Starting phenix.real_space_refine
on Sun Jun  8 11:34:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wsr_32765/06_2025/7wsr_32765.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wsr_32765/06_2025/7wsr_32765.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wsr_32765/06_2025/7wsr_32765.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wsr_32765/06_2025/7wsr_32765.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wsr_32765/06_2025/7wsr_32765.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wsr_32765/06_2025/7wsr_32765.cif"
  }
  resolution = 2.9
  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=  -0.003 sd=   0.061
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      74      5.16       5
     C    6268      2.51       5
     N    1446      2.21       5
     O    1578      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9366
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 600, 4613
          Classifications: {'peptide': 600}
          Link IDs: {'PTRANS': 29, 'TRANS': 570}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 600, 4613
          Classifications: {'peptide': 600}
          Link IDs: {'PTRANS': 29, 'TRANS': 570}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 70
          Unusual residues: {'Y01': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 70
          Unusual residues: {'Y01': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 7.27, per 1000 atoms: 0.78
  Number of scatterers: 9366
  At special positions: 0
  Unit cell: (101.905, 138.359, 82.0215, 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      74     16.00
     O    1578      8.00
     N    1446      7.00
     C    6268      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 250 " - pdb=" SG  CYS A 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 250 " - pdb=" SG  CYS B 671 " distance=2.03

  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: 2.99
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2152

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 1 sheets defined
      78.7% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 75
    Processing helix  chain 'A' and resid 81 through 104
      removed outlier: 3.642A  pdb=" N   ALA A  86 " --> pdb=" O   ASN A  82 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A  87 " --> pdb=" O   VAL A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 132
      removed outlier: 3.541A  pdb=" N   TYR A 126 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ILE A 128 " --> pdb=" O   ALA A 124 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ALA A 129 " --> pdb=" O   CYS A 125 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   PHE A 130 " --> pdb=" O   TYR A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 141
      removed outlier: 3.651A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 150
      removed outlier: 3.576A  pdb=" N   GLY A 150 " --> pdb=" O   TYR A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 191
      removed outlier: 4.256A  pdb=" N   PHE A 177 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   GLY A 178 " --> pdb=" O   ALA A 174 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   GLY A 179 " --> pdb=" O   CYS A 175 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   LEU A 180 " --> pdb=" O   SER A 176 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   LEU A 181 " --> pdb=" O   PHE A 177 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   THR A 182 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ILE A 184 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
      Proline residue:  A 185  - end of helix
      removed outlier: 3.982A  pdb=" N   GLN A 188 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL A 189 " --> pdb=" O   PRO A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 213
    Processing helix  chain 'A' and resid 219 through 243
      removed outlier: 3.564A  pdb=" N   TYR A 230 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   PHE A 243 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 265
    Processing helix  chain 'A' and resid 272 through 281
      removed outlier: 3.915A  pdb=" N   ILE A 281 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 299
    Processing helix  chain 'A' and resid 300 through 306
    Processing helix  chain 'A' and resid 307 through 309
      No H-bonds generated for 'chain 'A' and resid 307 through 309'
    Processing helix  chain 'A' and resid 325 through 359
      removed outlier: 3.674A  pdb=" N   LYS A 329 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   TYR A 343 " --> pdb=" O   GLY A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 416
      removed outlier: 3.927A  pdb=" N   TYR A 398 " --> pdb=" O   SER A 394 " (cutoff:3.500A)
      Proline residue:  A 413  - end of helix
    Processing helix  chain 'A' and resid 420 through 446
      removed outlier: 3.731A  pdb=" N   VAL A 424 " --> pdb=" O   LYS A 420 " (cutoff:3.500A)
      Proline residue:  A 432  - end of helix
      removed outlier: 3.553A  pdb=" N   LEU A 444 " --> pdb=" O   TYR A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 464
    Processing helix  chain 'A' and resid 470 through 501
      removed outlier: 3.539A  pdb=" N   GLN A 493 " --> pdb=" O   ALA A 489 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ASP A 494 " --> pdb=" O   ASP A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 534
      removed outlier: 3.562A  pdb=" N   ILE A 521 " --> pdb=" O   ALA A 517 " (cutoff:3.500A)
      Proline residue:  A 524  - end of helix
    Processing helix  chain 'A' and resid 545 through 560
      removed outlier: 3.936A  pdb=" N   LEU A 549 " --> pdb=" O   ALA A 545 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   GLU A 560 " --> pdb=" O   ILE A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 565
    Processing helix  chain 'A' and resid 568 through 590
      removed outlier: 3.639A  pdb=" N   ASP A 588 " --> pdb=" O   SER A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 610
      removed outlier: 3.801A  pdb=" N   VAL A 606 " --> pdb=" O   MET A 602 " (cutoff:3.500A)
      Proline residue:  A 607  - end of helix
      removed outlier: 3.561A  pdb=" N   VAL A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 632
    Processing helix  chain 'A' and resid 632 through 664
      removed outlier: 4.154A  pdb=" N   PHE A 638 " --> pdb=" O   LYS A 634 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL A 640 " --> pdb=" O   ALA A 636 " (cutoff:3.500A)
      Proline residue:  A 641  - end of helix
      removed outlier: 3.508A  pdb=" N   THR A 655 " --> pdb=" O   ASP A 651 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   PHE A 656 " --> pdb=" O   GLY A 652 " (cutoff:3.500A)
      Proline residue:  A 657  - end of helix
    Processing helix  chain 'B' and resid 50 through 75
    Processing helix  chain 'B' and resid 81 through 104
      removed outlier: 3.642A  pdb=" N   ALA B  86 " --> pdb=" O   ASN B  82 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU B  87 " --> pdb=" O   VAL B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 132
      removed outlier: 3.540A  pdb=" N   TYR B 126 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ILE B 128 " --> pdb=" O   ALA B 124 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ALA B 129 " --> pdb=" O   CYS B 125 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   PHE B 130 " --> pdb=" O   TYR B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 141
      removed outlier: 3.651A  pdb=" N   LEU B 141 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 150
      removed outlier: 3.575A  pdb=" N   GLY B 150 " --> pdb=" O   TYR B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 191
      removed outlier: 4.256A  pdb=" N   PHE B 177 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   GLY B 178 " --> pdb=" O   ALA B 174 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   GLY B 179 " --> pdb=" O   CYS B 175 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   LEU B 180 " --> pdb=" O   SER B 176 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   LEU B 181 " --> pdb=" O   PHE B 177 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   THR B 182 " --> pdb=" O   GLY B 178 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ILE B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
      Proline residue:  B 185  - end of helix
      removed outlier: 3.980A  pdb=" N   GLN B 188 " --> pdb=" O   ILE B 184 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL B 189 " --> pdb=" O   PRO B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 213
    Processing helix  chain 'B' and resid 219 through 243
      removed outlier: 3.565A  pdb=" N   TYR B 230 " --> pdb=" O   GLY B 226 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   PHE B 243 " --> pdb=" O   PHE B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 265
    Processing helix  chain 'B' and resid 272 through 281
      removed outlier: 3.914A  pdb=" N   ILE B 281 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 299
    Processing helix  chain 'B' and resid 300 through 306
    Processing helix  chain 'B' and resid 307 through 309
      No H-bonds generated for 'chain 'B' and resid 307 through 309'
    Processing helix  chain 'B' and resid 325 through 359
      removed outlier: 3.674A  pdb=" N   LYS B 329 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   TYR B 343 " --> pdb=" O   GLY B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 416
      removed outlier: 3.927A  pdb=" N   TYR B 398 " --> pdb=" O   SER B 394 " (cutoff:3.500A)
      Proline residue:  B 413  - end of helix
    Processing helix  chain 'B' and resid 420 through 446
      removed outlier: 3.732A  pdb=" N   VAL B 424 " --> pdb=" O   LYS B 420 " (cutoff:3.500A)
      Proline residue:  B 432  - end of helix
      removed outlier: 3.553A  pdb=" N   LEU B 444 " --> pdb=" O   TYR B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 464
    Processing helix  chain 'B' and resid 470 through 501
      removed outlier: 3.539A  pdb=" N   GLN B 493 " --> pdb=" O   ALA B 489 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ASP B 494 " --> pdb=" O   ASP B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 534
      removed outlier: 3.563A  pdb=" N   ILE B 521 " --> pdb=" O   ALA B 517 " (cutoff:3.500A)
      Proline residue:  B 524  - end of helix
    Processing helix  chain 'B' and resid 545 through 560
      removed outlier: 3.936A  pdb=" N   LEU B 549 " --> pdb=" O   ALA B 545 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   GLU B 560 " --> pdb=" O   ILE B 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 565
    Processing helix  chain 'B' and resid 568 through 590
      removed outlier: 3.639A  pdb=" N   ASP B 588 " --> pdb=" O   SER B 584 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 610
      removed outlier: 3.801A  pdb=" N   VAL B 606 " --> pdb=" O   MET B 602 " (cutoff:3.500A)
      Proline residue:  B 607  - end of helix
      removed outlier: 3.561A  pdb=" N   VAL B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 632
    Processing helix  chain 'B' and resid 632 through 664
      removed outlier: 4.153A  pdb=" N   PHE B 638 " --> pdb=" O   LYS B 634 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL B 640 " --> pdb=" O   ALA B 636 " (cutoff:3.500A)
      Proline residue:  B 641  - end of helix
      removed outlier: 3.508A  pdb=" N   THR B 655 " --> pdb=" O   ASP B 651 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   PHE B 656 " --> pdb=" O   GLY B 652 " (cutoff:3.500A)
      Proline residue:  B 657  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 671 through 675

    640 hydrogen bonds defined for protein.
    1896 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: 2.84

  Time building geometry restraints manager: 3.48 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: 2720
        1.35 -     1.47: 2551
        1.47 -     1.58: 4245
        1.58 -     1.70: 0
        1.70 -     1.82: 126
  Bond restraints: 9642
  Sorted by residual:
  bond pdb=" CAI Y01 A 802 "
       pdb=" CAK Y01 A 802 "
    ideal  model  delta    sigma   weight residual
    1.492  1.405  0.087 2.00e-02 2.50e+03 1.87e+01
  bond pdb=" CAI Y01 B 701 "
       pdb=" CAK Y01 B 701 "
    ideal  model  delta    sigma   weight residual
    1.492  1.406  0.086 2.00e-02 2.50e+03 1.86e+01
  bond pdb=" CAI Y01 B 702 "
       pdb=" CAK Y01 B 702 "
    ideal  model  delta    sigma   weight residual
    1.492  1.406  0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" CAI Y01 A 801 "
       pdb=" CAK Y01 A 801 "
    ideal  model  delta    sigma   weight residual
    1.492  1.406  0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" CAI Y01 B 701 "
       pdb=" CAZ Y01 B 701 "
    ideal  model  delta    sigma   weight residual
    1.332  1.382 -0.050 2.00e-02 2.50e+03 6.28e+00
  ... (remaining 9637 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 12973
        2.40 -     4.81: 115
        4.81 -     7.21: 18
        7.21 -     9.62: 8
        9.62 -    12.02: 8
  Bond angle restraints: 13122
  Sorted by residual:
  angle pdb=" OAG Y01 A 802 "
        pdb=" CAY Y01 A 802 "
        pdb=" OAW Y01 A 802 "
      ideal   model   delta    sigma   weight residual
     123.38  111.36   12.02 3.00e+00 1.11e-01 1.61e+01
  angle pdb=" OAG Y01 B 701 "
        pdb=" CAY Y01 B 701 "
        pdb=" OAW Y01 B 701 "
      ideal   model   delta    sigma   weight residual
     123.38  111.37   12.01 3.00e+00 1.11e-01 1.60e+01
  angle pdb=" OAG Y01 B 702 "
        pdb=" CAY Y01 B 702 "
        pdb=" OAW Y01 B 702 "
      ideal   model   delta    sigma   weight residual
     123.38  111.51   11.87 3.00e+00 1.11e-01 1.56e+01
  angle pdb=" OAG Y01 A 801 "
        pdb=" CAY Y01 A 801 "
        pdb=" OAW Y01 A 801 "
      ideal   model   delta    sigma   weight residual
     123.38  111.53   11.85 3.00e+00 1.11e-01 1.56e+01
  angle pdb=" CAM Y01 B 701 "
        pdb=" CAY Y01 B 701 "
        pdb=" OAW Y01 B 701 "
      ideal   model   delta    sigma   weight residual
     111.19  123.01  -11.82 3.00e+00 1.11e-01 1.55e+01
  ... (remaining 13117 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.38: 5427
       16.38 -    32.77: 215
       32.77 -    49.15: 70
       49.15 -    65.54: 16
       65.54 -    81.92: 2
  Dihedral angle restraints: 5730
    sinusoidal: 2324
      harmonic: 3406
  Sorted by residual:
  dihedral pdb=" CB  CYS A 250 "
           pdb=" SG  CYS A 250 "
           pdb=" SG  CYS A 671 "
           pdb=" CB  CYS A 671 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.84   31.84     1      1.00e+01 1.00e-02 1.44e+01
  dihedral pdb=" CB  CYS B 250 "
           pdb=" SG  CYS B 250 "
           pdb=" SG  CYS B 671 "
           pdb=" CB  CYS B 671 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.83   31.83     1      1.00e+01 1.00e-02 1.44e+01
  dihedral pdb=" CA  MET A 322 "
           pdb=" CB  MET A 322 "
           pdb=" CG  MET A 322 "
           pdb=" SD  MET A 322 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.05   55.05     3      1.50e+01 4.44e-03 9.32e+00
  ... (remaining 5727 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1157
       0.044 -    0.088: 263
       0.088 -    0.133: 54
       0.133 -    0.177: 6
       0.177 -    0.221: 6
  Chirality restraints: 1486
  Sorted by residual:
  chirality pdb=" CBF Y01 A 801 "
            pdb=" CAS Y01 A 801 "
            pdb=" CBD Y01 A 801 "
            pdb=" CBH Y01 A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.67    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CBF Y01 B 702 "
            pdb=" CAS Y01 B 702 "
            pdb=" CBD Y01 B 702 "
            pdb=" CBH Y01 B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.66    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CBG Y01 A 802 "
            pdb=" CAQ Y01 A 802 "
            pdb=" CBD Y01 A 802 "
            pdb=" CBI Y01 A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.52    0.19 2.00e-01 2.50e+01 8.98e-01
  ... (remaining 1483 not shown)

  Planarity restraints: 1576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 606 "   -0.019 5.00e-02 4.00e+02   2.89e-02 1.33e+00
        pdb=" N   PRO B 607 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 607 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 607 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 606 "    0.019 5.00e-02 4.00e+02   2.86e-02 1.31e+00
        pdb=" N   PRO A 607 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 607 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 607 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 156 "   -0.018 5.00e-02 4.00e+02   2.66e-02 1.13e+00
        pdb=" N   PRO B 157 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO B 157 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 157 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1573 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1980
        2.78 -     3.31: 9367
        3.31 -     3.84: 15499
        3.84 -     4.37: 18913
        4.37 -     4.90: 32771
  Nonbonded interactions: 78530
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 123 "
            pdb=" OG1 THR A 127 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   VAL B 123 "
            pdb=" OG1 THR B 127 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OD1 ASP A 446 "
            pdb=" NE2 GLN A 493 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OD1 ASP B 446 "
            pdb=" NE2 GLN B 493 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OH  TYR A 328 "
            pdb=" O   LYS A 567 "
     model   vdw
     2.311 3.040
  ... (remaining 78525 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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=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:             3.680
  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:             0.020
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.000
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
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      :  0.004   0.087   9644  Z= 0.184
  Angle     :  0.647  12.024  13126  Z= 0.295
  Chirality :  0.040   0.221   1486
  Planarity :  0.003   0.029   1576
  Dihedral  : 10.320  81.919   3572
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  2.49 %
    Favored  : 96.67 %
  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:  1.52 (0.24), residues: 1192
  helix:  1.70 (0.17), residues: 850
  sheet:  None (None), residues: 0
  loop : -0.72 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 167 
 HIS   0.001   0.001   HIS A 212 
 PHE   0.006   0.001   PHE B 110 
 TYR   0.007   0.001   TYR A 422 
 ARG   0.002   0.000   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21424 (  640)
  hydrogen bonds       : angle       6.89531 ( 1896)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       2.08817 (    4)
  covalent geometry    : bond        0.00373 ( 9642)
  covalent geometry    : angle       0.64569 (13122)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 190
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A  111 THR cc_start: 0.8030 (p) cc_final: 0.7715 (t)
REVERT: A  506 LYS cc_start: 0.7162 (pttp) cc_final: 0.6923 (ptmt)
REVERT: A  633 LYS cc_start: 0.8486 (tptm) cc_final: 0.8200 (tptt)
REVERT: B  111 THR cc_start: 0.8036 (p) cc_final: 0.7721 (t)
REVERT: B  506 LYS cc_start: 0.7160 (pttp) cc_final: 0.6926 (ptmt)
REVERT: B  633 LYS cc_start: 0.8486 (tptm) cc_final: 0.8200 (tptt)
  outliers start: 8
  outliers final: 2
  residues processed: 196
  average time/residue: 0.9955
  time to fit residues: 212.0077
Evaluate side-chains
  138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 136
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain B residue  192 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   chunk 70 optimal weight:    0.0040
   chunk 108 optimal weight:    2.9990
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 287 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 = 0.4134 r_free = 0.4134 target = 0.186074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.151537 restraints weight = 10894.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.82
r_work: 0.3490 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9644  Z= 0.153
  Angle     :  0.574   6.656  13126  Z= 0.290
  Chirality :  0.040   0.156   1486
  Planarity :  0.004   0.032   1576
  Dihedral  :  7.545  52.897   1564
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  :  9.98 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.25), residues: 1192
  helix:  2.26 (0.18), residues: 842
  sheet:  None (None), residues: 0
  loop : -0.40 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 654 
 HIS   0.002   0.001   HIS B 212 
 PHE   0.019   0.002   PHE A 638 
 TYR   0.011   0.001   TYR B 126 
 ARG   0.001   0.000   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04871 (  640)
  hydrogen bonds       : angle       4.55637 ( 1896)
  SS BOND              : bond        0.00105 (    2)
  SS BOND              : angle       2.06331 (    4)
  covalent geometry    : bond        0.00340 ( 9642)
  covalent geometry    : angle       0.57343 (13122)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 1.038 
Fit side-chains
REVERT: A  194 TYR cc_start: 0.8228 (m-10) cc_final: 0.8008 (m-10)
REVERT: A  396 MET cc_start: 0.7407 (mpp) cc_final: 0.6032 (tmt)
REVERT: A  440 TYR cc_start: 0.7945 (t80) cc_final: 0.7617 (t80)
REVERT: A  453 TYR cc_start: 0.8427 (m-10) cc_final: 0.8138 (m-10)
REVERT: A  506 LYS cc_start: 0.6533 (pttp) cc_final: 0.6254 (ptmt)
REVERT: A  509 MET cc_start: 0.6502 (OUTLIER) cc_final: 0.6149 (ttp)
REVERT: A  620 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8311 (tp)
REVERT: A  633 LYS cc_start: 0.8232 (tptm) cc_final: 0.7922 (tptt)
REVERT: B  194 TYR cc_start: 0.8238 (m-10) cc_final: 0.8015 (m-10)
REVERT: B  396 MET cc_start: 0.7425 (mpp) cc_final: 0.6038 (tmt)
REVERT: B  440 TYR cc_start: 0.7953 (t80) cc_final: 0.7631 (t80)
REVERT: B  453 TYR cc_start: 0.8440 (m-10) cc_final: 0.8153 (m-10)
REVERT: B  506 LYS cc_start: 0.6536 (pttp) cc_final: 0.6261 (ptmt)
REVERT: B  509 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.6189 (ttp)
REVERT: B  620 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8308 (tp)
REVERT: B  633 LYS cc_start: 0.8216 (tptm) cc_final: 0.7856 (tptt)
  outliers start: 30
  outliers final: 4
  residues processed: 160
  average time/residue: 1.0290
  time to fit residues: 178.1524
Evaluate side-chains
  142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  634 LYS
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  509 MET
Chi-restraints excluded: chain B residue  620 LEU
Chi-restraints excluded: chain B residue  634 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0980
   chunk 92 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 89 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 104 optimal weight:    0.0970
   chunk 68 optimal weight:    0.5980
   chunk 109 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 287 ASN
** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 287 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.186938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.151816 restraints weight = 10996.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 2.69
r_work: 0.3504 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9644  Z= 0.128
  Angle     :  0.532   7.588  13126  Z= 0.265
  Chirality :  0.039   0.123   1486
  Planarity :  0.004   0.034   1576
  Dihedral  :  7.272  52.163   1564
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 12.79 %
    Favored  : 84.62 %
  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:  2.41 (0.25), residues: 1192
  helix:  2.34 (0.18), residues: 864
  sheet:  None (None), residues: 0
  loop : -0.44 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 654 
 HIS   0.002   0.001   HIS A 212 
 PHE   0.020   0.001   PHE A 638 
 TYR   0.011   0.001   TYR A 126 
 ARG   0.001   0.000   ARG B 552 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04393 (  640)
  hydrogen bonds       : angle       4.24930 ( 1896)
  SS BOND              : bond        0.00143 (    2)
  SS BOND              : angle       1.88136 (    4)
  covalent geometry    : bond        0.00278 ( 9642)
  covalent geometry    : angle       0.53102 (13122)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 146
  time to evaluate  : 0.986 
Fit side-chains
REVERT: A  396 MET cc_start: 0.7357 (mpp) cc_final: 0.5980 (tmt)
REVERT: A  453 TYR cc_start: 0.8400 (m-10) cc_final: 0.8144 (m-10)
REVERT: A  506 LYS cc_start: 0.6406 (pttp) cc_final: 0.6074 (ptmt)
REVERT: A  591 PRO cc_start: 0.6950 (Cg_exo) cc_final: 0.6643 (Cg_endo)
REVERT: A  633 LYS cc_start: 0.8313 (tptm) cc_final: 0.8009 (tptt)
REVERT: B  396 MET cc_start: 0.7360 (mpp) cc_final: 0.5985 (tmt)
REVERT: B  453 TYR cc_start: 0.8399 (m-10) cc_final: 0.8140 (m-10)
REVERT: B  506 LYS cc_start: 0.6410 (pttp) cc_final: 0.6085 (ptmt)
REVERT: B  591 PRO cc_start: 0.6938 (Cg_exo) cc_final: 0.6628 (Cg_endo)
REVERT: B  633 LYS cc_start: 0.8305 (tptm) cc_final: 0.8008 (tptt)
  outliers start: 25
  outliers final: 10
  residues processed: 158
  average time/residue: 1.0779
  time to fit residues: 184.0310
Evaluate side-chains
  144 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  602 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  602 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 96 optimal weight:    0.5980
   chunk 118 optimal weight:    1.9990
   chunk 95 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 109 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 31 optimal weight:    0.3980
   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 155 ASN
B 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.186014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.150525 restraints weight = 10959.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 2.71
r_work: 0.3486 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9644  Z= 0.140
  Angle     :  0.542   7.897  13126  Z= 0.271
  Chirality :  0.040   0.131   1486
  Planarity :  0.004   0.037   1576
  Dihedral  :  7.184  49.125   1564
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 12.79 %
    Favored  : 84.30 %
  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:  2.32 (0.25), residues: 1192
  helix:  2.27 (0.18), residues: 864
  sheet:  None (None), residues: 0
  loop : -0.47 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 654 
 HIS   0.002   0.001   HIS A 344 
 PHE   0.020   0.002   PHE A 638 
 TYR   0.011   0.001   TYR A 194 
 ARG   0.001   0.000   ARG B 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04228 (  640)
  hydrogen bonds       : angle       4.19411 ( 1896)
  SS BOND              : bond        0.00129 (    2)
  SS BOND              : angle       1.90577 (    4)
  covalent geometry    : bond        0.00317 ( 9642)
  covalent geometry    : angle       0.54146 (13122)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 149
  time to evaluate  : 0.997 
Fit side-chains
REVERT: A  396 MET cc_start: 0.7294 (mpp) cc_final: 0.5947 (tmt)
REVERT: A  453 TYR cc_start: 0.8376 (m-10) cc_final: 0.8149 (m-10)
REVERT: A  506 LYS cc_start: 0.6412 (pttp) cc_final: 0.6117 (ptmt)
REVERT: A  509 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.5757 (ttt)
REVERT: A  633 LYS cc_start: 0.8235 (tptm) cc_final: 0.7921 (tptt)
REVERT: B  396 MET cc_start: 0.7303 (mpp) cc_final: 0.5955 (tmt)
REVERT: B  453 TYR cc_start: 0.8371 (m-10) cc_final: 0.8146 (m-10)
REVERT: B  506 LYS cc_start: 0.6408 (pttp) cc_final: 0.6106 (ptmt)
REVERT: B  509 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.5761 (ttt)
REVERT: B  633 LYS cc_start: 0.8263 (tptm) cc_final: 0.7947 (tptt)
  outliers start: 28
  outliers final: 10
  residues processed: 163
  average time/residue: 1.0196
  time to fit residues: 180.6516
Evaluate side-chains
  141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  509 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 33 optimal weight:    0.0970
   chunk 44 optimal weight:    0.6980
   chunk 60 optimal weight:    8.9990
   chunk 116 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 55 optimal weight:    0.3980
   chunk 87 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9980
   chunk 59 optimal weight:    0.2980
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
B 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.187640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.152244 restraints weight = 10890.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 2.47
r_work: 0.3515 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9644  Z= 0.122
  Angle     :  0.533   8.068  13126  Z= 0.264
  Chirality :  0.039   0.128   1486
  Planarity :  0.004   0.036   1576
  Dihedral  :  7.028  46.352   1564
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.97 %
    Favored  : 82.74 %
  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:  2.37 (0.25), residues: 1192
  helix:  2.31 (0.18), residues: 862
  sheet:  None (None), residues: 0
  loop : -0.44 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 654 
 HIS   0.001   0.001   HIS B 344 
 PHE   0.018   0.001   PHE A 638 
 TYR   0.010   0.001   TYR B 146 
 ARG   0.002   0.000   ARG A 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03974 (  640)
  hydrogen bonds       : angle       4.10531 ( 1896)
  SS BOND              : bond        0.00098 (    2)
  SS BOND              : angle       1.68401 (    4)
  covalent geometry    : bond        0.00263 ( 9642)
  covalent geometry    : angle       0.53269 (13122)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 155
  time to evaluate  : 0.946 
Fit side-chains
REVERT: A  396 MET cc_start: 0.7258 (mpp) cc_final: 0.5933 (tmt)
REVERT: A  453 TYR cc_start: 0.8313 (m-10) cc_final: 0.8083 (m-10)
REVERT: A  506 LYS cc_start: 0.6381 (pttp) cc_final: 0.6079 (ptmt)
REVERT: A  509 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.5718 (ttt)
REVERT: A  633 LYS cc_start: 0.8265 (tptm) cc_final: 0.7947 (tptt)
REVERT: B  396 MET cc_start: 0.7268 (mpp) cc_final: 0.5940 (tmt)
REVERT: B  453 TYR cc_start: 0.8312 (m-10) cc_final: 0.8082 (m-10)
REVERT: B  506 LYS cc_start: 0.6399 (pttp) cc_final: 0.6094 (ptmt)
REVERT: B  509 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.5713 (ttt)
REVERT: B  633 LYS cc_start: 0.8253 (tptm) cc_final: 0.7944 (tptt)
  outliers start: 22
  outliers final: 10
  residues processed: 171
  average time/residue: 1.2114
  time to fit residues: 222.1438
Evaluate side-chains
  152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  509 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 117 optimal weight:    0.2980
   chunk 99 optimal weight:    1.9990
   chunk 80 optimal weight:    0.2980
   chunk 39 optimal weight:    1.9990
   chunk 114 optimal weight:    0.7980
   chunk 90 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0980
   chunk 50 optimal weight:    0.8980
   chunk 59 optimal weight:    0.4980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
B 115 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.187077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.152917 restraints weight = 10849.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 2.49
r_work: 0.3533 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9644  Z= 0.121
  Angle     :  0.531   8.752  13126  Z= 0.263
  Chirality :  0.039   0.136   1486
  Planarity :  0.004   0.036   1576
  Dihedral  :  6.867  44.748   1564
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.35 %
    Favored  : 82.95 %
  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:  2.36 (0.25), residues: 1192
  helix:  2.30 (0.18), residues: 850
  sheet:  None (None), residues: 0
  loop : -0.34 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 654 
 HIS   0.002   0.001   HIS A 344 
 PHE   0.020   0.001   PHE B 638 
 TYR   0.010   0.001   TYR A 597 
 ARG   0.003   0.000   ARG A 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03871 (  640)
  hydrogen bonds       : angle       4.05318 ( 1896)
  SS BOND              : bond        0.00089 (    2)
  SS BOND              : angle       1.62916 (    4)
  covalent geometry    : bond        0.00264 ( 9642)
  covalent geometry    : angle       0.53071 (13122)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 1.032 
Fit side-chains
REVERT: A  396 MET cc_start: 0.7194 (mpp) cc_final: 0.5925 (tmt)
REVERT: A  440 TYR cc_start: 0.7856 (t80) cc_final: 0.7589 (t80)
REVERT: A  453 TYR cc_start: 0.8301 (m-10) cc_final: 0.8092 (m-10)
REVERT: A  509 MET cc_start: 0.6301 (OUTLIER) cc_final: 0.5594 (ttt)
REVERT: A  633 LYS cc_start: 0.8234 (tptm) cc_final: 0.7925 (tptt)
REVERT: B  396 MET cc_start: 0.7214 (mpp) cc_final: 0.5929 (tmt)
REVERT: B  440 TYR cc_start: 0.7868 (t80) cc_final: 0.7605 (t80)
REVERT: B  453 TYR cc_start: 0.8284 (m-10) cc_final: 0.8074 (m-10)
REVERT: B  633 LYS cc_start: 0.8246 (tptm) cc_final: 0.7936 (tptt)
  outliers start: 26
  outliers final: 14
  residues processed: 161
  average time/residue: 1.1132
  time to fit residues: 193.6988
Evaluate side-chains
  149 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  498 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 115 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 83 optimal weight:    0.1980
   chunk 13 optimal weight:    0.7980
   chunk 77 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 104 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 110 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4123 r_free = 0.4123 target = 0.186006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.152361 restraints weight = 10945.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 2.71
r_work: 0.3500 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9644  Z= 0.140
  Angle     :  0.560   8.429  13126  Z= 0.274
  Chirality :  0.039   0.122   1486
  Planarity :  0.004   0.037   1576
  Dihedral  :  6.895  45.421   1564
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.86 %
    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:  2.29 (0.25), residues: 1192
  helix:  2.22 (0.18), residues: 852
  sheet:  None (None), residues: 0
  loop : -0.29 (0.37), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 654 
 HIS   0.002   0.001   HIS A 212 
 PHE   0.016   0.001   PHE A 638 
 TYR   0.010   0.001   TYR A 244 
 ARG   0.003   0.000   ARG B 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04029 (  640)
  hydrogen bonds       : angle       4.10408 ( 1896)
  SS BOND              : bond        0.00067 (    2)
  SS BOND              : angle       1.64895 (    4)
  covalent geometry    : bond        0.00321 ( 9642)
  covalent geometry    : angle       0.55936 (13122)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 1.123 
Fit side-chains
REVERT: A  396 MET cc_start: 0.7259 (mpp) cc_final: 0.5970 (tmt)
REVERT: A  453 TYR cc_start: 0.8312 (m-10) cc_final: 0.8087 (m-10)
REVERT: A  633 LYS cc_start: 0.8244 (tptm) cc_final: 0.7933 (tptt)
REVERT: B  396 MET cc_start: 0.7265 (mpp) cc_final: 0.5968 (tmt)
REVERT: B  453 TYR cc_start: 0.8304 (m-10) cc_final: 0.8081 (m-10)
REVERT: B  509 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.5724 (ttt)
REVERT: B  633 LYS cc_start: 0.8277 (tptm) cc_final: 0.7958 (tptt)
  outliers start: 26
  outliers final: 18
  residues processed: 159
  average time/residue: 1.0820
  time to fit residues: 186.1129
Evaluate side-chains
  151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  509 MET
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 52 optimal weight:    0.2980
   chunk 106 optimal weight:    0.3980
   chunk 18 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0270
   chunk 110 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 116 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
A 483 GLN
B 483 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.186829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.152871 restraints weight = 11054.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3783 rms_B_bonded: 2.62
r_work: 0.3530 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9644  Z= 0.127
  Angle     :  0.563   8.863  13126  Z= 0.274
  Chirality :  0.039   0.139   1486
  Planarity :  0.004   0.036   1576
  Dihedral  :  6.808  45.336   1564
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.28 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.25), residues: 1192
  helix:  2.27 (0.18), residues: 860
  sheet:  None (None), residues: 0
  loop : -0.50 (0.37), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 654 
 HIS   0.001   0.001   HIS A 212 
 PHE   0.015   0.001   PHE B 638 
 TYR   0.009   0.001   TYR A 422 
 ARG   0.003   0.000   ARG A 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  640)
  hydrogen bonds       : angle       4.07683 ( 1896)
  SS BOND              : bond        0.00070 (    2)
  SS BOND              : angle       1.62103 (    4)
  covalent geometry    : bond        0.00285 ( 9642)
  covalent geometry    : angle       0.56205 (13122)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A  396 MET cc_start: 0.7247 (mpp) cc_final: 0.5963 (tmt)
REVERT: A  440 TYR cc_start: 0.7857 (t80) cc_final: 0.7575 (t80)
REVERT: A  453 TYR cc_start: 0.8281 (m-10) cc_final: 0.8058 (m-10)
REVERT: A  509 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.5616 (ttt)
REVERT: A  633 LYS cc_start: 0.8232 (tptm) cc_final: 0.7918 (tptt)
REVERT: B  396 MET cc_start: 0.7248 (mpp) cc_final: 0.5959 (tmt)
REVERT: B  440 TYR cc_start: 0.7851 (t80) cc_final: 0.7571 (t80)
REVERT: B  453 TYR cc_start: 0.8276 (m-10) cc_final: 0.8051 (m-10)
REVERT: B  509 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5561 (ttt)
REVERT: B  633 LYS cc_start: 0.8255 (tptm) cc_final: 0.7945 (tptt)
  outliers start: 26
  outliers final: 15
  residues processed: 153
  average time/residue: 1.1740
  time to fit residues: 194.2283
Evaluate side-chains
  149 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  509 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 114 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 483 GLN
B 483 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.183879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.150227 restraints weight = 10933.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.71
r_work: 0.3473 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9644  Z= 0.173
  Angle     :  0.609  10.202  13126  Z= 0.299
  Chirality :  0.041   0.154   1486
  Planarity :  0.004   0.039   1576
  Dihedral  :  7.094  49.125   1564
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 16.11 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.25), residues: 1192
  helix:  2.07 (0.18), residues: 860
  sheet:  None (None), residues: 0
  loop : -0.60 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 654 
 HIS   0.002   0.001   HIS B 212 
 PHE   0.013   0.002   PHE B 576 
 TYR   0.011   0.001   TYR A 244 
 ARG   0.003   0.000   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04318 (  640)
  hydrogen bonds       : angle       4.23439 ( 1896)
  SS BOND              : bond        0.00030 (    2)
  SS BOND              : angle       1.72854 (    4)
  covalent geometry    : bond        0.00413 ( 9642)
  covalent geometry    : angle       0.60841 (13122)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 1.156 
Fit side-chains
REVERT: A  396 MET cc_start: 0.7216 (mpp) cc_final: 0.5941 (tmt)
REVERT: A  440 TYR cc_start: 0.7992 (t80) cc_final: 0.7734 (t80)
REVERT: A  453 TYR cc_start: 0.8357 (m-10) cc_final: 0.8138 (m-10)
REVERT: A  509 MET cc_start: 0.6414 (OUTLIER) cc_final: 0.5705 (ttt)
REVERT: A  633 LYS cc_start: 0.8265 (tptm) cc_final: 0.7947 (tptt)
REVERT: B  396 MET cc_start: 0.7219 (mpp) cc_final: 0.5946 (tmt)
REVERT: B  440 TYR cc_start: 0.7993 (t80) cc_final: 0.7732 (t80)
REVERT: B  453 TYR cc_start: 0.8353 (m-10) cc_final: 0.8137 (m-10)
REVERT: B  509 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.5658 (ttt)
REVERT: B  633 LYS cc_start: 0.8289 (tptm) cc_final: 0.7963 (tptt)
  outliers start: 25
  outliers final: 17
  residues processed: 155
  average time/residue: 1.5186
  time to fit residues: 254.1562
Evaluate side-chains
  146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  509 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 108 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 56 optimal weight:    0.4980
   chunk 33 optimal weight:    0.0970
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.186048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.152149 restraints weight = 11052.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.58
r_work: 0.3521 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
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   0.042   9644  Z= 0.138
  Angle     :  0.591  10.061  13126  Z= 0.289
  Chirality :  0.040   0.140   1486
  Planarity :  0.004   0.037   1576
  Dihedral  :  7.012  55.827   1564
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.26 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.25), residues: 1192
  helix:  2.14 (0.18), residues: 860
  sheet:  None (None), residues: 0
  loop : -0.57 (0.37), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 654 
 HIS   0.002   0.001   HIS A 212 
 PHE   0.012   0.001   PHE B 576 
 TYR   0.010   0.001   TYR A 244 
 ARG   0.005   0.000   ARG A 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04014 (  640)
  hydrogen bonds       : angle       4.15583 ( 1896)
  SS BOND              : bond        0.00050 (    2)
  SS BOND              : angle       1.66268 (    4)
  covalent geometry    : bond        0.00316 ( 9642)
  covalent geometry    : angle       0.59025 (13122)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.996 
Fit side-chains
REVERT: A  396 MET cc_start: 0.7204 (mpp) cc_final: 0.5933 (tmt)
REVERT: A  440 TYR cc_start: 0.7891 (t80) cc_final: 0.7648 (t80)
REVERT: A  453 TYR cc_start: 0.8309 (m-10) cc_final: 0.8096 (m-10)
REVERT: A  509 MET cc_start: 0.6303 (OUTLIER) cc_final: 0.5563 (ttt)
REVERT: A  633 LYS cc_start: 0.8276 (tptm) cc_final: 0.7948 (tptt)
REVERT: B  396 MET cc_start: 0.7195 (mpp) cc_final: 0.5933 (tmt)
REVERT: B  440 TYR cc_start: 0.7899 (t80) cc_final: 0.7655 (t80)
REVERT: B  453 TYR cc_start: 0.8308 (m-10) cc_final: 0.8096 (m-10)
REVERT: B  509 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.5650 (ttt)
REVERT: B  633 LYS cc_start: 0.8278 (tptm) cc_final: 0.7950 (tptt)
  outliers start: 21
  outliers final: 13
  residues processed: 148
  average time/residue: 1.1283
  time to fit residues: 180.0092
Evaluate side-chains
  144 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  509 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 84 optimal weight:    0.6980
   chunk 113 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0870
   chunk 63 optimal weight:    0.9980
   chunk 110 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0670
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.4496

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

Flipped N/Q/H residues before XYZ refinement:
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.186679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.152480 restraints weight = 10953.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 2.62
r_work: 0.3532 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9644  Z= 0.130
  Angle     :  0.579   9.940  13126  Z= 0.283
  Chirality :  0.039   0.136   1486
  Planarity :  0.004   0.037   1576
  Dihedral  :  6.829  53.230   1564
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.57 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.25), residues: 1192
  helix:  2.20 (0.18), residues: 850
  sheet:  None (None), residues: 0
  loop : -0.47 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 654 
 HIS   0.002   0.001   HIS A 212 
 PHE   0.012   0.001   PHE B 576 
 TYR   0.009   0.001   TYR A 244 
 ARG   0.003   0.000   ARG A 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03896 (  640)
  hydrogen bonds       : angle       4.10944 ( 1896)
  SS BOND              : bond        0.00081 (    2)
  SS BOND              : angle       1.58508 (    4)
  covalent geometry    : bond        0.00295 ( 9642)
  covalent geometry    : angle       0.57883 (13122)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7043.91 seconds
wall clock time: 124 minutes 56.35 seconds (7496.35 seconds total)