Starting phenix.real_space_refine
on Thu Mar 13 11:24:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qpf_18549/03_2025/8qpf_18549.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qpf_18549/03_2025/8qpf_18549.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qpf_18549/03_2025/8qpf_18549.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qpf_18549/03_2025/8qpf_18549.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qpf_18549/03_2025/8qpf_18549.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qpf_18549/03_2025/8qpf_18549.cif"
  }
  resolution = 2.53
  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=   0.001 sd=   0.026
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    5850      2.51       5
     N    1434      2.21       5
     O    1744      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9085
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 2961
          Classifications: {'peptide': 389}
          Link IDs: {'PTRANS': 8, 'TRANS': 380}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 2961
          Classifications: {'peptide': 389}
          Link IDs: {'PTRANS': 8, 'TRANS': 380}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 2961
          Classifications: {'peptide': 389}
          Link IDs: {'PTRANS': 8, 'TRANS': 380}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 66
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 66
          Classifications: {'water': 66}
          Link IDs: {None: 65}
    Chain: "B"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 70
          Classifications: {'water': 70}
          Link IDs: {None: 69}
    Chain: "C"
      Number of atoms: 66
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 66
          Classifications: {'water': 66}
          Link IDs: {None: 65}
  Time building chain proxies: 5.45, per 1000 atoms: 0.60
  Number of scatterers: 9085
  At special positions: 0
  Unit cell: (87.36, 94.08, 80.64, 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    1744      8.00
     N    1434      7.00
     C    5850      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: 2.14
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2064

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 3 sheets defined
      78.3% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 32
      removed outlier: 3.511A  pdb=" N   ASN A  32 " --> pdb=" O   PHE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 59
      removed outlier: 4.054A  pdb=" N   PHE A  49 " --> pdb=" O   ASN A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 66
    Processing helix  chain 'A' and resid 87 through 110
      removed outlier: 4.010A  pdb=" N   GLY A 108 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ALA A 109 " --> pdb=" O   ILE A 105 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   VAL A 110 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 129
    Processing helix  chain 'A' and resid 129 through 140
    Processing helix  chain 'A' and resid 152 through 158
    Processing helix  chain 'A' and resid 168 through 184
    Processing helix  chain 'A' and resid 203 through 226
      removed outlier: 3.570A  pdb=" N   GLY A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 256
      removed outlier: 3.557A  pdb=" N   VAL A 236 " --> pdb=" O   MET A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 280
      removed outlier: 3.750A  pdb=" N   PHE A 266 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ALA A 280 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 311
    Processing helix  chain 'A' and resid 318 through 323
    Processing helix  chain 'A' and resid 323 through 338
      removed outlier: 4.215A  pdb=" N   ALA A 335 " --> pdb=" O   THR A 331 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ILE A 336 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 343
    Processing helix  chain 'A' and resid 348 through 382
      removed outlier: 3.532A  pdb=" N   PHE A 353 " --> pdb=" O   ARG A 349 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   LEU A 370 " --> pdb=" O   PHE A 366 " (cutoff:3.500A)
      Proline residue:  A 371  - end of helix
      removed outlier: 3.711A  pdb=" N   VAL A 381 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 394
    Processing helix  chain 'A' and resid 395 through 398
      removed outlier: 3.931A  pdb=" N   GLY A 398 " --> pdb=" O   LEU A 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 395 through 398'
    Processing helix  chain 'B' and resid 3 through 32
      removed outlier: 3.550A  pdb=" N   ASN B  32 " --> pdb=" O   PHE B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 59
      removed outlier: 4.012A  pdb=" N   PHE B  49 " --> pdb=" O   ASN B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 66
    Processing helix  chain 'B' and resid 87 through 108
      removed outlier: 3.636A  pdb=" N   ALA B 103 " --> pdb=" O   CYS B  99 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   GLY B 108 " --> pdb=" O   THR B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 111
      No H-bonds generated for 'chain 'B' and resid 109 through 111'
    Processing helix  chain 'B' and resid 115 through 129
    Processing helix  chain 'B' and resid 129 through 140
    Processing helix  chain 'B' and resid 152 through 158
    Processing helix  chain 'B' and resid 168 through 184
    Processing helix  chain 'B' and resid 203 through 226
      removed outlier: 3.558A  pdb=" N   GLY B 220 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 256
      removed outlier: 3.545A  pdb=" N   VAL B 236 " --> pdb=" O   MET B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 280
      removed outlier: 3.686A  pdb=" N   PHE B 266 " --> pdb=" O   LEU B 262 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ALA B 280 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 311
    Processing helix  chain 'B' and resid 318 through 323
    Processing helix  chain 'B' and resid 323 through 338
      removed outlier: 4.211A  pdb=" N   ALA B 335 " --> pdb=" O   THR B 331 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ILE B 336 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 343
    Processing helix  chain 'B' and resid 348 through 382
      removed outlier: 3.533A  pdb=" N   PHE B 353 " --> pdb=" O   ARG B 349 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LEU B 370 " --> pdb=" O   PHE B 366 " (cutoff:3.500A)
      Proline residue:  B 371  - end of helix
      removed outlier: 3.666A  pdb=" N   VAL B 381 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 394
    Processing helix  chain 'B' and resid 395 through 398
      removed outlier: 3.967A  pdb=" N   GLY B 398 " --> pdb=" O   LEU B 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 395 through 398'
    Processing helix  chain 'C' and resid 3 through 32
      removed outlier: 3.547A  pdb=" N   ASN C  32 " --> pdb=" O   PHE C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 59
      removed outlier: 4.001A  pdb=" N   PHE C  49 " --> pdb=" O   ASN C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 66
    Processing helix  chain 'C' and resid 87 through 110
      removed outlier: 3.981A  pdb=" N   GLY C 108 " --> pdb=" O   THR C 104 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ALA C 109 " --> pdb=" O   ILE C 105 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   VAL C 110 " --> pdb=" O   ILE C 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 129
    Processing helix  chain 'C' and resid 129 through 140
    Processing helix  chain 'C' and resid 152 through 158
    Processing helix  chain 'C' and resid 168 through 184
    Processing helix  chain 'C' and resid 203 through 226
      removed outlier: 3.505A  pdb=" N   GLY C 220 " --> pdb=" O   LEU C 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 256
      removed outlier: 3.567A  pdb=" N   VAL C 236 " --> pdb=" O   MET C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 262 through 280
      removed outlier: 3.738A  pdb=" N   PHE C 266 " --> pdb=" O   LEU C 262 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ALA C 280 " --> pdb=" O   VAL C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 311
    Processing helix  chain 'C' and resid 318 through 323
    Processing helix  chain 'C' and resid 323 through 338
      removed outlier: 4.200A  pdb=" N   ALA C 335 " --> pdb=" O   THR C 331 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ILE C 336 " --> pdb=" O   LEU C 332 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 339 through 343
    Processing helix  chain 'C' and resid 348 through 382
      removed outlier: 3.516A  pdb=" N   PHE C 353 " --> pdb=" O   ARG C 349 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   LEU C 370 " --> pdb=" O   PHE C 366 " (cutoff:3.500A)
      Proline residue:  C 371  - end of helix
      removed outlier: 3.628A  pdb=" N   VAL C 381 " --> pdb=" O   LEU C 377 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 387 through 394
    Processing helix  chain 'C' and resid 395 through 398
      removed outlier: 3.975A  pdb=" N   GLY C 398 " --> pdb=" O   LEU C 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 395 through 398'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 191
    Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 191
      removed outlier: 3.515A  pdb=" N   GLY B 195 " --> pdb=" O   ASN B 191 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 190 through 191

    653 hydrogen bonds defined for protein.
    1935 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: 2.49

  Time building geometry restraints manager: 2.54 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2735
        1.35 -     1.47: 2435
        1.47 -     1.59: 3851
        1.59 -     1.71: 0
        1.71 -     1.83: 78
  Bond restraints: 9099
  Sorted by residual:
  bond pdb=" CB  TRP B 218 "
       pdb=" CG  TRP B 218 "
    ideal  model  delta    sigma   weight residual
    1.498  1.419  0.079 3.10e-02 1.04e+03 6.43e+00
  bond pdb=" CB  TRP A 218 "
       pdb=" CG  TRP A 218 "
    ideal  model  delta    sigma   weight residual
    1.498  1.421  0.077 3.10e-02 1.04e+03 6.17e+00
  bond pdb=" CB  TRP C 218 "
       pdb=" CG  TRP C 218 "
    ideal  model  delta    sigma   weight residual
    1.498  1.424  0.074 3.10e-02 1.04e+03 5.64e+00
  bond pdb=" CG  LEU B 216 "
       pdb=" CD2 LEU B 216 "
    ideal  model  delta    sigma   weight residual
    1.521  1.452  0.069 3.30e-02 9.18e+02 4.41e+00
  bond pdb=" CG  LEU A 216 "
       pdb=" CD2 LEU A 216 "
    ideal  model  delta    sigma   weight residual
    1.521  1.457  0.064 3.30e-02 9.18e+02 3.80e+00
  ... (remaining 9094 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.47: 12270
        3.47 -     6.95: 81
        6.95 -    10.42: 19
       10.42 -    13.89: 0
       13.89 -    17.36: 2
  Bond angle restraints: 12372
  Sorted by residual:
  angle pdb=" CB  MET A  97 "
        pdb=" CG  MET A  97 "
        pdb=" SD  MET A  97 "
      ideal   model   delta    sigma   weight residual
     112.70  130.06  -17.36 3.00e+00 1.11e-01 3.35e+01
  angle pdb=" CB  MET C  97 "
        pdb=" CG  MET C  97 "
        pdb=" SD  MET C  97 "
      ideal   model   delta    sigma   weight residual
     112.70  127.04  -14.34 3.00e+00 1.11e-01 2.28e+01
  angle pdb=" C   CYS B 255 "
        pdb=" N   ILE B 256 "
        pdb=" CA  ILE B 256 "
      ideal   model   delta    sigma   weight residual
     121.97  129.84   -7.87 1.80e+00 3.09e-01 1.91e+01
  angle pdb=" C   CYS A 255 "
        pdb=" N   ILE A 256 "
        pdb=" CA  ILE A 256 "
      ideal   model   delta    sigma   weight residual
     121.97  129.82   -7.85 1.80e+00 3.09e-01 1.90e+01
  angle pdb=" C   CYS C 255 "
        pdb=" N   ILE C 256 "
        pdb=" CA  ILE C 256 "
      ideal   model   delta    sigma   weight residual
     121.97  129.80   -7.83 1.80e+00 3.09e-01 1.89e+01
  ... (remaining 12367 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.18: 4515
       17.18 -    34.36: 453
       34.36 -    51.54: 103
       51.54 -    68.72: 20
       68.72 -    85.90: 6
  Dihedral angle restraints: 5097
    sinusoidal: 1842
      harmonic: 3255
  Sorted by residual:
  dihedral pdb=" CA  THR A 104 "
           pdb=" C   THR A 104 "
           pdb=" N   ILE A 105 "
           pdb=" CA  ILE A 105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.80   18.20     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  THR C 104 "
           pdb=" C   THR C 104 "
           pdb=" N   ILE C 105 "
           pdb=" CA  ILE C 105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.86   18.14     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  THR B 104 "
           pdb=" C   THR B 104 "
           pdb=" N   ILE B 105 "
           pdb=" CA  ILE B 105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.95   18.05     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 5094 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1269
       0.072 -    0.144: 153
       0.144 -    0.215: 15
       0.215 -    0.287: 0
       0.287 -    0.359: 3
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CB  ILE C 256 "
            pdb=" CA  ILE C 256 "
            pdb=" CG1 ILE C 256 "
            pdb=" CG2 ILE C 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.36 2.00e-01 2.50e+01 3.22e+00
  chirality pdb=" CB  ILE B 256 "
            pdb=" CA  ILE B 256 "
            pdb=" CG1 ILE B 256 "
            pdb=" CG2 ILE B 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.35 2.00e-01 2.50e+01 3.13e+00
  chirality pdb=" CB  ILE A 256 "
            pdb=" CA  ILE A 256 "
            pdb=" CG1 ILE A 256 "
            pdb=" CG2 ILE A 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.92e+00
  ... (remaining 1437 not shown)

  Planarity restraints: 1533
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 204 "   -0.037 5.00e-02 4.00e+02   5.60e-02 5.02e+00
        pdb=" N   PRO C 205 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO C 205 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 205 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 204 "    0.037 5.00e-02 4.00e+02   5.52e-02 4.88e+00
        pdb=" N   PRO B 205 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B 205 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 205 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 204 "   -0.037 5.00e-02 4.00e+02   5.52e-02 4.88e+00
        pdb=" N   PRO A 205 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 205 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 205 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1530 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2211
        2.79 -     3.31: 8642
        3.31 -     3.84: 17312
        3.84 -     4.37: 20634
        4.37 -     4.90: 34349
  Nonbonded interactions: 83148
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 234 "
            pdb=" OG  SER B  90 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   LEU B 204 "
            pdb=" OG1 THR B 207 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   LEU A 204 "
            pdb=" OG1 THR A 207 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" NE1 TRP C 218 "
            pdb=" OG1 THR C 279 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" O   PHE B  79 "
            pdb=" O   HOH B 701 "
     model   vdw
     2.334 3.040
  ... (remaining 83143 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  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 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:             0.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.650
  Find NCS groups from input model:        0.280
  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:11.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
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   0.079   9099  Z= 0.343
  Angle     :  0.838  17.365  12372  Z= 0.464
  Chirality :  0.049   0.359   1440
  Planarity :  0.007   0.072   1533
  Dihedral  : 14.754  85.903   3033
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.25 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 13.95 %
    Favored  : 85.30 %
  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: -0.50 (0.22), residues: 1155
  helix:  0.25 (0.16), residues: 837
  sheet:  None (None), residues: 0
  loop : -1.69 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 218 
 HIS   0.005   0.001   HIS A 169 
 PHE   0.020   0.002   PHE B 221 
 TYR   0.026   0.003   TYR C 119 
 ARG   0.017   0.002   ARG A 376 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 169
  time to evaluate  : 0.946 
Fit side-chains
  outliers start: 7
  outliers final: 5
  residues processed: 174
  average time/residue: 1.3430
  time to fit residues: 250.0671
Evaluate side-chains
  123 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 118
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain B residue  231 ASP
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  231 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 89 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 103 optimal weight:    9.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A  95 GLN
A 259 GLN
B  22 GLN
B 259 GLN
C 197 ASN
C 259 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.093658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.074772 restraints weight = 16252.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.2780 rms_B_bonded: 2.97
r_work: 0.2650 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9099  Z= 0.180
  Angle     :  0.540   8.815  12372  Z= 0.291
  Chirality :  0.038   0.208   1440
  Planarity :  0.004   0.040   1533
  Dihedral  :  4.618  24.072   1235
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  1.73 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 15.55 %
    Favored  : 82.43 %
  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:  1.38 (0.24), residues: 1155
  helix:  1.67 (0.17), residues: 846
  sheet:  None (None), residues: 0
  loop : -1.20 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 257 
 HIS   0.004   0.001   HIS C 323 
 PHE   0.019   0.001   PHE C 221 
 TYR   0.025   0.002   TYR A 119 
 ARG   0.004   0.001   ARG C 376 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
REVERT: A  202 ASP cc_start: 0.8471 (m-30) cc_final: 0.8241 (m-30)
REVERT: A  259 GLN cc_start: 0.8114 (pt0) cc_final: 0.7344 (pp30)
REVERT: A  339 ASP cc_start: 0.8113 (t0) cc_final: 0.7831 (t0)
REVERT: B   64 MET cc_start: 0.8624 (ttt) cc_final: 0.8266 (ttt)
REVERT: B  218 TRP cc_start: 0.8419 (OUTLIER) cc_final: 0.7481 (m-90)
REVERT: B  339 ASP cc_start: 0.8139 (t0) cc_final: 0.7808 (t0)
REVERT: C  161 ASP cc_start: 0.9182 (t70) cc_final: 0.8975 (t70)
REVERT: C  259 GLN cc_start: 0.8136 (pt0) cc_final: 0.7886 (pp30)
REVERT: C  339 ASP cc_start: 0.7987 (t0) cc_final: 0.7657 (t0)
REVERT: C  341 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8526 (pp30)
  outliers start: 19
  outliers final: 8
  residues processed: 152
  average time/residue: 1.2311
  time to fit residues: 200.2290
Evaluate side-chains
  135 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  218 TRP
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue  218 TRP
Chi-restraints excluded: chain C residue  191 ASN
Chi-restraints excluded: chain C residue  218 TRP
Chi-restraints excluded: chain C residue  341 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   chunk 16 optimal weight:    8.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A  45 ASN
B  22 GLN
C  45 ASN
C  95 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.090872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.071984 restraints weight = 16766.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.2752 rms_B_bonded: 2.99
r_work: 0.2618 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9099  Z= 0.193
  Angle     :  0.508   7.063  12372  Z= 0.276
  Chirality :  0.039   0.179   1440
  Planarity :  0.003   0.034   1533
  Dihedral  :  4.144  14.427   1227
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.08 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.72 %
    Favored  : 81.26 %
  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 (0.25), residues: 1155
  helix:  2.37 (0.17), residues: 834
  sheet:  None (None), residues: 0
  loop : -1.05 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 257 
 HIS   0.005   0.001   HIS B 323 
 PHE   0.014   0.001   PHE A 221 
 TYR   0.025   0.002   TYR B 119 
 ARG   0.004   0.000   ARG A 376 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 GLU cc_start: 0.9541 (mt-10) cc_final: 0.9241 (mt-10)
REVERT: A  156 GLN cc_start: 0.9020 (tt0) cc_final: 0.8556 (tm-30)
REVERT: A  202 ASP cc_start: 0.8632 (m-30) cc_final: 0.8431 (m-30)
REVERT: A  259 GLN cc_start: 0.8198 (pt0) cc_final: 0.7389 (pp30)
REVERT: A  339 ASP cc_start: 0.8117 (t0) cc_final: 0.7792 (t0)
REVERT: B  156 GLN cc_start: 0.9117 (tt0) cc_final: 0.8656 (tm-30)
REVERT: B  339 ASP cc_start: 0.8211 (t0) cc_final: 0.7881 (t0)
REVERT: B  399 GLU cc_start: 0.3800 (OUTLIER) cc_final: 0.3510 (pt0)
REVERT: C  259 GLN cc_start: 0.8295 (pt0) cc_final: 0.8021 (pp30)
REVERT: C  339 ASP cc_start: 0.8105 (t0) cc_final: 0.7656 (t0)
REVERT: C  341 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8574 (pt0)
  outliers start: 19
  outliers final: 12
  residues processed: 145
  average time/residue: 1.1784
  time to fit residues: 183.0863
Evaluate side-chains
  138 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  218 TRP
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue  218 TRP
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  399 GLU
Chi-restraints excluded: chain C residue  218 TRP
Chi-restraints excluded: chain C residue  231 ASP
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain C residue  341 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 81 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 21 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 109 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 77 optimal weight:    8.9990
   chunk 103 optimal weight:    0.8980
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
B  22 GLN
B 323 HIS
C  45 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.086914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.068084 restraints weight = 16846.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.2686 rms_B_bonded: 2.99
r_work: 0.2551 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9099  Z= 0.270
  Angle     :  0.539   7.447  12372  Z= 0.289
  Chirality :  0.040   0.179   1440
  Planarity :  0.003   0.030   1533
  Dihedral  :  4.088  15.837   1227
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  1.90 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 18.21 %
    Favored  : 79.98 %
  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:  2.51 (0.25), residues: 1155
  helix:  2.60 (0.17), residues: 834
  sheet:  None (None), residues: 0
  loop : -0.97 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 257 
 HIS   0.004   0.001   HIS B 323 
 PHE   0.026   0.001   PHE B 221 
 TYR   0.020   0.002   TYR A 119 
 ARG   0.003   0.000   ARG B 376 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.981 
Fit side-chains
REVERT: A  156 GLN cc_start: 0.9044 (tt0) cc_final: 0.8586 (tm-30)
REVERT: A  339 ASP cc_start: 0.8172 (t0) cc_final: 0.7828 (t0)
REVERT: A  399 GLU cc_start: 0.5310 (pm20) cc_final: 0.4958 (pt0)
REVERT: B  156 GLN cc_start: 0.9111 (tt0) cc_final: 0.8666 (tm-30)
REVERT: B  259 GLN cc_start: 0.8154 (pt0) cc_final: 0.7475 (pp30)
REVERT: B  339 ASP cc_start: 0.8273 (t0) cc_final: 0.7940 (t0)
REVERT: B  399 GLU cc_start: 0.3790 (OUTLIER) cc_final: 0.3516 (pt0)
REVERT: C  218 TRP cc_start: 0.8880 (OUTLIER) cc_final: 0.7481 (t-100)
REVERT: C  259 GLN cc_start: 0.8319 (pt0) cc_final: 0.8028 (pp30)
REVERT: C  339 ASP cc_start: 0.8178 (t0) cc_final: 0.7731 (t0)
REVERT: C  341 GLN cc_start: 0.8942 (pt0) cc_final: 0.8622 (pt0)
  outliers start: 17
  outliers final: 12
  residues processed: 136
  average time/residue: 1.2732
  time to fit residues: 184.9991
Evaluate side-chains
  129 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  218 TRP
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue  218 TRP
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  399 GLU
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue  191 ASN
Chi-restraints excluded: chain C residue  218 TRP
Chi-restraints excluded: chain C residue  278 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 86 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 258 GLN
B  22 GLN
C  45 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.088517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.069752 restraints weight = 16871.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.2711 rms_B_bonded: 2.99
r_work: 0.2580 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9099  Z= 0.207
  Angle     :  0.518   7.629  12372  Z= 0.278
  Chirality :  0.039   0.180   1440
  Planarity :  0.003   0.030   1533
  Dihedral  :  4.063  16.235   1227
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.25 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.00 %
    Favored  : 79.77 %
  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:  2.72 (0.25), residues: 1155
  helix:  2.75 (0.17), residues: 834
  sheet:  None (None), residues: 0
  loop : -0.90 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 257 
 HIS   0.002   0.001   HIS C 323 
 PHE   0.024   0.001   PHE B 221 
 TYR   0.028   0.002   TYR B 119 
 ARG   0.003   0.000   ARG B 376 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 1.006 
Fit side-chains
REVERT: A  156 GLN cc_start: 0.9059 (tt0) cc_final: 0.8605 (tm-30)
REVERT: A  258 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7400 (mm-40)
REVERT: A  259 GLN cc_start: 0.8279 (pt0) cc_final: 0.7528 (pp30)
REVERT: A  339 ASP cc_start: 0.8178 (t0) cc_final: 0.7823 (t0)
REVERT: A  399 GLU cc_start: 0.5252 (pm20) cc_final: 0.4921 (pt0)
REVERT: B  156 GLN cc_start: 0.9119 (tt0) cc_final: 0.8644 (tm-30)
REVERT: B  161 ASP cc_start: 0.8994 (t70) cc_final: 0.8640 (t0)
REVERT: B  259 GLN cc_start: 0.8266 (pt0) cc_final: 0.7562 (pp30)
REVERT: B  289 ASP cc_start: 0.8417 (m-30) cc_final: 0.8206 (m-30)
REVERT: B  339 ASP cc_start: 0.8279 (t0) cc_final: 0.7922 (t0)
REVERT: B  399 GLU cc_start: 0.3798 (OUTLIER) cc_final: 0.3542 (pt0)
REVERT: C  218 TRP cc_start: 0.8948 (OUTLIER) cc_final: 0.7849 (t-100)
REVERT: C  221 PHE cc_start: 0.8492 (t80) cc_final: 0.8266 (t80)
REVERT: C  259 GLN cc_start: 0.8369 (pt0) cc_final: 0.8087 (pp30)
REVERT: C  339 ASP cc_start: 0.8204 (t0) cc_final: 0.7619 (t0)
  outliers start: 21
  outliers final: 12
  residues processed: 143
  average time/residue: 1.2090
  time to fit residues: 185.0457
Evaluate side-chains
  133 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  218 TRP
Chi-restraints excluded: chain A residue  258 GLN
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue  218 TRP
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  399 GLU
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue  191 ASN
Chi-restraints excluded: chain C residue  218 TRP
Chi-restraints excluded: chain C residue  278 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   chunk 69 optimal weight:    9.9990
   chunk 67 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 258 GLN
B 258 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.086202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.067603 restraints weight = 16834.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.2685 rms_B_bonded: 2.96
r_work: 0.2552 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9099  Z= 0.257
  Angle     :  0.538   8.554  12372  Z= 0.289
  Chirality :  0.039   0.181   1440
  Planarity :  0.003   0.029   1533
  Dihedral  :  4.039  16.350   1227
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.16 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.53 %
    Favored  : 78.81 %
  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:  2.74 (0.25), residues: 1155
  helix:  2.76 (0.17), residues: 834
  sheet:  None (None), residues: 0
  loop : -0.88 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 257 
 HIS   0.002   0.001   HIS A 323 
 PHE   0.022   0.001   PHE B 221 
 TYR   0.022   0.002   TYR A 119 
 ARG   0.002   0.000   ARG B 376 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 1.051 
Fit side-chains
REVERT: A  156 GLN cc_start: 0.9059 (tt0) cc_final: 0.8605 (tm-30)
REVERT: A  259 GLN cc_start: 0.8251 (pt0) cc_final: 0.7494 (pp30)
REVERT: A  339 ASP cc_start: 0.8197 (t0) cc_final: 0.7840 (t0)
REVERT: B   80 TYR cc_start: 0.6137 (t80) cc_final: 0.5908 (t80)
REVERT: B  156 GLN cc_start: 0.9127 (tt0) cc_final: 0.8661 (tm-30)
REVERT: B  161 ASP cc_start: 0.9010 (t70) cc_final: 0.8695 (t0)
REVERT: B  259 GLN cc_start: 0.8322 (pt0) cc_final: 0.7634 (pp30)
REVERT: B  289 ASP cc_start: 0.8419 (m-30) cc_final: 0.8197 (m-30)
REVERT: B  339 ASP cc_start: 0.8323 (t0) cc_final: 0.7964 (t0)
REVERT: B  399 GLU cc_start: 0.3886 (OUTLIER) cc_final: 0.3659 (pt0)
REVERT: C  218 TRP cc_start: 0.9083 (OUTLIER) cc_final: 0.7315 (t-100)
REVERT: C  259 GLN cc_start: 0.8406 (pt0) cc_final: 0.8117 (pp30)
REVERT: C  339 ASP cc_start: 0.8243 (t0) cc_final: 0.7636 (t0)
  outliers start: 25
  outliers final: 16
  residues processed: 141
  average time/residue: 1.3152
  time to fit residues: 198.1371
Evaluate side-chains
  137 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  218 TRP
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  218 TRP
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  307 LEU
Chi-restraints excluded: chain B residue  399 GLU
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue  191 ASN
Chi-restraints excluded: chain C residue  218 TRP
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain C residue  307 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0670
   chunk 2 optimal weight:    1.9990
   chunk 99 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 75 optimal weight:    0.5980
   chunk 100 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
B  22 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.092488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.073832 restraints weight = 16783.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 2.97
r_work: 0.2643 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9099  Z= 0.162
  Angle     :  0.516   8.748  12372  Z= 0.276
  Chirality :  0.038   0.186   1440
  Planarity :  0.003   0.030   1533
  Dihedral  :  4.003  15.896   1227
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.25 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 19.60 %
    Favored  : 78.59 %
  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:  2.77 (0.25), residues: 1155
  helix:  2.93 (0.17), residues: 816
  sheet:  None (None), residues: 0
  loop : -1.08 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 257 
 HIS   0.003   0.001   HIS C 323 
 PHE   0.020   0.001   PHE A 221 
 TYR   0.029   0.001   TYR B 119 
 ARG   0.002   0.000   ARG B 376 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: A  156 GLN cc_start: 0.9049 (tt0) cc_final: 0.8565 (tm-30)
REVERT: A  259 GLN cc_start: 0.8385 (pt0) cc_final: 0.7659 (pp30)
REVERT: A  339 ASP cc_start: 0.8189 (t0) cc_final: 0.7819 (t0)
REVERT: B  112 GLU cc_start: 0.9338 (mt-10) cc_final: 0.9130 (mt-10)
REVERT: B  156 GLN cc_start: 0.9122 (tt0) cc_final: 0.8660 (tm-30)
REVERT: B  161 ASP cc_start: 0.9001 (t70) cc_final: 0.8698 (t0)
REVERT: B  289 ASP cc_start: 0.8379 (m-30) cc_final: 0.8140 (m-30)
REVERT: B  339 ASP cc_start: 0.8249 (t0) cc_final: 0.7885 (t0)
REVERT: C  218 TRP cc_start: 0.9010 (OUTLIER) cc_final: 0.7927 (t-100)
REVERT: C  259 GLN cc_start: 0.8399 (pt0) cc_final: 0.8100 (pp30)
REVERT: C  339 ASP cc_start: 0.8207 (t0) cc_final: 0.7642 (t0)
  outliers start: 17
  outliers final: 9
  residues processed: 150
  average time/residue: 1.1730
  time to fit residues: 188.8606
Evaluate side-chains
  130 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  218 TRP
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue  218 TRP
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue  191 ASN
Chi-restraints excluded: chain C residue  218 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 45 optimal weight:    8.9990
   chunk 98 optimal weight:    3.9990
   chunk 32 optimal weight:    9.9990
   chunk 92 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 70 optimal weight:    9.9990
   chunk 95 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 191 ASN
A 197 ASN
B  45 ASN
C 258 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.087238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.068549 restraints weight = 17159.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.2704 rms_B_bonded: 3.02
r_work: 0.2568 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9099  Z= 0.246
  Angle     :  0.560  10.413  12372  Z= 0.296
  Chirality :  0.039   0.189   1440
  Planarity :  0.003   0.028   1533
  Dihedral  :  3.963  16.072   1227
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  1.90 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 19.91 %
    Favored  : 78.17 %
  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:  2.90 (0.25), residues: 1155
  helix:  2.87 (0.17), residues: 834
  sheet:  None (None), residues: 0
  loop : -0.78 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 257 
 HIS   0.002   0.001   HIS A 323 
 PHE   0.024   0.001   PHE C 221 
 TYR   0.021   0.002   TYR C 119 
 ARG   0.002   0.000   ARG B 376 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 1.081 
Fit side-chains
REVERT: A  156 GLN cc_start: 0.9061 (tt0) cc_final: 0.8602 (tm-30)
REVERT: A  259 GLN cc_start: 0.8390 (pt0) cc_final: 0.7673 (pp30)
REVERT: A  339 ASP cc_start: 0.8233 (t0) cc_final: 0.7871 (t0)
REVERT: B   80 TYR cc_start: 0.6023 (t80) cc_final: 0.5813 (t80)
REVERT: B  156 GLN cc_start: 0.9123 (tt0) cc_final: 0.8676 (tm-30)
REVERT: B  161 ASP cc_start: 0.8999 (t70) cc_final: 0.8694 (t0)
REVERT: B  259 GLN cc_start: 0.8397 (pt0) cc_final: 0.7729 (pp30)
REVERT: B  289 ASP cc_start: 0.8416 (m-30) cc_final: 0.8136 (m-30)
REVERT: B  339 ASP cc_start: 0.8329 (t0) cc_final: 0.7966 (t0)
REVERT: C  218 TRP cc_start: 0.9151 (OUTLIER) cc_final: 0.7292 (t-100)
REVERT: C  259 GLN cc_start: 0.8450 (pt0) cc_final: 0.8159 (pp30)
REVERT: C  339 ASP cc_start: 0.8290 (t0) cc_final: 0.7693 (t0)
REVERT: C  341 GLN cc_start: 0.9127 (pt0) cc_final: 0.8773 (pt0)
  outliers start: 18
  outliers final: 12
  residues processed: 139
  average time/residue: 1.5083
  time to fit residues: 224.9639
Evaluate side-chains
  134 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  191 ASN
Chi-restraints excluded: chain A residue  218 TRP
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  218 TRP
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue  160 ILE
Chi-restraints excluded: chain C residue  191 ASN
Chi-restraints excluded: chain C residue  218 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 76 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 111 optimal weight:    3.9990
   chunk 95 optimal weight:    0.5980
   chunk 11 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   chunk 14 optimal weight:    0.0770
   chunk 69 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 107 optimal weight:    0.5980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
B  22 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.093321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.074652 restraints weight = 16556.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.2792 rms_B_bonded: 3.00
r_work: 0.2663 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9099  Z= 0.164
  Angle     :  0.542  10.834  12372  Z= 0.285
  Chirality :  0.038   0.196   1440
  Planarity :  0.003   0.029   1533
  Dihedral  :  3.967  14.995   1227
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.60 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 20.55 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.83 (0.25), residues: 1155
  helix:  2.96 (0.17), residues: 816
  sheet:  None (None), residues: 0
  loop : -1.01 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 257 
 HIS   0.002   0.001   HIS C 323 
 PHE   0.024   0.001   PHE B 221 
 TYR   0.027   0.001   TYR B 119 
 ARG   0.002   0.000   ARG B 376 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.942 
Fit side-chains
REVERT: A  156 GLN cc_start: 0.9075 (tt0) cc_final: 0.8586 (tm-30)
REVERT: A  259 GLN cc_start: 0.8419 (pt0) cc_final: 0.7677 (pp30)
REVERT: A  339 ASP cc_start: 0.8219 (t0) cc_final: 0.7873 (t0)
REVERT: B  156 GLN cc_start: 0.9119 (tt0) cc_final: 0.8642 (tm-30)
REVERT: B  161 ASP cc_start: 0.8914 (t70) cc_final: 0.8663 (t0)
REVERT: B  259 GLN cc_start: 0.8429 (pt0) cc_final: 0.7753 (pp30)
REVERT: B  289 ASP cc_start: 0.8399 (m-30) cc_final: 0.8091 (m-30)
REVERT: B  339 ASP cc_start: 0.8316 (t0) cc_final: 0.7936 (t0)
REVERT: C  218 TRP cc_start: 0.9054 (OUTLIER) cc_final: 0.8004 (t-100)
REVERT: C  259 GLN cc_start: 0.8389 (pt0) cc_final: 0.7850 (pp30)
REVERT: C  339 ASP cc_start: 0.8257 (t0) cc_final: 0.7664 (t0)
REVERT: C  341 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8812 (pt0)
  outliers start: 14
  outliers final: 12
  residues processed: 142
  average time/residue: 1.2186
  time to fit residues: 185.2470
Evaluate side-chains
  139 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  218 TRP
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  218 TRP
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue  160 ILE
Chi-restraints excluded: chain C residue  191 ASN
Chi-restraints excluded: chain C residue  218 TRP
Chi-restraints excluded: chain C residue  231 ASP
Chi-restraints excluded: chain C residue  341 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 19 optimal weight:    0.0670
   chunk 16 optimal weight:    0.9980
   chunk 109 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 89 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.0122

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

Flipped N/Q/H residues before XYZ refinement:
B  22 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.091645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.073182 restraints weight = 16772.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.2776 rms_B_bonded: 2.98
r_work: 0.2646 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9099  Z= 0.183
  Angle     :  0.556  12.193  12372  Z= 0.293
  Chirality :  0.039   0.198   1440
  Planarity :  0.003   0.029   1533
  Dihedral  :  3.933  15.731   1227
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.34 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 20.55 %
    Favored  : 78.06 %
  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:  2.84 (0.25), residues: 1155
  helix:  2.97 (0.17), residues: 816
  sheet:  None (None), residues: 0
  loop : -1.01 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 257 
 HIS   0.003   0.001   HIS A 323 
 PHE   0.023   0.001   PHE B 221 
 TYR   0.022   0.001   TYR C 119 
 ARG   0.002   0.000   ARG B 376 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A  156 GLN cc_start: 0.9067 (tt0) cc_final: 0.8581 (tm-30)
REVERT: A  259 GLN cc_start: 0.8434 (pt0) cc_final: 0.7710 (pp30)
REVERT: A  339 ASP cc_start: 0.8216 (t0) cc_final: 0.7861 (t0)
REVERT: B  156 GLN cc_start: 0.9122 (tt0) cc_final: 0.8647 (tm-30)
REVERT: B  161 ASP cc_start: 0.8918 (t70) cc_final: 0.8679 (t0)
REVERT: B  259 GLN cc_start: 0.8437 (pt0) cc_final: 0.7790 (pp30)
REVERT: B  289 ASP cc_start: 0.8398 (m-30) cc_final: 0.8092 (m-30)
REVERT: B  339 ASP cc_start: 0.8336 (t0) cc_final: 0.7946 (t0)
REVERT: C  218 TRP cc_start: 0.9114 (OUTLIER) cc_final: 0.8102 (t-100)
REVERT: C  259 GLN cc_start: 0.8399 (pt0) cc_final: 0.7858 (pp30)
REVERT: C  339 ASP cc_start: 0.8274 (t0) cc_final: 0.7683 (t0)
REVERT: C  341 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8796 (pt0)
  outliers start: 13
  outliers final: 10
  residues processed: 139
  average time/residue: 1.2575
  time to fit residues: 186.6817
Evaluate side-chains
  135 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  218 TRP
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue  218 TRP
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  307 LEU
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue  191 ASN
Chi-restraints excluded: chain C residue  218 TRP
Chi-restraints excluded: chain C residue  231 ASP
Chi-restraints excluded: chain C residue  341 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 3 optimal weight:    0.3980
   chunk 93 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 73 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 59 optimal weight:    8.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B  22 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.093980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.076565 restraints weight = 16672.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 2.81
r_work: 0.2747 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9099  Z= 0.174
  Angle     :  0.559  13.027  12372  Z= 0.293
  Chirality :  0.039   0.199   1440
  Planarity :  0.003   0.028   1533
  Dihedral  :  3.929  15.112   1227
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.42 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 21.09 %
    Favored  : 77.64 %
  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:  2.86 (0.25), residues: 1155
  helix:  2.99 (0.17), residues: 816
  sheet:  None (None), residues: 0
  loop : -1.00 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 257 
 HIS   0.003   0.001   HIS C 323 
 PHE   0.023   0.001   PHE B 221 
 TYR   0.028   0.001   TYR B 119 
 ARG   0.002   0.000   ARG B 376 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6007.83 seconds
wall clock time: 104 minutes 24.44 seconds (6264.44 seconds total)