Starting phenix.real_space_refine
on Tue Jan 14 23:18:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xda_38271/01_2025/8xda_38271_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xda_38271/01_2025/8xda_38271.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xda_38271/01_2025/8xda_38271.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xda_38271/01_2025/8xda_38271.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xda_38271/01_2025/8xda_38271_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xda_38271/01_2025/8xda_38271_neut.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.169
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    5100      2.51       5
     N    1158      2.21       5
     O    1305      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 7620
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2530
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 328, 2510
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 306}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
      Conformer: "B"
        Number of residues, atoms: 328, 2510
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 306}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
          bond proxies already assigned to first conformer: 2565
    Chain: "B"
      Number of atoms: 2530
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 328, 2510
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 306}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
      Conformer: "B"
        Number of residues, atoms: 328, 2510
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 306}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
          bond proxies already assigned to first conformer: 2565
    Chain: "C"
      Number of atoms: 2530
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 328, 2510
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 306}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
      Conformer: "B"
        Number of residues, atoms: 328, 2510
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 306}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
          bond proxies already assigned to first conformer: 2565
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 2, 8
          Unusual residues: {'URE': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 2, 8
          Unusual residues: {'URE': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 2, 8
          Unusual residues: {'URE': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N  APHE A 120 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 120 " occ=0.50
    residue:
      pdb=" N  APHE B 120 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE B 120 " occ=0.50
    residue:
      pdb=" N  APHE C 120 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE C 120 " occ=0.50
    residue:
      pdb=" C  AURE A 401 " occ=0.25
      ... (2 atoms not shown)
      pdb=" N2 AURE A 401 " occ=0.25
    residue:
      pdb=" C  AURE B 401 " occ=0.25
      ... (2 atoms not shown)
      pdb=" N2 AURE B 401 " occ=0.25
    residue:
      pdb=" C  AURE C 401 " occ=0.25
      ... (2 atoms not shown)
      pdb=" N2 AURE C 401 " occ=0.25
  Time building chain proxies: 9.11, per 1000 atoms: 1.20
  Number of scatterers: 7620
  At special positions: 0
  Unit cell: (94.76, 89.24, 71.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    1305      8.00
     N    1158      7.00
     C    5100      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: 2.21
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1830

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 0 sheets defined
      77.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 52 through 68
      removed outlier: 3.867A  pdb=" N   VAL A  68 " --> pdb=" O   GLY A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 88
      removed outlier: 3.759A  pdb=" N   ASN A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 109
    Processing helix  chain 'A' and resid 112 through 117
    Processing helix  chain 'A' and resid 122 through 135
      removed outlier: 4.018A  pdb=" N   LEU A 127 " --> pdb=" O   TYR A 123 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL A 128 " --> pdb=" O   ASN A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 144
      No H-bonds generated for 'chain 'A' and resid 142 through 144'
    Processing helix  chain 'A' and resid 145 through 167
      Proline residue:  A 157  - end of helix
      removed outlier: 3.970A  pdb=" N   GLY A 164 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 191
    Processing helix  chain 'A' and resid 212 through 216
      removed outlier: 3.885A  pdb=" N   VAL A 216 " --> pdb=" O   TRP A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 231
      removed outlier: 4.334A  pdb=" N   ILE A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      Proline residue:  A 226  - end of helix
    Processing helix  chain 'A' and resid 232 through 234
      No H-bonds generated for 'chain 'A' and resid 232 through 234'
    Processing helix  chain 'A' and resid 237 through 252
      removed outlier: 3.642A  pdb=" N   SER A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 273
    Processing helix  chain 'A' and resid 276 through 283
      removed outlier: 3.535A  pdb=" N   ILE A 280 " --> pdb=" O   PRO A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 297
    Processing helix  chain 'A' and resid 304 through 330
    Processing helix  chain 'A' and resid 338 through 350
    Processing helix  chain 'A' and resid 362 through 366
    Processing helix  chain 'A' and resid 368 through 379
    Processing helix  chain 'B' and resid 53 through 67
    Processing helix  chain 'B' and resid 68 through 70
      No H-bonds generated for 'chain 'B' and resid 68 through 70'
    Processing helix  chain 'B' and resid 73 through 88
      removed outlier: 3.759A  pdb=" N   ASN B  88 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 109
    Processing helix  chain 'B' and resid 112 through 117
    Processing helix  chain 'B' and resid 122 through 135
      removed outlier: 4.018A  pdb=" N   LEU B 127 " --> pdb=" O   TYR B 123 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL B 128 " --> pdb=" O   ASN B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 144
      No H-bonds generated for 'chain 'B' and resid 142 through 144'
    Processing helix  chain 'B' and resid 145 through 167
      Proline residue:  B 157  - end of helix
      removed outlier: 3.969A  pdb=" N   GLY B 164 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 191
    Processing helix  chain 'B' and resid 212 through 216
      removed outlier: 3.885A  pdb=" N   VAL B 216 " --> pdb=" O   TRP B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 231
      removed outlier: 4.334A  pdb=" N   ILE B 225 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      Proline residue:  B 226  - end of helix
    Processing helix  chain 'B' and resid 232 through 234
      No H-bonds generated for 'chain 'B' and resid 232 through 234'
    Processing helix  chain 'B' and resid 237 through 252
      removed outlier: 3.643A  pdb=" N   SER B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 273
    Processing helix  chain 'B' and resid 276 through 283
      removed outlier: 3.535A  pdb=" N   ILE B 280 " --> pdb=" O   PRO B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 297
    Processing helix  chain 'B' and resid 304 through 330
    Processing helix  chain 'B' and resid 338 through 350
    Processing helix  chain 'B' and resid 362 through 366
    Processing helix  chain 'B' and resid 368 through 379
    Processing helix  chain 'C' and resid 53 through 67
    Processing helix  chain 'C' and resid 68 through 70
      No H-bonds generated for 'chain 'C' and resid 68 through 70'
    Processing helix  chain 'C' and resid 73 through 88
      removed outlier: 3.758A  pdb=" N   ASN C  88 " --> pdb=" O   LEU C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 109
    Processing helix  chain 'C' and resid 112 through 117
    Processing helix  chain 'C' and resid 122 through 135
      removed outlier: 4.018A  pdb=" N   LEU C 127 " --> pdb=" O   TYR C 123 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL C 128 " --> pdb=" O   ASN C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 144
      No H-bonds generated for 'chain 'C' and resid 142 through 144'
    Processing helix  chain 'C' and resid 145 through 167
      Proline residue:  C 157  - end of helix
      removed outlier: 3.969A  pdb=" N   GLY C 164 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 191
    Processing helix  chain 'C' and resid 212 through 216
      removed outlier: 3.885A  pdb=" N   VAL C 216 " --> pdb=" O   TRP C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 231
      removed outlier: 4.334A  pdb=" N   ILE C 225 " --> pdb=" O   LEU C 221 " (cutoff:3.500A)
      Proline residue:  C 226  - end of helix
    Processing helix  chain 'C' and resid 232 through 234
      No H-bonds generated for 'chain 'C' and resid 232 through 234'
    Processing helix  chain 'C' and resid 237 through 252
      removed outlier: 3.642A  pdb=" N   SER C 251 " --> pdb=" O   ALA C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 273
    Processing helix  chain 'C' and resid 276 through 283
      removed outlier: 3.535A  pdb=" N   ILE C 280 " --> pdb=" O   PRO C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 297
    Processing helix  chain 'C' and resid 304 through 330
    Processing helix  chain 'C' and resid 338 through 350
    Processing helix  chain 'C' and resid 362 through 366
    Processing helix  chain 'C' and resid 368 through 379

    502 hydrogen bonds defined for protein.
    1479 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.31

  Time building geometry restraints manager: 2.50 seconds

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

  Histogram of bond lengths:
        1.11 -     1.25: 1113
        1.25 -     1.39: 2034
        1.39 -     1.53: 4350
        1.53 -     1.67: 273
        1.67 -     1.81: 87
  Bond restraints: 7857
  Sorted by residual:
  bond pdb=" C   URE A 402 "
       pdb=" O   URE A 402 "
    ideal  model  delta    sigma   weight residual
    1.225  1.115  0.110 2.00e-02 2.50e+03 3.05e+01
  bond pdb=" C   URE C 402 "
       pdb=" O   URE C 402 "
    ideal  model  delta    sigma   weight residual
    1.225  1.115  0.110 2.00e-02 2.50e+03 3.04e+01
  bond pdb=" C   URE B 402 "
       pdb=" O   URE B 402 "
    ideal  model  delta    sigma   weight residual
    1.225  1.115  0.110 2.00e-02 2.50e+03 3.04e+01
  bond pdb=" CA  SER C 168 "
       pdb=" C   SER C 168 "
    ideal  model  delta    sigma   weight residual
    1.523  1.449  0.074 1.41e-02 5.03e+03 2.72e+01
  bond pdb=" CA  SER A 168 "
       pdb=" C   SER A 168 "
    ideal  model  delta    sigma   weight residual
    1.523  1.449  0.073 1.41e-02 5.03e+03 2.70e+01
  ... (remaining 7852 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 10560
        2.60 -     5.20: 197
        5.20 -     7.80: 22
        7.80 -    10.40: 6
       10.40 -    13.00: 6
  Bond angle restraints: 10791
  Sorted by residual:
  angle pdb=" N   THR C 165 "
        pdb=" CA  THR C 165 "
        pdb=" C   THR C 165 "
      ideal   model   delta    sigma   weight residual
     114.31  101.31   13.00 1.29e+00 6.01e-01 1.02e+02
  angle pdb=" N   THR B 165 "
        pdb=" CA  THR B 165 "
        pdb=" C   THR B 165 "
      ideal   model   delta    sigma   weight residual
     114.31  101.33   12.98 1.29e+00 6.01e-01 1.01e+02
  angle pdb=" N   THR A 165 "
        pdb=" CA  THR A 165 "
        pdb=" C   THR A 165 "
      ideal   model   delta    sigma   weight residual
     114.31  101.34   12.97 1.29e+00 6.01e-01 1.01e+02
  angle pdb=" N   TRP B 170 "
        pdb=" CA  TRP B 170 "
        pdb=" C   TRP B 170 "
      ideal   model   delta    sigma   weight residual
     113.61  104.49    9.12 1.50e+00 4.44e-01 3.70e+01
  angle pdb=" N   TRP A 170 "
        pdb=" CA  TRP A 170 "
        pdb=" C   TRP A 170 "
      ideal   model   delta    sigma   weight residual
     113.61  104.49    9.12 1.50e+00 4.44e-01 3.70e+01
  ... (remaining 10786 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.31: 3836
       12.31 -    24.62: 442
       24.62 -    36.92: 133
       36.92 -    49.23: 29
       49.23 -    61.54: 18
  Dihedral angle restraints: 4458
    sinusoidal: 1593
      harmonic: 2865
  Sorted by residual:
  dihedral pdb=" C   THR A 338 "
           pdb=" N   THR A 338 "
           pdb=" CA  THR A 338 "
           pdb=" CB  THR A 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.47   13.47     0      2.50e+00 1.60e-01 2.90e+01
  dihedral pdb=" C   THR B 338 "
           pdb=" N   THR B 338 "
           pdb=" CA  THR B 338 "
           pdb=" CB  THR B 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.41   13.41     0      2.50e+00 1.60e-01 2.88e+01
  dihedral pdb=" C   THR C 338 "
           pdb=" N   THR C 338 "
           pdb=" CA  THR C 338 "
           pdb=" CB  THR C 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.37   13.37     0      2.50e+00 1.60e-01 2.86e+01
  ... (remaining 4455 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 1219
       0.107 -    0.214: 48
       0.214 -    0.321: 2
       0.321 -    0.428: 0
       0.428 -    0.534: 6
  Chirality restraints: 1275
  Sorted by residual:
  chirality pdb=" CA  PHE C  70 "
            pdb=" N   PHE C  70 "
            pdb=" C   PHE C  70 "
            pdb=" CB  PHE C  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 7.14e+00
  chirality pdb=" CA  PHE A  70 "
            pdb=" N   PHE A  70 "
            pdb=" C   PHE A  70 "
            pdb=" CB  PHE A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 7.10e+00
  chirality pdb=" CA  PHE B  70 "
            pdb=" N   PHE B  70 "
            pdb=" C   PHE B  70 "
            pdb=" CB  PHE B  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 7.09e+00
  ... (remaining 1272 not shown)

  Planarity restraints: 1314
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 305 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.83e+00
        pdb=" C   TRP A 305 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   TRP A 305 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLN A 306 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 305 "   -0.010 2.00e-02 2.50e+03   1.94e-02 3.78e+00
        pdb=" C   TRP B 305 "    0.034 2.00e-02 2.50e+03
        pdb=" O   TRP B 305 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLN B 306 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP C 305 "    0.010 2.00e-02 2.50e+03   1.93e-02 3.71e+00
        pdb=" C   TRP C 305 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   TRP C 305 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLN C 306 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1311 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2295
        2.81 -     3.33: 7825
        3.33 -     3.86: 13491
        3.86 -     4.38: 16568
        4.38 -     4.90: 27256
  Nonbonded interactions: 67435
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 180 "
            pdb=" O   CYS A 337 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" ND2 ASN B 180 "
            pdb=" O   CYS B 337 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" ND2 ASN C 180 "
            pdb=" O   CYS C 337 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" OG  SER A 102 "
            pdb=" O   HIS A 121 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" OG  SER B 102 "
            pdb=" O   HIS B 121 "
     model   vdw
     2.326 3.040
  ... (remaining 67430 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.25 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     28.250
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.070
  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:14.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
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      :  0.008   0.110   7857  Z= 0.553
  Angle     :  0.862  13.001  10791  Z= 0.495
  Chirality :  0.061   0.534   1275
  Planarity :  0.006   0.040   1314
  Dihedral  : 12.749  61.536   2628
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  0.73 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.33 %
  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 (0.27), residues: 990
  helix:  0.66 (0.19), residues: 693
  sheet:  None (None), residues: 0
  loop : -0.04 (0.39), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 305 
 HIS   0.004   0.002   HIS A 258 
 PHE   0.013   0.002   PHE B 287 
 TYR   0.014   0.002   TYR C 123 
 ARG   0.001   0.000   ARG A 223 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.819 
Fit side-chains
  outliers start: 8
  outliers final: 0
  residues processed: 57
  average time/residue: 1.0747
  time to fit residues: 66.3877
Evaluate side-chains
  45 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 75 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  72 ASN
C  72 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.128268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.112159 restraints weight = 29069.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 2.50
r_work: 0.3240 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2934
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7857  Z= 0.258
  Angle     :  0.609   7.385  10791  Z= 0.302
  Chirality :  0.044   0.143   1275
  Planarity :  0.005   0.038   1314
  Dihedral  :  4.656  18.917   1044
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  4.76 %
    Favored  : 94.51 %
  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:  0.90 (0.26), residues: 990
  helix:  0.88 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.13 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 339 
 HIS   0.003   0.001   HIS A 258 
 PHE   0.014   0.001   PHE A 287 
 TYR   0.010   0.001   TYR C 123 
 ARG   0.001   0.000   ARG A  63 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A  168 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.8224 (p)
  outliers start: 6
  outliers final: 3
  residues processed: 49
  average time/residue: 1.1722
  time to fit residues: 61.8119
Evaluate side-chains
  47 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain C residue  160 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 86 optimal weight:    0.4980
   chunk 95 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.120483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.104718 restraints weight = 27941.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 2.38
r_work: 0.3139 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7857  Z= 0.255
  Angle     :  0.570   7.277  10791  Z= 0.284
  Chirality :  0.042   0.120   1275
  Planarity :  0.005   0.039   1314
  Dihedral  :  4.420  15.983   1044
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  6.47 %
    Favored  : 93.04 %
  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:  1.22 (0.27), residues: 990
  helix:  1.11 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.25 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 170 
 HIS   0.003   0.001   HIS A 258 
 PHE   0.012   0.001   PHE A 287 
 TYR   0.009   0.001   TYR C 123 
 ARG   0.001   0.000   ARG B 223 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.720 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7919 (pt)
REVERT: A  202 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8247 (mp)
REVERT: B   84 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7746 (pt)
REVERT: C  168 SER cc_start: 0.8325 (OUTLIER) cc_final: 0.8111 (p)
  outliers start: 4
  outliers final: 0
  residues processed: 61
  average time/residue: 0.9133
  time to fit residues: 60.7911
Evaluate side-chains
  51 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain C residue  168 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 92 optimal weight:    0.3980
   chunk 44 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.118093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.102818 restraints weight = 26405.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 2.28
r_work: 0.3106 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3037
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3037
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7857  Z= 0.270
  Angle     :  0.566   7.349  10791  Z= 0.279
  Chirality :  0.043   0.120   1275
  Planarity :  0.005   0.039   1314
  Dihedral  :  4.405  15.741   1044
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  8.79 %
    Favored  : 90.23 %
  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:  1.25 (0.27), residues: 990
  helix:  1.09 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.40 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 170 
 HIS   0.003   0.001   HIS A 258 
 PHE   0.013   0.001   PHE C 287 
 TYR   0.010   0.001   TYR C 123 
 ARG   0.000   0.000   ARG B 223 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.767 
Fit side-chains
REVERT: A  168 SER cc_start: 0.8413 (t) cc_final: 0.8209 (p)
REVERT: A  202 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8230 (mp)
REVERT: A  273 ILE cc_start: 0.7596 (tp) cc_final: 0.7384 (tp)
REVERT: B   84 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7899 (pt)
REVERT: C  168 SER cc_start: 0.8225 (OUTLIER) cc_final: 0.7936 (p)
  outliers start: 8
  outliers final: 4
  residues processed: 65
  average time/residue: 0.8883
  time to fit residues: 63.0692
Evaluate side-chains
  66 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  250 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 94 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 76 optimal weight:    0.2980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3373 r_free = 0.3373 target = 0.117501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.102265 restraints weight = 26913.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.28
r_work: 0.3095 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.3559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7857  Z= 0.264
  Angle     :  0.565   7.321  10791  Z= 0.278
  Chirality :  0.043   0.120   1275
  Planarity :  0.005   0.041   1314
  Dihedral  :  4.401  15.266   1044
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  9.52 %
    Favored  : 88.64 %
  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:  1.34 (0.27), residues: 990
  helix:  1.14 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.46 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 339 
 HIS   0.003   0.001   HIS A 258 
 PHE   0.012   0.001   PHE A 287 
 TYR   0.009   0.001   TYR C 123 
 ARG   0.000   0.000   ARG B 223 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.812 
Fit side-chains
REVERT: A  168 SER cc_start: 0.8416 (t) cc_final: 0.8173 (p)
REVERT: A  202 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8224 (mp)
REVERT: A  273 ILE cc_start: 0.7783 (tp) cc_final: 0.7562 (tp)
REVERT: B   84 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7979 (pt)
REVERT: B  273 ILE cc_start: 0.7878 (tp) cc_final: 0.7628 (tp)
REVERT: C  168 SER cc_start: 0.8297 (OUTLIER) cc_final: 0.7969 (p)
  outliers start: 15
  outliers final: 6
  residues processed: 68
  average time/residue: 0.9468
  time to fit residues: 70.4666
Evaluate side-chains
  70 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain C residue  160 SER
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  250 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 92 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0020
   chunk 80 optimal weight:    0.0570
   chunk 15 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.4906

-------------------------------------------------------------------------------
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 = 0.3360 r_free = 0.3360 target = 0.117796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.102305 restraints weight = 30262.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 2.40
r_work: 0.3065 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2998
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2998
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.3692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7857  Z= 0.203
  Angle     :  0.527   6.340  10791  Z= 0.260
  Chirality :  0.041   0.121   1275
  Planarity :  0.005   0.041   1314
  Dihedral  :  4.249  15.363   1044
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  :  9.40 %
    Favored  : 88.16 %
  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:  1.57 (0.27), residues: 990
  helix:  1.32 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.54 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 339 
 HIS   0.002   0.001   HIS C 258 
 PHE   0.011   0.001   PHE C 287 
 TYR   0.008   0.001   TYR C 123 
 ARG   0.001   0.000   ARG C  63 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 60
  time to evaluate  : 0.852 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8005 (pt)
REVERT: A  168 SER cc_start: 0.8312 (t) cc_final: 0.8058 (p)
REVERT: A  273 ILE cc_start: 0.7678 (tp) cc_final: 0.7431 (tp)
REVERT: B   84 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7891 (pt)
REVERT: B  273 ILE cc_start: 0.7787 (tp) cc_final: 0.7515 (tp)
REVERT: C  168 SER cc_start: 0.8141 (OUTLIER) cc_final: 0.7852 (p)
  outliers start: 20
  outliers final: 7
  residues processed: 68
  average time/residue: 0.8839
  time to fit residues: 65.5876
Evaluate side-chains
  69 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  374 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 80 optimal weight:    0.4980
   chunk 49 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.116746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.102580 restraints weight = 20729.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.90
r_work: 0.3085 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7857  Z= 0.233
  Angle     :  0.560   7.979  10791  Z= 0.277
  Chirality :  0.042   0.120   1275
  Planarity :  0.005   0.042   1314
  Dihedral  :  4.282  18.292   1044
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  9.65 %
    Favored  : 88.77 %
  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 (0.27), residues: 990
  helix:  1.35 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.64 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 339 
 HIS   0.003   0.001   HIS A 258 
 PHE   0.011   0.001   PHE C 287 
 TYR   0.009   0.001   TYR C 123 
 ARG   0.001   0.000   ARG A  63 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.735 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8118 (pt)
REVERT: A  168 SER cc_start: 0.8298 (t) cc_final: 0.8063 (p)
REVERT: A  273 ILE cc_start: 0.7729 (tp) cc_final: 0.7483 (tp)
REVERT: B   84 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7959 (pt)
REVERT: B  273 ILE cc_start: 0.7842 (tp) cc_final: 0.7577 (tp)
REVERT: C  168 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7879 (p)
  outliers start: 13
  outliers final: 8
  residues processed: 62
  average time/residue: 1.0042
  time to fit residues: 67.4935
Evaluate side-chains
  69 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  374 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 92 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   chunk 12 optimal weight:    0.4980
   chunk 56 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.118405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.102677 restraints weight = 30194.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.47
r_work: 0.3102 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2885
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2885 r_free = 0.2885    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2885 r_free = 0.2885    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2885
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7857  Z= 0.249
  Angle     :  0.565   7.715  10791  Z= 0.280
  Chirality :  0.042   0.121   1275
  Planarity :  0.005   0.042   1314
  Dihedral  :  4.313  18.961   1044
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  9.77 %
    Favored  : 88.40 %
  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:  1.66 (0.27), residues: 990
  helix:  1.35 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.66 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 339 
 HIS   0.003   0.001   HIS A 258 
 PHE   0.012   0.001   PHE C 287 
 TYR   0.009   0.001   TYR C 123 
 ARG   0.001   0.000   ARG C 373 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.791 
Fit side-chains
REVERT: A  168 SER cc_start: 0.8321 (t) cc_final: 0.8049 (p)
REVERT: A  273 ILE cc_start: 0.7601 (tp) cc_final: 0.7341 (tp)
REVERT: B   84 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7956 (pt)
REVERT: B  273 ILE cc_start: 0.7920 (tp) cc_final: 0.7642 (tp)
REVERT: C  168 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7847 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 64
  average time/residue: 0.9548
  time to fit residues: 66.3050
Evaluate side-chains
  70 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain C residue  160 SER
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  374 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 43 optimal weight:    0.1980
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 85 optimal weight:    0.7980
   chunk 44 optimal weight:    0.2980
   chunk 72 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   chunk 22 optimal weight:    0.4980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.118143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.102431 restraints weight = 31884.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 2.46
r_work: 0.3059 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7857  Z= 0.203
  Angle     :  0.543   9.414  10791  Z= 0.268
  Chirality :  0.041   0.124   1275
  Planarity :  0.005   0.042   1314
  Dihedral  :  4.198  18.158   1044
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.62 %
    Favored  : 87.79 %
  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:  1.76 (0.27), residues: 990
  helix:  1.45 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.65 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 339 
 HIS   0.002   0.001   HIS A 258 
 PHE   0.011   0.001   PHE C 287 
 TYR   0.008   0.001   TYR B 123 
 ARG   0.002   0.000   ARG C 373 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.897 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8020 (pt)
REVERT: A  273 ILE cc_start: 0.7643 (tp) cc_final: 0.7359 (tp)
REVERT: B   84 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7868 (pt)
REVERT: B  273 ILE cc_start: 0.7802 (tp) cc_final: 0.7506 (tp)
REVERT: C  168 SER cc_start: 0.8137 (OUTLIER) cc_final: 0.7826 (p)
  outliers start: 13
  outliers final: 8
  residues processed: 61
  average time/residue: 1.0117
  time to fit residues: 66.8351
Evaluate side-chains
  66 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  374 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0670
   chunk 12 optimal weight:    0.0270
   chunk 38 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0980
   chunk 27 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.3176

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

Flipped N/Q/H residues before XYZ refinement:
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.120512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.105456 restraints weight = 26760.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.21
r_work: 0.3121 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3072
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3072 r_free = 0.3072    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3072 r_free = 0.3072    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3072
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7857  Z= 0.175
  Angle     :  0.526   8.419  10791  Z= 0.260
  Chirality :  0.040   0.120   1275
  Planarity :  0.004   0.042   1314
  Dihedral  :  4.096  19.050   1044
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 10.99 %
    Favored  : 87.67 %
  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:  1.89 (0.27), residues: 990
  helix:  1.54 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.67 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 339 
 HIS   0.002   0.001   HIS A 258 
 PHE   0.010   0.001   PHE C 287 
 TYR   0.008   0.001   TYR C 123 
 ARG   0.002   0.000   ARG C 373 

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.788 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7880 (pt)
REVERT: B   84 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7787 (pt)
REVERT: C  168 SER cc_start: 0.8097 (OUTLIER) cc_final: 0.7767 (p)
  outliers start: 11
  outliers final: 7
  residues processed: 62
  average time/residue: 1.0007
  time to fit residues: 67.2900
Evaluate side-chains
  65 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  250 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 76 optimal weight:    0.0370
   chunk 68 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0370
   chunk 46 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.4536

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

Flipped N/Q/H residues before XYZ refinement:
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.119260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.104410 restraints weight = 26054.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.17
r_work: 0.3103 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7857  Z= 0.197
  Angle     :  0.545   9.924  10791  Z= 0.268
  Chirality :  0.041   0.120   1275
  Planarity :  0.005   0.042   1314
  Dihedral  :  4.123  18.470   1044
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 11.23 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.27), residues: 990
  helix:  1.54 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.73 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 339 
 HIS   0.002   0.001   HIS C 258 
 PHE   0.010   0.001   PHE C 287 
 TYR   0.009   0.001   TYR B 123 
 ARG   0.001   0.000   ARG A  63 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4685.13 seconds
wall clock time: 84 minutes 29.64 seconds (5069.64 seconds total)