 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.5908 (mt-10)
  outliers start: 19
  outliers final: 13
  residues processed: 125
  average time/residue: 0.1778
  time to fit residues: 34.4593
Evaluate side-chains
  118 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  296 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   chunk 111 optimal weight:    6.9990
   chunk 114 optimal weight:    6.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
B  49 GLN
** B 131 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 = 0.4077 r_free = 0.4077 target = 0.144564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.115895 restraints weight = 16450.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.114381 restraints weight = 17425.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.114719 restraints weight = 18472.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.3599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  10221  Z= 0.284
  Angle     :  0.621   6.961  14067  Z= 0.334
  Chirality :  0.044   0.210   1619
  Planarity :  0.004   0.061   1589
  Dihedral  : 20.749 144.280   1939
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 18.90 %
    Favored  : 79.02 %
  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: -1.15 (0.25), residues: 1103
  helix:  1.07 (0.29), residues: 334
  sheet: -1.49 (0.28), residues: 285
  loop : -1.56 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  28 
 HIS   0.003   0.001   HIS D  63 
 PHE   0.017   0.002   PHE D  68 
 TYR   0.010   0.002   TYR C 239 
 ARG   0.003   0.000   ARG C  61 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 1.034 
Fit side-chains
REVERT: B   37 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8285 (tt)
REVERT: A   75 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7078 (tmm)
REVERT: A  119 MET cc_start: 0.7096 (ppp) cc_final: 0.6595 (ppp)
REVERT: A  131 GLN cc_start: 0.8103 (pm20) cc_final: 0.7610 (pm20)
REVERT: C   25 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7366 (mm-30)
REVERT: C   68 MET cc_start: 0.8650 (pmm) cc_final: 0.8244 (pmm)
  outliers start: 20
  outliers final: 18
  residues processed: 121
  average time/residue: 0.1723
  time to fit residues: 32.1411
Evaluate side-chains
  122 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  244 MET
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   58 ASP
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  296 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 10 optimal weight:    0.4980
   chunk 30 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 76 optimal weight:    0.7980
   chunk 111 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 131 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 = 0.4087 r_free = 0.4087 target = 0.145333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.115708 restraints weight = 16463.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.115900 restraints weight = 18007.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.116911 restraints weight = 19499.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  10221  Z= 0.243
  Angle     :  0.611   6.985  14067  Z= 0.330
  Chirality :  0.043   0.211   1619
  Planarity :  0.004   0.063   1589
  Dihedral  : 20.745 144.384   1939
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 19.73 %
    Favored  : 78.09 %
  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: -1.13 (0.25), residues: 1103
  helix:  1.11 (0.29), residues: 334
  sheet: -1.49 (0.28), residues: 287
  loop : -1.55 (0.26), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  28 
 HIS   0.003   0.001   HIS D  63 
 PHE   0.020   0.001   PHE D  68 
 TYR   0.011   0.002   TYR C 239 
 ARG   0.004   0.000   ARG A 146 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 1.030 
Fit side-chains
REVERT: B    1 MET cc_start: 0.7274 (ppp) cc_final: 0.6811 (ptt)
REVERT: B   37 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8303 (tt)
REVERT: B   90 LEU cc_start: 0.9018 (mm) cc_final: 0.8678 (mp)
REVERT: A   75 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7409 (tmm)
REVERT: A  131 GLN cc_start: 0.8011 (pm20) cc_final: 0.7532 (pm20)
REVERT: C   68 MET cc_start: 0.8602 (pmm) cc_final: 0.8181 (pmm)
REVERT: D  160 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5960 (mt-10)
  outliers start: 21
  outliers final: 16
  residues processed: 120
  average time/residue: 0.1733
  time to fit residues: 32.2891
Evaluate side-chains
  121 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  244 MET
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  296 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0370
   chunk 72 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0970
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.5056

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

Flipped N/Q/H residues before XYZ refinement:
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  48 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 = 0.4100 r_free = 0.4100 target = 0.146398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.117012 restraints weight = 16324.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.116637 restraints weight = 18033.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.117953 restraints weight = 19016.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10221  Z= 0.212
  Angle     :  0.606  11.710  14067  Z= 0.325
  Chirality :  0.043   0.211   1619
  Planarity :  0.004   0.061   1589
  Dihedral  : 20.714 144.542   1939
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 20.35 %
    Favored  : 77.57 %
  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: -1.06 (0.25), residues: 1103
  helix:  1.16 (0.29), residues: 334
  sheet: -1.48 (0.28), residues: 287
  loop : -1.50 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  28 
 HIS   0.004   0.001   HIS D  63 
 PHE   0.021   0.001   PHE D  68 
 TYR   0.010   0.001   TYR C 239 
 ARG   0.002   0.000   ARG B 149 

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 1.076 
Fit side-chains
REVERT: B    1 MET cc_start: 0.7397 (ppp) cc_final: 0.6920 (ptt)
REVERT: B   37 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8275 (tt)
REVERT: B   90 LEU cc_start: 0.8985 (mm) cc_final: 0.8652 (mp)
REVERT: A   75 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7387 (tmm)
REVERT: A  131 GLN cc_start: 0.7981 (pm20) cc_final: 0.7514 (pm20)
REVERT: C   25 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7299 (mm-30)
REVERT: C   68 MET cc_start: 0.8569 (pmm) cc_final: 0.8118 (pmm)
REVERT: D   40 TYR cc_start: 0.7802 (m-80) cc_final: 0.7356 (m-10)
REVERT: D   77 ASN cc_start: 0.7181 (t0) cc_final: 0.6941 (t0)
REVERT: D  160 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.5887 (mt-10)
  outliers start: 20
  outliers final: 16
  residues processed: 119
  average time/residue: 0.1775
  time to fit residues: 33.1153
Evaluate side-chains
  122 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  244 MET
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  296 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 115 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 109 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 104 optimal weight:    6.9990
   chunk 107 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** B 131 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 = 0.4058 r_free = 0.4058 target = 0.143140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.113163 restraints weight = 16491.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.112586 restraints weight = 18091.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.113725 restraints weight = 21048.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.3868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  10221  Z= 0.347
  Angle     :  0.656   9.479  14067  Z= 0.351
  Chirality :  0.045   0.206   1619
  Planarity :  0.004   0.061   1589
  Dihedral  : 20.794 143.787   1939
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.83 %
    Favored  : 77.88 %
  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: -1.18 (0.25), residues: 1103
  helix:  1.06 (0.28), residues: 334
  sheet: -1.58 (0.28), residues: 291
  loop : -1.55 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  28 
 HIS   0.005   0.001   HIS D 208 
 PHE   0.017   0.002   PHE D  68 
 TYR   0.014   0.002   TYR C 239 
 ARG   0.004   0.000   ARG C  61 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2767.00 seconds
wall clock time: 50 minutes 58.86 seconds (3058.86 seconds total)