Starting phenix.real_space_refine
on Mon Apr 28 08:27:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g79_51116/04_2025/9g79_51116.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g79_51116/04_2025/9g79_51116.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g79_51116/04_2025/9g79_51116.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g79_51116/04_2025/9g79_51116.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g79_51116/04_2025/9g79_51116.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g79_51116/04_2025/9g79_51116.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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      40      5.16       5
     C    4644      2.51       5
     N    1212      2.21       5
     O    1336      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7232
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3616
          Classifications: {'peptide': 449}
          Link IDs: {'PTRANS': 23, 'TRANS': 425}
    Chain: "A"
      Number of atoms: 3616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3616
          Classifications: {'peptide': 449}
          Link IDs: {'PTRANS': 23, 'TRANS': 425}
  Time building chain proxies: 5.32, per 1000 atoms: 0.74
  Number of scatterers: 7232
  At special positions: 0
  Unit cell: (119.652, 77.172, 75.048, 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      40     16.00
     O    1336      8.00
     N    1212      7.00
     C    4644      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: 1.87
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1636

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 10 sheets defined
      39.4% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'B' and resid 17 through 25
      removed outlier: 3.813A  pdb=" N   THR B  21 " --> pdb=" O   ASN B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 31
      removed outlier: 3.653A  pdb=" N   ALA B  30 " --> pdb=" O   ASP B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 34
      No H-bonds generated for 'chain 'B' and resid 32 through 34'
    Processing helix  chain 'B' and resid 35 through 40
    Processing helix  chain 'B' and resid 43 through 49
    Processing helix  chain 'B' and resid 49 through 54
    Processing helix  chain 'B' and resid 76 through 94
    Processing helix  chain 'B' and resid 109 through 122
      removed outlier: 3.523A  pdb=" N   TYR B 113 " --> pdb=" O   SER B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 146
    Processing helix  chain 'B' and resid 156 through 160
      removed outlier: 3.620A  pdb=" N   ILE B 160 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 165
    Processing helix  chain 'B' and resid 187 through 193
      removed outlier: 3.818A  pdb=" N   GLN B 193 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 241
      removed outlier: 4.325A  pdb=" N   GLN B 233 " --> pdb=" O   GLU B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 264
    Processing helix  chain 'B' and resid 266 through 272
      removed outlier: 3.564A  pdb=" N   TRP B 270 " --> pdb=" O   ILE B 266 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASN B 272 " --> pdb=" O   ALA B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 296
    Processing helix  chain 'B' and resid 303 through 313
    Processing helix  chain 'B' and resid 314 through 320
      removed outlier: 3.777A  pdb=" N   ALA B 318 " --> pdb=" O   GLY B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 348
    Processing helix  chain 'B' and resid 422 through 428
    Processing helix  chain 'A' and resid 17 through 25
      removed outlier: 3.643A  pdb=" N   THR A  21 " --> pdb=" O   ASN A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 31
      removed outlier: 3.676A  pdb=" N   ALA A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 34
      No H-bonds generated for 'chain 'A' and resid 32 through 34'
    Processing helix  chain 'A' and resid 35 through 40
    Processing helix  chain 'A' and resid 43 through 49
    Processing helix  chain 'A' and resid 49 through 54
    Processing helix  chain 'A' and resid 76 through 94
    Processing helix  chain 'A' and resid 109 through 122
    Processing helix  chain 'A' and resid 134 through 145
    Processing helix  chain 'A' and resid 156 through 160
      removed outlier: 3.555A  pdb=" N   ILE A 160 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 165
    Processing helix  chain 'A' and resid 187 through 193
      removed outlier: 3.664A  pdb=" N   GLN A 193 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 241
      removed outlier: 4.327A  pdb=" N   GLN A 233 " --> pdb=" O   GLU A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 264
    Processing helix  chain 'A' and resid 266 through 272
      removed outlier: 3.590A  pdb=" N   TRP A 270 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ASN A 272 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 296
    Processing helix  chain 'A' and resid 303 through 314
    Processing helix  chain 'A' and resid 314 through 321
      removed outlier: 3.676A  pdb=" N   ALA A 318 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   TYR A 321 " --> pdb=" O   MET A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 348
      removed outlier: 3.731A  pdb=" N   ILE A 341 " --> pdb=" O   ASN A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 428
      removed outlier: 3.660A  pdb=" N   TYR A 426 " --> pdb=" O   ASN A 422 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 71 through 75
      removed outlier: 6.207A  pdb=" N   ALA B  62 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
      removed outlier: 7.503A  pdb=" N   ILE B 278 " --> pdb=" O   ALA B  62 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   TYR B  64 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   CYS B 252 " --> pdb=" O   VAL B 277 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   VAL B 279 " --> pdb=" O   CYS B 252 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   ILE B 249 " --> pdb=" O   VAL B 299 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   TYR B 301 " --> pdb=" O   ILE B 249 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   TRP B 251 " --> pdb=" O   TYR B 301 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   VAL B 329 " --> pdb=" O   HIS B 353 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   THR B 355 " --> pdb=" O   VAL B 329 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   SER B 331 " --> pdb=" O   THR B 355 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE B 366 " --> pdb=" O   TRP B 356 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 125 through 128
      removed outlier: 6.435A  pdb=" N   VAL B 102 " --> pdb=" O   GLY B 127 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL B 149 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 208 through 214
      removed outlier: 3.525A  pdb=" N   LEU B 210 " --> pdb=" O   HIS B 226 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   THR B 418 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 388 through 391
      removed outlier: 3.552A  pdb=" N   GLY B 404 " --> pdb=" O   ALA B 442 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   ASP B 440 " --> pdb=" O   LEU B 406 " (cutoff:3.500A)
      removed outlier: 9.315A  pdb=" N   ILE B 408 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   SER B 438 " --> pdb=" O   ILE B 408 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   TRP B 435 " --> pdb=" O   MET B 431 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 388 through 391
      removed outlier: 3.552A  pdb=" N   GLY B 404 " --> pdb=" O   ALA B 442 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   ASP B 440 " --> pdb=" O   LEU B 406 " (cutoff:3.500A)
      removed outlier: 9.315A  pdb=" N   ILE B 408 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   SER B 438 " --> pdb=" O   ILE B 408 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 75
      removed outlier: 6.256A  pdb=" N   ALA A  62 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   ILE A 278 " --> pdb=" O   ALA A  62 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   TYR A  64 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   CYS A 252 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   VAL A 279 " --> pdb=" O   CYS A 252 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   ILE A 249 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   TYR A 301 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   TRP A 251 " --> pdb=" O   TYR A 301 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   VAL A 329 " --> pdb=" O   HIS A 353 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   THR A 355 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   SER A 331 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A 366 " --> pdb=" O   TRP A 356 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 125 through 129
      removed outlier: 6.416A  pdb=" N   VAL A 102 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   LEU A 129 " --> pdb=" O   VAL A 102 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ILE A 104 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL A 149 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.519A  pdb=" N   LEU A 210 " --> pdb=" O   HIS A 226 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   THR A 418 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 388 through 391
      removed outlier: 3.596A  pdb=" N   GLY A 404 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   ASP A 440 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
      removed outlier: 9.288A  pdb=" N   ILE A 408 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   SER A 438 " --> pdb=" O   ILE A 408 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   TRP A 435 " --> pdb=" O   MET A 431 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 388 through 391
      removed outlier: 3.596A  pdb=" N   GLY A 404 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   ASP A 440 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
      removed outlier: 9.288A  pdb=" N   ILE A 408 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   SER A 438 " --> pdb=" O   ILE A 408 " (cutoff:3.500A)

    262 hydrogen bonds defined for protein.
    756 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: 2.10

  Time building geometry restraints manager: 2.23 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2324
        1.34 -     1.46: 1665
        1.46 -     1.57: 3387
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 7450
  Sorted by residual:
  bond pdb=" C   GLU B 334 "
       pdb=" N   PRO B 335 "
    ideal  model  delta    sigma   weight residual
    1.333  1.348 -0.014 1.01e-02 9.80e+03 1.97e+00
  bond pdb=" CB  PRO B 335 "
       pdb=" CG  PRO B 335 "
    ideal  model  delta    sigma   weight residual
    1.492  1.551 -0.059 5.00e-02 4.00e+02 1.40e+00
  bond pdb=" CB  ASN B 349 "
       pdb=" CG  ASN B 349 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.14e+00
  bond pdb=" CB  GLU A  10 "
       pdb=" CG  GLU A  10 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.13e+00
  bond pdb=" CB  ASP A  12 "
       pdb=" CG  ASP A  12 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.12e+00
  ... (remaining 7445 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 9643
        1.23 -     2.45: 357
        2.45 -     3.68: 82
        3.68 -     4.90: 21
        4.90 -     6.13: 3
  Bond angle restraints: 10106
  Sorted by residual:
  angle pdb=" N   LEU B 310 "
        pdb=" CA  LEU B 310 "
        pdb=" C   LEU B 310 "
      ideal   model   delta    sigma   weight residual
     111.14  105.48    5.66 1.08e+00 8.57e-01 2.75e+01
  angle pdb=" N   LEU A 336 "
        pdb=" CA  LEU A 336 "
        pdb=" C   LEU A 336 "
      ideal   model   delta    sigma   weight residual
     108.96  115.09   -6.13 1.59e+00 3.96e-01 1.49e+01
  angle pdb=" CA  PRO B 335 "
        pdb=" N   PRO B 335 "
        pdb=" CD  PRO B 335 "
      ideal   model   delta    sigma   weight residual
     112.00  106.87    5.13 1.40e+00 5.10e-01 1.34e+01
  angle pdb=" N   MET B 309 "
        pdb=" CA  MET B 309 "
        pdb=" C   MET B 309 "
      ideal   model   delta    sigma   weight residual
     111.82  108.38    3.44 1.16e+00 7.43e-01 8.81e+00
  angle pdb=" N   ASN B 349 "
        pdb=" CA  ASN B 349 "
        pdb=" C   ASN B 349 "
      ideal   model   delta    sigma   weight residual
     111.24  107.43    3.81 1.38e+00 5.25e-01 7.63e+00
  ... (remaining 10101 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 3792
       17.80 -    35.61: 417
       35.61 -    53.41: 106
       53.41 -    71.21: 19
       71.21 -    89.01: 4
  Dihedral angle restraints: 4338
    sinusoidal: 1760
      harmonic: 2578
  Sorted by residual:
  dihedral pdb=" CA  PRO B 335 "
           pdb=" C   PRO B 335 "
           pdb=" N   LEU B 336 "
           pdb=" CA  LEU B 336 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.44  -17.56     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  LEU A  63 "
           pdb=" C   LEU A  63 "
           pdb=" N   TYR A  64 "
           pdb=" CA  TYR A  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.46   16.54     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  TRP B 202 "
           pdb=" C   TRP B 202 "
           pdb=" N   MET B 203 "
           pdb=" CA  MET B 203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.60  -16.40     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 4335 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 710
       0.038 -    0.076: 221
       0.076 -    0.115: 73
       0.115 -    0.153: 18
       0.153 -    0.191: 2
  Chirality restraints: 1024
  Sorted by residual:
  chirality pdb=" CA  GLU A 334 "
            pdb=" N   GLU A 334 "
            pdb=" C   GLU A 334 "
            pdb=" CB  GLU A 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.12e-01
  chirality pdb=" CA  TRP A  36 "
            pdb=" N   TRP A  36 "
            pdb=" C   TRP A  36 "
            pdb=" CB  TRP A  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.88e-01
  chirality pdb=" CA  PRO B 335 "
            pdb=" N   PRO B 335 "
            pdb=" C   PRO B 335 "
            pdb=" CB  PRO B 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.96e-01
  ... (remaining 1021 not shown)

  Planarity restraints: 1304
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 334 "   -0.066 5.00e-02 4.00e+02   9.75e-02 1.52e+01
        pdb=" N   PRO B 335 "    0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO B 335 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO B 335 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 349 "    0.011 2.00e-02 2.50e+03   2.30e-02 5.27e+00
        pdb=" C   ASN B 349 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ASN B 349 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LYS B 350 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 334 "   -0.034 5.00e-02 4.00e+02   5.12e-02 4.19e+00
        pdb=" N   PRO A 335 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 335 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 335 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1301 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1506
        2.77 -     3.31: 6540
        3.31 -     3.84: 12487
        3.84 -     4.37: 15193
        4.37 -     4.90: 26101
  Nonbonded interactions: 61827
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 265 "
            pdb=" ND2 ASN B 276 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" NZ  LYS B  66 "
            pdb=" OE1 GLN B 294 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" N   GLU B 316 "
            pdb=" OE1 GLU B 316 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" O   GLY A 265 "
            pdb=" ND2 ASN A 276 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OH  TYR A  65 "
            pdb=" OD2 ASP A  67 "
     model   vdw
     2.274 3.040
  ... (remaining 61822 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'
}

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:             3.970
  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:                     21.740
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  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:11.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
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      :  0.003   0.059   7450  Z= 0.140
  Angle     :  0.591   6.128  10106  Z= 0.343
  Chirality :  0.044   0.191   1024
  Planarity :  0.006   0.097   1304
  Dihedral  : 15.637  89.013   2702
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 24.73 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.29), residues: 894
  helix:  0.22 (0.32), residues: 274
  sheet: -0.08 (0.38), residues: 180
  loop :  1.04 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  36 
 HIS   0.003   0.001   HIS A 226 
 PHE   0.008   0.001   PHE A 209 
 TYR   0.019   0.001   TYR A 264 
 ARG   0.008   0.001   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17763 (  250)
  hydrogen bonds       : angle       7.90556 (  756)
  covalent geometry    : bond        0.00299 ( 7450)
  covalent geometry    : angle       0.59068 (10106)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  346 LYS cc_start: 0.8958 (ttpt) cc_final: 0.8712 (ttmm)
REVERT: A  308 ARG cc_start: 0.7607 (mtt90) cc_final: 0.7239 (mtm110)
REVERT: A  334 GLU cc_start: 0.8010 (tt0) cc_final: 0.7714 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 1.4401
  time to fit residues: 164.7471
Evaluate side-chains
  98 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 26 optimal weight:    0.2980
   chunk 41 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0970
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B  14 ASN
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 144 ASN
B 170 HIS
B 212 HIS
B 228 HIS
B 393 ASN
A  14 ASN
A 144 ASN
A 170 HIS
A 212 HIS
A 228 HIS
A 294 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.134655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.104788 restraints weight = 9673.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.38
r_work: 0.3130 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.1058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7450  Z= 0.117
  Angle     :  0.484   4.277  10106  Z= 0.259
  Chirality :  0.044   0.142   1024
  Planarity :  0.004   0.045   1304
  Dihedral  :  4.252  17.268    978
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 19.68 %
    Favored  : 76.33 %
  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:  0.68 (0.29), residues: 894
  helix:  0.37 (0.32), residues: 302
  sheet: -0.30 (0.38), residues: 182
  loop :  1.18 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  36 
 HIS   0.003   0.001   HIS A 226 
 PHE   0.008   0.001   PHE A 209 
 TYR   0.019   0.001   TYR A 264 
 ARG   0.005   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03641 (  250)
  hydrogen bonds       : angle       5.73388 (  756)
  covalent geometry    : bond        0.00273 ( 7450)
  covalent geometry    : angle       0.48443 (10106)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  346 LYS cc_start: 0.9122 (ttpt) cc_final: 0.8904 (ttmm)
REVERT: A  308 ARG cc_start: 0.7842 (mtt90) cc_final: 0.7518 (mtm110)
REVERT: A  334 GLU cc_start: 0.8244 (tt0) cc_final: 0.8029 (tt0)
REVERT: A  349 ASN cc_start: 0.8766 (t0) cc_final: 0.8520 (t0)
  outliers start: 30
  outliers final: 7
  residues processed: 128
  average time/residue: 1.3034
  time to fit residues: 175.8611
Evaluate side-chains
  104 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  378 SER
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  378 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 67 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 393 ASN
A 294 GLN
A 393 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.130066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.099283 restraints weight = 9909.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 2.43
r_work: 0.3043 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7450  Z= 0.215
  Angle     :  0.545   4.770  10106  Z= 0.289
  Chirality :  0.046   0.138   1024
  Planarity :  0.004   0.034   1304
  Dihedral  :  4.590  18.171    978
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 19.41 %
    Favored  : 76.46 %
  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:  0.48 (0.29), residues: 894
  helix:  0.24 (0.31), residues: 302
  sheet: -0.46 (0.38), residues: 182
  loop :  1.05 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  36 
 HIS   0.005   0.001   HIS B 226 
 PHE   0.014   0.002   PHE A 267 
 TYR   0.019   0.002   TYR B 264 
 ARG   0.002   0.000   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04200 (  250)
  hydrogen bonds       : angle       5.66970 (  756)
  covalent geometry    : bond        0.00515 ( 7450)
  covalent geometry    : angle       0.54463 (10106)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 104
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7783 (pp20)
REVERT: B  156 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8159 (mm)
REVERT: B  193 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8541 (mp10)
REVERT: B  349 ASN cc_start: 0.8830 (t0) cc_final: 0.8465 (t0)
REVERT: A  308 ARG cc_start: 0.7919 (mtt90) cc_final: 0.7595 (mtm110)
REVERT: A  311 MET cc_start: 0.8138 (mtp) cc_final: 0.7807 (mtp)
REVERT: A  334 GLU cc_start: 0.8318 (tt0) cc_final: 0.8030 (tt0)
REVERT: A  349 ASN cc_start: 0.8748 (t0) cc_final: 0.8363 (t0)
  outliers start: 31
  outliers final: 12
  residues processed: 124
  average time/residue: 1.8133
  time to fit residues: 236.0749
Evaluate side-chains
  112 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  140 ASP
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain B residue  378 SER
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  379 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   chunk 43 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 393 ASN
A 294 GLN
A 393 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.131771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.101863 restraints weight = 9850.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.37
r_work: 0.3080 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7450  Z= 0.166
  Angle     :  0.508   5.919  10106  Z= 0.267
  Chirality :  0.045   0.139   1024
  Planarity :  0.004   0.036   1304
  Dihedral  :  4.443  18.224    978
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 19.55 %
    Favored  : 75.80 %
  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:  0.47 (0.29), residues: 894
  helix:  0.31 (0.31), residues: 302
  sheet: -0.53 (0.38), residues: 182
  loop :  1.02 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  36 
 HIS   0.003   0.001   HIS A 226 
 PHE   0.011   0.001   PHE A 267 
 TYR   0.017   0.002   TYR B 264 
 ARG   0.002   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03582 (  250)
  hydrogen bonds       : angle       5.53512 (  756)
  covalent geometry    : bond        0.00398 ( 7450)
  covalent geometry    : angle       0.50783 (10106)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 101
  time to evaluate  : 0.797 
Fit side-chains
REVERT: B   97 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7791 (pp20)
REVERT: B  156 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8243 (mm)
REVERT: B  349 ASN cc_start: 0.8841 (t0) cc_final: 0.8389 (t0)
REVERT: B  397 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7642 (mp0)
REVERT: A  156 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8302 (mm)
REVERT: A  169 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7533 (mp10)
REVERT: A  193 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8536 (mm-40)
REVERT: A  205 LYS cc_start: 0.8784 (ptpp) cc_final: 0.8337 (ptpp)
REVERT: A  308 ARG cc_start: 0.7917 (mtt90) cc_final: 0.7569 (mtt90)
REVERT: A  311 MET cc_start: 0.8095 (mtp) cc_final: 0.7693 (mtp)
REVERT: A  334 GLU cc_start: 0.8319 (tt0) cc_final: 0.7949 (tt0)
REVERT: A  349 ASN cc_start: 0.8741 (t0) cc_final: 0.8305 (t0)
  outliers start: 35
  outliers final: 12
  residues processed: 125
  average time/residue: 1.6729
  time to fit residues: 219.3699
Evaluate side-chains
  114 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain B residue  378 SER
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  379 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 69 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
B 393 ASN
A 294 GLN
A 393 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.132399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.103009 restraints weight = 9789.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 2.35
r_work: 0.3071 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7450  Z= 0.162
  Angle     :  0.507   6.743  10106  Z= 0.266
  Chirality :  0.045   0.139   1024
  Planarity :  0.004   0.036   1304
  Dihedral  :  4.391  18.530    978
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 19.02 %
    Favored  : 76.20 %
  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:  0.51 (0.29), residues: 894
  helix:  0.39 (0.31), residues: 302
  sheet: -0.61 (0.37), residues: 182
  loop :  1.05 (0.33), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  36 
 HIS   0.002   0.001   HIS B 226 
 PHE   0.011   0.001   PHE A 267 
 TYR   0.016   0.002   TYR A 264 
 ARG   0.002   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03500 (  250)
  hydrogen bonds       : angle       5.48471 (  756)
  covalent geometry    : bond        0.00391 ( 7450)
  covalent geometry    : angle       0.50682 (10106)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.8256 (ttp-110) cc_final: 0.7934 (mtm-85)
REVERT: B   97 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7783 (pp20)
REVERT: B  156 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8309 (mm)
REVERT: B  349 ASN cc_start: 0.8853 (t0) cc_final: 0.8362 (t0)
REVERT: B  364 GLN cc_start: 0.8910 (mt0) cc_final: 0.8643 (mt0)
REVERT: B  397 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7588 (mp0)
REVERT: A   23 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7972 (mtm-85)
REVERT: A  156 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8383 (mm)
REVERT: A  169 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7541 (mp10)
REVERT: A  199 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.7939 (p0)
REVERT: A  205 LYS cc_start: 0.8734 (ptpp) cc_final: 0.8108 (pttm)
REVERT: A  308 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7577 (mtm110)
REVERT: A  311 MET cc_start: 0.8025 (mtp) cc_final: 0.7624 (mtp)
REVERT: A  334 GLU cc_start: 0.8301 (tt0) cc_final: 0.8001 (tt0)
REVERT: A  349 ASN cc_start: 0.8729 (t0) cc_final: 0.8239 (t0)
  outliers start: 36
  outliers final: 12
  residues processed: 126
  average time/residue: 1.6794
  time to fit residues: 221.8739
Evaluate side-chains
  118 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 1.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  229 GLU
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain B residue  378 SER
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  379 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 63 optimal weight:    0.2980
   chunk 86 optimal weight:    0.3980
   chunk 58 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0020
   chunk 76 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0070
   chunk 45 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.3406

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 393 ASN
A 186 ASN
A 294 GLN
A 393 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.134868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.105417 restraints weight = 9734.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.35
r_work: 0.3149 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7450  Z= 0.094
  Angle     :  0.477   7.590  10106  Z= 0.249
  Chirality :  0.043   0.142   1024
  Planarity :  0.004   0.035   1304
  Dihedral  :  4.084  16.448    978
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.68 %
    Favored  : 76.60 %
  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:  0.74 (0.30), residues: 894
  helix:  0.74 (0.32), residues: 290
  sheet: -0.58 (0.37), residues: 182
  loop :  1.08 (0.33), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  36 
 HIS   0.002   0.001   HIS A  52 
 PHE   0.007   0.001   PHE B 283 
 TYR   0.014   0.001   TYR A 264 
 ARG   0.002   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02743 (  250)
  hydrogen bonds       : angle       5.26290 (  756)
  covalent geometry    : bond        0.00221 ( 7450)
  covalent geometry    : angle       0.47734 (10106)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 2.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.8235 (ttp-110) cc_final: 0.8013 (mtm-85)
REVERT: B   97 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7691 (pp20)
REVERT: B  164 LYS cc_start: 0.7545 (mppt) cc_final: 0.7198 (mttm)
REVERT: B  169 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7345 (mp10)
REVERT: B  349 ASN cc_start: 0.8815 (t0) cc_final: 0.8304 (t0)
REVERT: B  364 GLN cc_start: 0.8788 (mt0) cc_final: 0.8566 (mt0)
REVERT: B  408 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8437 (mm)
REVERT: B  415 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7592 (ttm)
REVERT: A   23 ARG cc_start: 0.8213 (ttp-110) cc_final: 0.7993 (mtm-85)
REVERT: A  205 LYS cc_start: 0.8702 (ptpp) cc_final: 0.8059 (pttm)
REVERT: A  308 ARG cc_start: 0.7818 (mtt90) cc_final: 0.7501 (mtm110)
REVERT: A  311 MET cc_start: 0.7985 (mtp) cc_final: 0.7590 (mtp)
REVERT: A  334 GLU cc_start: 0.8212 (tt0) cc_final: 0.7989 (tt0)
REVERT: A  349 ASN cc_start: 0.8688 (t0) cc_final: 0.8166 (t0)
REVERT: A  364 GLN cc_start: 0.8804 (mt0) cc_final: 0.8449 (mt0)
REVERT: A  415 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7494 (ttm)
  outliers start: 28
  outliers final: 12
  residues processed: 124
  average time/residue: 2.0532
  time to fit residues: 269.4589
Evaluate side-chains
  116 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  169 GLN
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  229 GLU
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  378 SER
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain A residue  140 ASP
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  415 MET
Chi-restraints excluded: chain A residue  425 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 52 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 393 ASN
A 368 ASN
A 393 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.131923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.102010 restraints weight = 9732.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.37
r_work: 0.3081 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7450  Z= 0.163
  Angle     :  0.519   7.392  10106  Z= 0.272
  Chirality :  0.045   0.140   1024
  Planarity :  0.004   0.035   1304
  Dihedral  :  4.265  18.588    978
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.95 %
    Favored  : 76.33 %
  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:  0.61 (0.30), residues: 894
  helix:  0.54 (0.31), residues: 300
  sheet: -0.63 (0.37), residues: 182
  loop :  1.10 (0.34), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  36 
 HIS   0.002   0.001   HIS B 167 
 PHE   0.011   0.001   PHE A 267 
 TYR   0.014   0.002   TYR B 264 
 ARG   0.001   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03320 (  250)
  hydrogen bonds       : angle       5.38170 (  756)
  covalent geometry    : bond        0.00395 ( 7450)
  covalent geometry    : angle       0.51936 (10106)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.8051 (mtm-85)
REVERT: B   97 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7734 (pp20)
REVERT: B  164 LYS cc_start: 0.7658 (mppt) cc_final: 0.7340 (mttm)
REVERT: B  169 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7453 (mp10)
REVERT: B  349 ASN cc_start: 0.8852 (t0) cc_final: 0.8340 (t0)
REVERT: B  364 GLN cc_start: 0.8900 (mt0) cc_final: 0.8605 (mt0)
REVERT: B  408 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8471 (mm)
REVERT: A   23 ARG cc_start: 0.8228 (ttp-110) cc_final: 0.7996 (mtm-85)
REVERT: A  164 LYS cc_start: 0.7653 (mppt) cc_final: 0.7368 (mttp)
REVERT: A  205 LYS cc_start: 0.8739 (ptpp) cc_final: 0.8496 (ptpp)
REVERT: A  308 ARG cc_start: 0.7873 (mtt90) cc_final: 0.7553 (mtm110)
REVERT: A  311 MET cc_start: 0.8022 (mtp) cc_final: 0.7637 (mtp)
REVERT: A  317 MET cc_start: 0.8130 (tpt) cc_final: 0.7874 (tpp)
REVERT: A  334 GLU cc_start: 0.8307 (tt0) cc_final: 0.8072 (tt0)
REVERT: A  349 ASN cc_start: 0.8732 (t0) cc_final: 0.8191 (t0)
  outliers start: 28
  outliers final: 14
  residues processed: 123
  average time/residue: 1.5306
  time to fit residues: 197.8442
Evaluate side-chains
  114 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  169 GLN
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain B residue  378 SER
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  425 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   chunk 75 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 85 optimal weight:    0.3980
   chunk 8 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 393 ASN
A 294 GLN
A 393 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.133155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.103345 restraints weight = 9832.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.38
r_work: 0.3106 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7450  Z= 0.130
  Angle     :  0.512   6.172  10106  Z= 0.268
  Chirality :  0.044   0.141   1024
  Planarity :  0.004   0.035   1304
  Dihedral  :  4.209  18.066    978
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.88 %
    Favored  : 76.06 %
  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:  0.63 (0.30), residues: 894
  helix:  0.60 (0.31), residues: 300
  sheet: -0.66 (0.37), residues: 182
  loop :  1.09 (0.34), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  36 
 HIS   0.002   0.001   HIS A  52 
 PHE   0.009   0.001   PHE A 267 
 TYR   0.015   0.001   TYR A 264 
 ARG   0.001   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03070 (  250)
  hydrogen bonds       : angle       5.33088 (  756)
  covalent geometry    : bond        0.00315 ( 7450)
  covalent geometry    : angle       0.51152 (10106)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.8242 (ttp-110) cc_final: 0.8019 (mtm-85)
REVERT: B   97 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7723 (pp20)
REVERT: B  205 LYS cc_start: 0.8575 (ptpp) cc_final: 0.8024 (pttm)
REVERT: B  349 ASN cc_start: 0.8853 (t0) cc_final: 0.8339 (t0)
REVERT: B  364 GLN cc_start: 0.8863 (mt0) cc_final: 0.8560 (mt0)
REVERT: B  408 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8474 (mm)
REVERT: A   23 ARG cc_start: 0.8224 (ttp-110) cc_final: 0.8005 (mtm-85)
REVERT: A  205 LYS cc_start: 0.8759 (ptpp) cc_final: 0.8193 (pttm)
REVERT: A  308 ARG cc_start: 0.7856 (mtt90) cc_final: 0.7549 (mtm110)
REVERT: A  311 MET cc_start: 0.7984 (mtp) cc_final: 0.7604 (mtp)
REVERT: A  317 MET cc_start: 0.8116 (tpt) cc_final: 0.7836 (tpp)
REVERT: A  334 GLU cc_start: 0.8277 (tt0) cc_final: 0.8041 (tt0)
REVERT: A  349 ASN cc_start: 0.8700 (t0) cc_final: 0.8155 (t0)
  outliers start: 23
  outliers final: 15
  residues processed: 123
  average time/residue: 1.3462
  time to fit residues: 173.9089
Evaluate side-chains
  118 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  378 SER
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  425 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 25 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0980
   chunk 63 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 393 ASN
A 294 GLN
A 393 ASN
A 453 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.133519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.103811 restraints weight = 9815.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.37
r_work: 0.3116 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7450  Z= 0.126
  Angle     :  0.522   8.904  10106  Z= 0.272
  Chirality :  0.044   0.141   1024
  Planarity :  0.004   0.035   1304
  Dihedral  :  4.169  17.997    978
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 21.14 %
    Favored  : 75.80 %
  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:  0.68 (0.30), residues: 894
  helix:  0.63 (0.31), residues: 300
  sheet: -0.66 (0.37), residues: 182
  loop :  1.14 (0.34), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  36 
 HIS   0.002   0.001   HIS A  52 
 PHE   0.009   0.001   PHE A 267 
 TYR   0.014   0.001   TYR A 264 
 ARG   0.001   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03000 (  250)
  hydrogen bonds       : angle       5.30955 (  756)
  covalent geometry    : bond        0.00305 ( 7450)
  covalent geometry    : angle       0.52232 (10106)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.8240 (ttp-110) cc_final: 0.8037 (mtm-85)
REVERT: B   97 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7705 (pp20)
REVERT: B  164 LYS cc_start: 0.7516 (mppt) cc_final: 0.7299 (mttp)
REVERT: B  169 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7466 (mp10)
REVERT: B  349 ASN cc_start: 0.8841 (t0) cc_final: 0.8326 (t0)
REVERT: B  364 GLN cc_start: 0.8841 (mt0) cc_final: 0.8542 (mt0)
REVERT: B  408 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8470 (mm)
REVERT: A  199 ASP cc_start: 0.8498 (t0) cc_final: 0.7981 (p0)
REVERT: A  205 LYS cc_start: 0.8730 (ptpp) cc_final: 0.8074 (pttm)
REVERT: A  308 ARG cc_start: 0.7871 (mtt90) cc_final: 0.7548 (mtm110)
REVERT: A  311 MET cc_start: 0.7990 (mtp) cc_final: 0.7619 (mtp)
REVERT: A  317 MET cc_start: 0.8098 (tpt) cc_final: 0.7802 (tpp)
REVERT: A  334 GLU cc_start: 0.8216 (tt0) cc_final: 0.7979 (tt0)
REVERT: A  349 ASN cc_start: 0.8693 (t0) cc_final: 0.8141 (t0)
REVERT: A  408 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8509 (mm)
  outliers start: 23
  outliers final: 14
  residues processed: 127
  average time/residue: 1.4845
  time to fit residues: 199.5611
Evaluate side-chains
  116 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  169 GLN
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  378 SER
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  425 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 393 ASN
A 393 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.133636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.103674 restraints weight = 9923.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.39
r_work: 0.3117 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7450  Z= 0.131
  Angle     :  0.533   8.081  10106  Z= 0.279
  Chirality :  0.044   0.140   1024
  Planarity :  0.004   0.035   1304
  Dihedral  :  4.166  17.914    978
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 22.07 %
    Favored  : 75.00 %
  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:  0.69 (0.30), residues: 894
  helix:  0.65 (0.31), residues: 300
  sheet: -0.69 (0.37), residues: 182
  loop :  1.16 (0.34), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  36 
 HIS   0.002   0.001   HIS A  52 
 PHE   0.009   0.001   PHE A 267 
 TYR   0.014   0.001   TYR A 264 
 ARG   0.002   0.000   ARG B 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03016 (  250)
  hydrogen bonds       : angle       5.30120 (  756)
  covalent geometry    : bond        0.00319 ( 7450)
  covalent geometry    : angle       0.53270 (10106)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7715 (pp20)
REVERT: B  164 LYS cc_start: 0.7531 (mppt) cc_final: 0.7236 (mttp)
REVERT: B  169 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7470 (mp10)
REVERT: B  349 ASN cc_start: 0.8848 (t0) cc_final: 0.8321 (t0)
REVERT: B  364 GLN cc_start: 0.8840 (mt0) cc_final: 0.8537 (mt0)
REVERT: A  199 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.7995 (p0)
REVERT: A  205 LYS cc_start: 0.8714 (ptpp) cc_final: 0.8047 (pttm)
REVERT: A  308 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7539 (mtm110)
REVERT: A  311 MET cc_start: 0.7974 (mtp) cc_final: 0.7605 (mtp)
REVERT: A  317 MET cc_start: 0.8072 (tpt) cc_final: 0.7766 (tpp)
REVERT: A  334 GLU cc_start: 0.8207 (tt0) cc_final: 0.7973 (tt0)
REVERT: A  349 ASN cc_start: 0.8686 (t0) cc_final: 0.8142 (t0)
REVERT: A  403 MET cc_start: 0.7933 (tpp) cc_final: 0.7682 (tpt)
REVERT: A  408 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8509 (mm)
  outliers start: 22
  outliers final: 14
  residues processed: 121
  average time/residue: 1.6458
  time to fit residues: 209.8600
Evaluate side-chains
  117 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  169 GLN
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  378 SER
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  425 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.0670
   chunk 55 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0010
   chunk 32 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 84 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.4524

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

Flipped N/Q/H residues before XYZ refinement:
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 393 ASN
A 294 GLN
A 393 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.135323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.105825 restraints weight = 9743.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.39
r_work: 0.3133 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7450  Z= 0.111
  Angle     :  0.531  10.231  10106  Z= 0.277
  Chirality :  0.043   0.141   1024
  Planarity :  0.004   0.037   1304
  Dihedral  :  4.088  17.082    978
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 21.94 %
    Favored  : 74.87 %
  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:  0.79 (0.30), residues: 894
  helix:  0.83 (0.31), residues: 288
  sheet: -0.59 (0.38), residues: 174
  loop :  1.07 (0.33), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  36 
 HIS   0.002   0.000   HIS A  52 
 PHE   0.007   0.001   PHE A 105 
 TYR   0.013   0.001   TYR A 264 
 ARG   0.003   0.000   ARG B 402 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02769 (  250)
  hydrogen bonds       : angle       5.21909 (  756)
  covalent geometry    : bond        0.00269 ( 7450)
  covalent geometry    : angle       0.53124 (10106)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7522.98 seconds
wall clock time: 135 minutes 38.41 seconds (8138.41 seconds total)