Starting phenix.real_space_refine
on Sun May 11 01:47:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g79_51116/05_2025/9g79_51116.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g79_51116/05_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_51116/05_2025/9g79_51116.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g79_51116/05_2025/9g79_51116.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g79_51116/05_2025/9g79_51116.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g79_51116/05_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-5687/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: 5.39, per 1000 atoms: 0.75
  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: 1.75
  Conformation dependent library (CDL) restraints added in 1.0 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: 1.06
  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: 2.35

  Time building geometry restraints manager: 2.08 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: 0.04
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:             3.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.580
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.760
-------------------------------------------------------------------------------
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  : 0.799 
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: 1.3059
  time to fit residues: 149.7210
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  : 0.820 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 41 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0970
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3707 r_free = 0.3707 target = 0.134476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.104715 restraints weight = 9679.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 2.37
r_work: 0.3127 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.1000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7450  Z= 0.121
  Angle     :  0.487   4.265  10106  Z= 0.261
  Chirality :  0.044   0.143   1024
  Planarity :  0.004   0.045   1304
  Dihedral  :  4.265  17.132    978
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 19.81 %
    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:  0.66 (0.29), residues: 894
  helix:  0.35 (0.31), residues: 302
  sheet: -0.30 (0.38), residues: 182
  loop :  1.17 (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 B 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        0.03872 (  250)
  hydrogen bonds       : angle       5.80235 (  756)
  covalent geometry    : bond        0.00283 ( 7450)
  covalent geometry    : angle       0.48703 (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
  140 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  346 LYS cc_start: 0.9113 (ttpt) cc_final: 0.8896 (ttmm)
REVERT: A  308 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7501 (mtm110)
REVERT: A  334 GLU cc_start: 0.8269 (tt0) cc_final: 0.8058 (tt0)
REVERT: A  349 ASN cc_start: 0.8738 (t0) cc_final: 0.8496 (t0)
  outliers start: 30
  outliers final: 7
  residues processed: 127
  average time/residue: 1.3753
  time to fit residues: 183.9552
Evaluate side-chains
  102 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0980
   chunk 75 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 77 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.134503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.104908 restraints weight = 9876.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.39
r_work: 0.3107 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7450  Z= 0.117
  Angle     :  0.475   5.005  10106  Z= 0.251
  Chirality :  0.044   0.138   1024
  Planarity :  0.004   0.032   1304
  Dihedral  :  4.195  16.632    978
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 19.28 %
    Favored  : 76.86 %
  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:  0.75 (0.29), residues: 894
  helix:  0.50 (0.32), residues: 302
  sheet: -0.37 (0.38), residues: 182
  loop :  1.21 (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   0.009   0.001   PHE A 267 
 TYR   0.016   0.001   TYR B 264 
 ARG   0.003   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03356 (  250)
  hydrogen bonds       : angle       5.43695 (  756)
  covalent geometry    : bond        0.00278 ( 7450)
  covalent geometry    : angle       0.47539 (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
  133 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.8270 (ttp-110) cc_final: 0.8005 (mtm-85)
REVERT: B   97 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7692 (pp20)
REVERT: B  349 ASN cc_start: 0.8749 (t0) cc_final: 0.8344 (t0)
REVERT: B  415 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7686 (ttm)
REVERT: A   23 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.8039 (mtm-85)
REVERT: A  308 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7523 (mtm110)
REVERT: A  349 ASN cc_start: 0.8717 (t0) cc_final: 0.8324 (t0)
  outliers start: 29
  outliers final: 11
  residues processed: 123
  average time/residue: 1.2803
  time to fit residues: 165.7988
Evaluate side-chains
  112 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
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  325 SER
Chi-restraints excluded: chain B residue  378 SER
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain B residue  415 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
Chi-restraints excluded: chain A residue  425 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 59 optimal weight:    0.3980
   chunk 68 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 39 optimal weight:    0.2980
   chunk 3 optimal weight:    0.7980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3687 r_free = 0.3687 target = 0.132180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.102204 restraints weight = 9857.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.37
r_work: 0.3088 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.1610

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= 0.167
  Angle     :  0.505   5.707  10106  Z= 0.265
  Chirality :  0.045   0.139   1024
  Planarity :  0.004   0.038   1304
  Dihedral  :  4.366  18.388    978
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 18.35 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.29), residues: 894
  helix:  0.38 (0.31), residues: 302
  sheet: -0.43 (0.38), residues: 182
  loop :  1.17 (0.33), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  36 
 HIS   0.004   0.001   HIS A 226 
 PHE   0.012   0.002   PHE A 267 
 TYR   0.017   0.002   TYR B 264 
 ARG   0.002   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03647 (  250)
  hydrogen bonds       : angle       5.46722 (  756)
  covalent geometry    : bond        0.00401 ( 7450)
  covalent geometry    : angle       0.50537 (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
  140 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 107
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.8279 (ttp-110) cc_final: 0.7964 (mtm-85)
REVERT: B   97 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7768 (pp20)
REVERT: B  311 MET cc_start: 0.7936 (mtp) cc_final: 0.7641 (mtp)
REVERT: B  349 ASN cc_start: 0.8825 (t0) cc_final: 0.8341 (t0)
REVERT: A   23 ARG cc_start: 0.8267 (ttp-110) cc_final: 0.8003 (mtm-85)
REVERT: A  349 ASN cc_start: 0.8740 (t0) cc_final: 0.8291 (t0)
  outliers start: 33
  outliers final: 12
  residues processed: 128
  average time/residue: 1.4168
  time to fit residues: 190.0903
Evaluate side-chains
  108 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 1.303 
-------------------------------------------------------------------------------
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  160 ILE
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 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  331 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:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 3 optimal weight:    0.4980
   chunk 6 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 186 ASN
A 294 GLN
A 393 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.135114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.105428 restraints weight = 9705.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.38
r_work: 0.3128 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7450  Z= 0.099
  Angle     :  0.466   6.734  10106  Z= 0.244
  Chirality :  0.043   0.141   1024
  Planarity :  0.004   0.033   1304
  Dihedral  :  4.104  16.648    978
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.48 %
    Favored  : 77.53 %
  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 (0.29), residues: 894
  helix:  0.69 (0.32), residues: 290
  sheet: -0.46 (0.37), residues: 182
  loop :  1.15 (0.33), residues: 422

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   0.007   0.001   PHE B 283 
 TYR   0.015   0.001   TYR A 264 
 ARG   0.002   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02864 (  250)
  hydrogen bonds       : angle       5.25431 (  756)
  covalent geometry    : bond        0.00234 ( 7450)
  covalent geometry    : angle       0.46573 (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
  139 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 109
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.8015 (mtm-85)
REVERT: B   97 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7682 (pp20)
REVERT: B  169 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7514 (mp10)
REVERT: B  311 MET cc_start: 0.7733 (mtp) cc_final: 0.7475 (mtp)
REVERT: B  349 ASN cc_start: 0.8811 (t0) cc_final: 0.8296 (t0)
REVERT: B  415 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7675 (ttm)
REVERT: A   23 ARG cc_start: 0.8225 (ttp-110) cc_final: 0.7991 (mtm-85)
REVERT: A  169 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7546 (mp10)
REVERT: A  349 ASN cc_start: 0.8676 (t0) cc_final: 0.8145 (t0)
REVERT: A  415 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7521 (ttm)
  outliers start: 30
  outliers final: 15
  residues processed: 128
  average time/residue: 1.4347
  time to fit residues: 192.8799
Evaluate side-chains
  120 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
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  169 GLN
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain B residue  214 THR
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  415 MET
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  229 GLU
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  415 MET
Chi-restraints excluded: chain A residue  425 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 368 ASN
A 393 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.132108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.102050 restraints weight = 9781.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.39
r_work: 0.3072 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7450  Z= 0.173
  Angle     :  0.511   7.173  10106  Z= 0.267
  Chirality :  0.045   0.139   1024
  Planarity :  0.004   0.035   1304
  Dihedral  :  4.315  18.644    978
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 18.62 %
    Favored  : 76.86 %
  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:  0.58 (0.29), residues: 894
  helix:  0.43 (0.31), residues: 302
  sheet: -0.55 (0.37), residues: 182
  loop :  1.10 (0.33), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  36 
 HIS   0.003   0.001   HIS B 226 
 PHE   0.012   0.002   PHE A 267 
 TYR   0.015   0.002   TYR A 443 
 ARG   0.002   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03471 (  250)
  hydrogen bonds       : angle       5.39626 (  756)
  covalent geometry    : bond        0.00417 ( 7450)
  covalent geometry    : angle       0.51126 (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
  137 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 103
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.8257 (ttp-110) cc_final: 0.7986 (mtm-85)
REVERT: B   97 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7755 (pp20)
REVERT: B  156 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8141 (mm)
REVERT: B  349 ASN cc_start: 0.8844 (t0) cc_final: 0.8340 (t0)
REVERT: B  364 GLN cc_start: 0.8903 (mt0) cc_final: 0.8652 (mt0)
REVERT: A   23 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7996 (mtm-85)
REVERT: A  156 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8244 (mm)
REVERT: A  349 ASN cc_start: 0.8713 (t0) cc_final: 0.8170 (t0)
  outliers start: 34
  outliers final: 15
  residues processed: 125
  average time/residue: 1.3512
  time to fit residues: 177.1804
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  : 0.744 
-------------------------------------------------------------------------------
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  160 ILE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  199 ASP
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 A residue  156 LEU
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
Chi-restraints excluded: chain A residue  403 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3686 r_free = 0.3686 target = 0.132384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.102665 restraints weight = 9779.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.37
r_work: 0.3091 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7450  Z= 0.167
  Angle     :  0.525   7.467  10106  Z= 0.275
  Chirality :  0.045   0.139   1024
  Planarity :  0.004   0.034   1304
  Dihedral  :  4.312  18.366    978
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 19.41 %
    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:  0.57 (0.29), residues: 894
  helix:  0.49 (0.31), residues: 300
  sheet: -0.60 (0.37), residues: 182
  loop :  1.04 (0.33), 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 226 
 PHE   0.011   0.001   PHE A 267 
 TYR   0.015   0.002   TYR A 264 
 ARG   0.002   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03386 (  250)
  hydrogen bonds       : angle       5.41053 (  756)
  covalent geometry    : bond        0.00403 ( 7450)
  covalent geometry    : angle       0.52481 (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
  134 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.8049 (mtm-85)
REVERT: B   97 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7747 (pp20)
REVERT: B  156 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8210 (mm)
REVERT: B  164 LYS cc_start: 0.7588 (mppt) cc_final: 0.7282 (mttp)
REVERT: B  349 ASN cc_start: 0.8845 (t0) cc_final: 0.8336 (t0)
REVERT: B  364 GLN cc_start: 0.8897 (mt0) cc_final: 0.8613 (mt0)
REVERT: B  408 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8490 (mm)
REVERT: A   23 ARG cc_start: 0.8245 (ttp-110) cc_final: 0.8001 (mtm-85)
REVERT: A  164 LYS cc_start: 0.7572 (mppt) cc_final: 0.7263 (mttp)
REVERT: A  199 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.7913 (p0)
REVERT: A  205 LYS cc_start: 0.8667 (ptpp) cc_final: 0.8234 (pttm)
REVERT: A  349 ASN cc_start: 0.8719 (t0) cc_final: 0.8163 (t0)
  outliers start: 30
  outliers final: 14
  residues processed: 123
  average time/residue: 1.3025
  time to fit residues: 168.6904
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  : 0.763 
-------------------------------------------------------------------------------
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  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  199 ASP
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  403 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 83 optimal weight:    0.0470
   chunk 75 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 85 optimal weight:    0.0060
   chunk 8 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.5094

-------------------------------------------------------------------------------
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 = 0.3720 r_free = 0.3720 target = 0.134571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.104941 restraints weight = 9826.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.41
r_work: 0.3119 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7450  Z= 0.111
  Angle     :  0.501   6.161  10106  Z= 0.263
  Chirality :  0.043   0.142   1024
  Planarity :  0.004   0.035   1304
  Dihedral  :  4.092  16.769    978
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.74 %
    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:  0.73 (0.30), residues: 894
  helix:  0.74 (0.32), residues: 288
  sheet: -0.59 (0.37), residues: 182
  loop :  1.08 (0.34), residues: 424

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        0.02830 (  250)
  hydrogen bonds       : angle       5.28326 (  756)
  covalent geometry    : bond        0.00269 ( 7450)
  covalent geometry    : angle       0.50108 (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
  131 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.8044 (mtm-85)
REVERT: B   97 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7722 (pp20)
REVERT: B  349 ASN cc_start: 0.8829 (t0) cc_final: 0.8308 (t0)
REVERT: B  364 GLN cc_start: 0.8827 (mt0) cc_final: 0.8570 (mt0)
REVERT: B  408 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8456 (mm)
REVERT: A   23 ARG cc_start: 0.8238 (ttp-110) cc_final: 0.8035 (mtm-85)
REVERT: A  199 ASP cc_start: 0.8496 (t0) cc_final: 0.7956 (p0)
REVERT: A  205 LYS cc_start: 0.8584 (ptpp) cc_final: 0.8153 (pttm)
REVERT: A  349 ASN cc_start: 0.8661 (t0) cc_final: 0.8085 (t0)
  outliers start: 23
  outliers final: 13
  residues processed: 125
  average time/residue: 1.2696
  time to fit residues: 167.0790
Evaluate side-chains
  120 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
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  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  140 ASP
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  331 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:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0040
   chunk 27 optimal weight:    0.9990
   chunk 68 optimal weight:    0.1980
   chunk 63 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.5192

-------------------------------------------------------------------------------
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 = 0.3719 r_free = 0.3719 target = 0.134550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.104962 restraints weight = 9814.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.37
r_work: 0.3131 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7450  Z= 0.115
  Angle     :  0.522   8.894  10106  Z= 0.272
  Chirality :  0.043   0.141   1024
  Planarity :  0.004   0.035   1304
  Dihedral  :  4.056  16.915    978
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 20.88 %
    Favored  : 75.93 %
  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:  0.75 (0.32), residues: 288
  sheet: -0.61 (0.37), residues: 182
  loop :  1.11 (0.34), residues: 424

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   0.008   0.001   PHE A 267 
 TYR   0.013   0.001   TYR A 264 
 ARG   0.002   0.000   ARG B 402 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02803 (  250)
  hydrogen bonds       : angle       5.26140 (  756)
  covalent geometry    : bond        0.00280 ( 7450)
  covalent geometry    : angle       0.52176 (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
  127 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7732 (pp20)
REVERT: B  164 LYS cc_start: 0.7512 (mppt) cc_final: 0.7200 (mttp)
REVERT: B  349 ASN cc_start: 0.8830 (t0) cc_final: 0.8297 (t0)
REVERT: B  364 GLN cc_start: 0.8791 (mt0) cc_final: 0.8542 (mt0)
REVERT: B  403 MET cc_start: 0.7918 (tpp) cc_final: 0.7671 (tpt)
REVERT: B  408 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8456 (mm)
REVERT: A  164 LYS cc_start: 0.7552 (mppt) cc_final: 0.7289 (mttp)
REVERT: A  199 ASP cc_start: 0.8486 (t0) cc_final: 0.7965 (p0)
REVERT: A  205 LYS cc_start: 0.8564 (ptpp) cc_final: 0.8136 (pttm)
REVERT: A  349 ASN cc_start: 0.8650 (t0) cc_final: 0.8060 (t0)
  outliers start: 24
  outliers final: 15
  residues processed: 123
  average time/residue: 1.2632
  time to fit residues: 163.9044
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  : 0.755 
-------------------------------------------------------------------------------
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  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  140 ASP
Chi-restraints excluded: chain A residue  174 VAL
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  331 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=1.00
-------------------------------------------------------------------------------
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:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 21 optimal weight:    0.1980
   chunk 79 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   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 = 0.3716 r_free = 0.3716 target = 0.134879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.105607 restraints weight = 9950.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.38
r_work: 0.3128 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.2308

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   8.285  10106  Z= 0.278
  Chirality :  0.044   0.141   1024
  Planarity :  0.004   0.035   1304
  Dihedral  :  4.107  17.365    978
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 21.01 %
    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:  0.70 (0.29), residues: 894
  helix:  0.73 (0.31), residues: 288
  sheet: -0.62 (0.37), residues: 182
  loop :  1.05 (0.33), residues: 424

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        0.02989 (  250)
  hydrogen bonds       : angle       5.28546 (  756)
  covalent geometry    : bond        0.00320 ( 7450)
  covalent geometry    : angle       0.53263 (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
  124 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7721 (pp20)
REVERT: B  164 LYS cc_start: 0.7504 (mppt) cc_final: 0.7219 (mttp)
REVERT: B  205 LYS cc_start: 0.8482 (ptpp) cc_final: 0.8176 (ttpt)
REVERT: B  349 ASN cc_start: 0.8839 (t0) cc_final: 0.8304 (t0)
REVERT: B  364 GLN cc_start: 0.8830 (mt0) cc_final: 0.8564 (mt0)
REVERT: B  403 MET cc_start: 0.7902 (tpp) cc_final: 0.7663 (tpt)
REVERT: B  408 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8459 (mm)
REVERT: B  415 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7598 (ttm)
REVERT: A  164 LYS cc_start: 0.7543 (mppt) cc_final: 0.7271 (mttp)
REVERT: A  199 ASP cc_start: 0.8508 (t0) cc_final: 0.7980 (p0)
REVERT: A  205 LYS cc_start: 0.8563 (ptpp) cc_final: 0.8129 (pttm)
REVERT: A  349 ASN cc_start: 0.8655 (t0) cc_final: 0.8062 (t0)
REVERT: A  415 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7515 (ttm)
  outliers start: 22
  outliers final: 15
  residues processed: 118
  average time/residue: 1.2290
  time to fit residues: 153.1348
Evaluate side-chains
  114 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
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  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 B residue  415 MET
Chi-restraints excluded: chain A residue  140 ASP
Chi-restraints excluded: chain A residue  174 VAL
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  331 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  415 MET
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:    0.0770
   chunk 55 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0770
   chunk 32 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.7098

-------------------------------------------------------------------------------
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 = 0.3710 r_free = 0.3710 target = 0.133909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.104299 restraints weight = 9776.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.35
r_work: 0.3119 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7450  Z= 0.132
  Angle     :  0.529   7.902  10106  Z= 0.277
  Chirality :  0.044   0.141   1024
  Planarity :  0.004   0.038   1304
  Dihedral  :  4.129  17.507    978
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.28 %
    Favored  : 75.93 %
  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 (0.29), residues: 894
  helix:  0.72 (0.31), residues: 288
  sheet: -0.62 (0.37), residues: 182
  loop :  1.04 (0.33), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  36 
 HIS   0.002   0.001   HIS B  52 
 PHE   0.011   0.001   PHE A 105 
 TYR   0.014   0.001   TYR A 264 
 ARG   0.002   0.000   ARG B 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02984 (  250)
  hydrogen bonds       : angle       5.30056 (  756)
  covalent geometry    : bond        0.00323 ( 7450)
  covalent geometry    : angle       0.52949 (10106)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5811.96 seconds
wall clock time: 101 minutes 0.91 seconds (6060.91 seconds total)