Starting phenix.real_space_refine
on Wed Sep 17 08:40:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g79_51116/09_2025/9g79_51116.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g79_51116/09_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_51116/09_2025/9g79_51116.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g79_51116/09_2025/9g79_51116.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g79_51116/09_2025/9g79_51116.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g79_51116/09_2025/9g79_51116.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.92, per 1000 atoms: 0.27
  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: 0.60
  Conformation dependent library (CDL) restraints added in 414.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.31
  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: 1.21

  Time building geometry restraints manager: 0.84 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: 0.01
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:             3.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.710
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  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:6.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.270
-------------------------------------------------------------------------------
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 : 9.11
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.008   0.001   ARG A 342 
 TYR   0.019   0.001   TYR A 264 
 PHE   0.008   0.001   PHE A 209 
 TRP   0.011   0.001   TRP A  36 
 HIS   0.003   0.001   HIS A 226 

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

*********************** 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  : 0.286 
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: 0.7225
  time to fit residues: 82.4010
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  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0870
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.7364

-------------------------------------------------------------------------------
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 = 0.3699 r_free = 0.3699 target = 0.133820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.103754 restraints weight = 9823.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.39
r_work: 0.3114 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7450  Z= 0.131
  Angle     :  0.493   4.259  10106  Z= 0.264
  Chirality :  0.044   0.142   1024
  Planarity :  0.004   0.046   1304
  Dihedral  :  4.311  17.223    978
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 19.68 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.29), residues: 894
  helix:  0.32 (0.31), residues: 302
  sheet: -0.32 (0.38), residues: 182
  loop :  1.16 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 342 
 TYR   0.019   0.002   TYR B 264 
 PHE   0.009   0.001   PHE A 209 
 TRP   0.012   0.001   TRP A  36 
 HIS   0.004   0.001   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7450)
  covalent geometry    : angle       0.49345 (10106)
  hydrogen bonds       : bond        0.03980 (  250)
  hydrogen bonds       : angle       5.78906 (  756)

*********************** 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: 31
    poor density    : 109
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  346 LYS cc_start: 0.9127 (ttpt) cc_final: 0.8912 (ttmm)
REVERT: A  308 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7540 (mtm110)
REVERT: A  349 ASN cc_start: 0.8772 (t0) cc_final: 0.8536 (t0)
  outliers start: 31
  outliers final: 9
  residues processed: 127
  average time/residue: 0.6656
  time to fit residues: 88.6032
Evaluate side-chains
  107 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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 B residue  403 MET
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0970
   chunk 48 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0970
   chunk 30 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 2 optimal weight:    0.3980
   chunk 68 optimal weight:    0.3980
   chunk 80 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.3976

-------------------------------------------------------------------------------
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 = 0.3722 r_free = 0.3722 target = 0.135668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.105850 restraints weight = 9768.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.40
r_work: 0.3141 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7450  Z= 0.096
  Angle     :  0.461   4.664  10106  Z= 0.243
  Chirality :  0.043   0.139   1024
  Planarity :  0.004   0.033   1304
  Dihedral  :  4.061  16.463    978
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 18.88 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.29), residues: 894
  helix:  0.55 (0.32), residues: 302
  sheet: -0.37 (0.38), residues: 182
  loop :  1.24 (0.33), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 342 
 TYR   0.016   0.001   TYR A 264 
 PHE   0.007   0.001   PHE A 267 
 TRP   0.010   0.001   TRP A  36 
 HIS   0.002   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 7450)
  covalent geometry    : angle       0.46135 (10106)
  hydrogen bonds       : bond        0.03086 (  250)
  hydrogen bonds       : angle       5.38129 (  756)

*********************** 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
  136 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7661 (pp20)
REVERT: B  349 ASN cc_start: 0.8738 (t0) cc_final: 0.8338 (t0)
REVERT: B  415 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7554 (ttm)
REVERT: A   23 ARG cc_start: 0.8295 (ttp-110) cc_final: 0.7998 (mtm-85)
REVERT: A  308 ARG cc_start: 0.7968 (mtt90) cc_final: 0.7616 (mtm110)
REVERT: A  349 ASN cc_start: 0.8691 (t0) cc_final: 0.8307 (t0)
REVERT: A  415 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7463 (ttm)
  outliers start: 29
  outliers final: 10
  residues processed: 126
  average time/residue: 0.6209
  time to fit residues: 82.3224
Evaluate side-chains
  111 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
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  415 MET
Chi-restraints excluded: chain A residue  214 THR
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 44 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 83 optimal weight:    0.1980
   chunk 87 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0070
   chunk 80 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.6202

-------------------------------------------------------------------------------
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 = 0.3719 r_free = 0.3719 target = 0.135069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.105319 restraints weight = 9869.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.39
r_work: 0.3134 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.1624

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= 0.114
  Angle     :  0.470   5.289  10106  Z= 0.246
  Chirality :  0.043   0.140   1024
  Planarity :  0.004   0.036   1304
  Dihedral  :  4.072  16.476    978
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 18.88 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.29), residues: 894
  helix:  0.58 (0.32), residues: 302
  sheet: -0.45 (0.37), residues: 182
  loop :  1.22 (0.33), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 108 
 TYR   0.015   0.001   TYR A 264 
 PHE   0.009   0.001   PHE A 267 
 TRP   0.011   0.001   TRP A  36 
 HIS   0.002   0.001   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7450)
  covalent geometry    : angle       0.46997 (10106)
  hydrogen bonds       : bond        0.03073 (  250)
  hydrogen bonds       : angle       5.30564 (  756)

*********************** 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
  138 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7687 (pp20)
REVERT: B  349 ASN cc_start: 0.8770 (t0) cc_final: 0.8265 (t0)
REVERT: B  415 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7679 (ttm)
REVERT: A   23 ARG cc_start: 0.8265 (ttp-110) cc_final: 0.8055 (mtm-85)
REVERT: A  308 ARG cc_start: 0.7984 (mtt90) cc_final: 0.7603 (mtm110)
REVERT: A  349 ASN cc_start: 0.8712 (t0) cc_final: 0.8247 (t0)
REVERT: A  415 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7560 (ttm)
  outliers start: 32
  outliers final: 12
  residues processed: 124
  average time/residue: 0.6762
  time to fit residues: 87.9866
Evaluate side-chains
  111 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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  140 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 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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 78 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0870
   chunk 57 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.6758

-------------------------------------------------------------------------------
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 = 0.3719 r_free = 0.3719 target = 0.134661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.104705 restraints weight = 9839.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.40
r_work: 0.3122 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.1787

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= 0.119
  Angle     :  0.480   6.536  10106  Z= 0.250
  Chirality :  0.044   0.140   1024
  Planarity :  0.004   0.033   1304
  Dihedral  :  4.101  16.687    978
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 19.15 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.29), residues: 894
  helix:  0.64 (0.32), residues: 302
  sheet: -0.48 (0.37), residues: 182
  loop :  1.23 (0.33), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 108 
 TYR   0.017   0.001   TYR A 264 
 PHE   0.009   0.001   PHE A 267 
 TRP   0.011   0.001   TRP A  36 
 HIS   0.002   0.001   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7450)
  covalent geometry    : angle       0.47980 (10106)
  hydrogen bonds       : bond        0.03060 (  250)
  hydrogen bonds       : angle       5.26664 (  756)

*********************** 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
  133 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 100
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7735 (pp20)
REVERT: B  349 ASN cc_start: 0.8789 (t0) cc_final: 0.8257 (t0)
REVERT: B  415 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7669 (ttm)
REVERT: A   23 ARG cc_start: 0.8272 (ttp-110) cc_final: 0.8061 (mtm-85)
REVERT: A  169 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7502 (mp10)
REVERT: A  308 ARG cc_start: 0.7990 (mtt90) cc_final: 0.7607 (mtm110)
REVERT: A  349 ASN cc_start: 0.8686 (t0) cc_final: 0.8173 (t0)
REVERT: A  415 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7613 (ttm)
  outliers start: 33
  outliers final: 13
  residues processed: 123
  average time/residue: 0.6160
  time to fit residues: 79.7049
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  : 0.259 
-------------------------------------------------------------------------------
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  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  415 MET
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
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 58 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3706 r_free = 0.3706 target = 0.133948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.104051 restraints weight = 9853.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.39
r_work: 0.3100 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7450  Z= 0.133
  Angle     :  0.491   7.434  10106  Z= 0.255
  Chirality :  0.044   0.140   1024
  Planarity :  0.004   0.034   1304
  Dihedral  :  4.174  17.456    978
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 18.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.29), residues: 894
  helix:  0.61 (0.32), residues: 302
  sheet: -0.55 (0.37), residues: 182
  loop :  1.18 (0.33), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 101 
 TYR   0.017   0.002   TYR A 264 
 PHE   0.010   0.001   PHE A 267 
 TRP   0.011   0.001   TRP A  36 
 HIS   0.003   0.001   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7450)
  covalent geometry    : angle       0.49127 (10106)
  hydrogen bonds       : bond        0.03201 (  250)
  hydrogen bonds       : angle       5.30843 (  756)

*********************** 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
  139 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 103
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7765 (pp20)
REVERT: B  164 LYS cc_start: 0.7562 (mppt) cc_final: 0.7177 (mttp)
REVERT: B  169 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7393 (mp10)
REVERT: B  229 GLU cc_start: 0.8354 (tt0) cc_final: 0.8140 (tt0)
REVERT: B  349 ASN cc_start: 0.8812 (t0) cc_final: 0.8298 (t0)
REVERT: A  308 ARG cc_start: 0.7979 (mtt90) cc_final: 0.7607 (mtm110)
REVERT: A  349 ASN cc_start: 0.8700 (t0) cc_final: 0.8150 (t0)
REVERT: A  415 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7731 (ttm)
  outliers start: 36
  outliers final: 16
  residues processed: 126
  average time/residue: 0.6096
  time to fit residues: 80.5477
Evaluate side-chains
  113 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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  378 SER
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain A residue  140 ASP
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  415 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3712 r_free = 0.3712 target = 0.133954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.103956 restraints weight = 9862.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.40
r_work: 0.3102 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.2007

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= 0.127
  Angle     :  0.492   7.400  10106  Z= 0.257
  Chirality :  0.044   0.141   1024
  Planarity :  0.004   0.033   1304
  Dihedral  :  4.149  17.499    978
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.61 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.29), residues: 894
  helix:  0.65 (0.32), residues: 300
  sheet: -0.58 (0.37), residues: 182
  loop :  1.15 (0.33), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 141 
 TYR   0.016   0.001   TYR A 264 
 PHE   0.009   0.001   PHE A 267 
 TRP   0.010   0.001   TRP A  36 
 HIS   0.002   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7450)
  covalent geometry    : angle       0.49241 (10106)
  hydrogen bonds       : bond        0.03078 (  250)
  hydrogen bonds       : angle       5.28824 (  756)

*********************** 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
  121 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7747 (pp20)
REVERT: B  349 ASN cc_start: 0.8814 (t0) cc_final: 0.8292 (t0)
REVERT: A  164 LYS cc_start: 0.7529 (mppt) cc_final: 0.7215 (mttp)
REVERT: A  308 ARG cc_start: 0.7991 (mtt90) cc_final: 0.7627 (mtm110)
REVERT: A  349 ASN cc_start: 0.8703 (t0) cc_final: 0.8131 (t0)
REVERT: A  415 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7713 (ttm)
  outliers start: 23
  outliers final: 14
  residues processed: 113
  average time/residue: 0.6249
  time to fit residues: 74.1859
Evaluate side-chains
  110 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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  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  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  415 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 43 optimal weight:    7.9990
   chunk 66 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    0.2980
   chunk 23 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0370
   chunk 75 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.5660

-------------------------------------------------------------------------------
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 = 0.3721 r_free = 0.3721 target = 0.135046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.105333 restraints weight = 9947.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.39
r_work: 0.3121 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.2146

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= 0.111
  Angle     :  0.489   8.284  10106  Z= 0.254
  Chirality :  0.043   0.142   1024
  Planarity :  0.004   0.034   1304
  Dihedral  :  4.056  17.021    978
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.54 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.29), residues: 894
  helix:  0.79 (0.32), residues: 288
  sheet: -0.60 (0.37), residues: 182
  loop :  1.09 (0.33), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 342 
 TYR   0.016   0.001   TYR A 264 
 PHE   0.008   0.001   PHE A 105 
 TRP   0.010   0.001   TRP A  36 
 HIS   0.002   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7450)
  covalent geometry    : angle       0.48872 (10106)
  hydrogen bonds       : bond        0.02873 (  250)
  hydrogen bonds       : angle       5.23253 (  756)

*********************** 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
  125 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7729 (pp20)
REVERT: B  164 LYS cc_start: 0.7508 (mppt) cc_final: 0.7258 (mttp)
REVERT: B  169 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7430 (mp10)
REVERT: B  349 ASN cc_start: 0.8814 (t0) cc_final: 0.8283 (t0)
REVERT: A  349 ASN cc_start: 0.8665 (t0) cc_final: 0.8078 (t0)
REVERT: A  415 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7533 (ttm)
  outliers start: 21
  outliers final: 15
  residues processed: 119
  average time/residue: 0.6152
  time to fit residues: 77.0067
Evaluate side-chains
  119 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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  140 ASP
Chi-restraints excluded: chain B residue  169 GLN
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  140 ASP
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  415 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 23 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 85 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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
A 453 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.132791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.102863 restraints weight = 9791.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.37
r_work: 0.3088 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7450  Z= 0.162
  Angle     :  0.537   8.971  10106  Z= 0.280
  Chirality :  0.044   0.140   1024
  Planarity :  0.004   0.033   1304
  Dihedral  :  4.246  18.273    978
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 21.68 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.29), residues: 894
  helix:  0.60 (0.31), residues: 300
  sheet: -0.66 (0.37), residues: 182
  loop :  1.08 (0.33), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 402 
 TYR   0.016   0.002   TYR A 264 
 PHE   0.011   0.002   PHE A 267 
 TRP   0.011   0.001   TRP A  36 
 HIS   0.003   0.001   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 7450)
  covalent geometry    : angle       0.53721 (10106)
  hydrogen bonds       : bond        0.03288 (  250)
  hydrogen bonds       : angle       5.35187 (  756)

*********************** 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
  128 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7744 (pp20)
REVERT: B  164 LYS cc_start: 0.7548 (mppt) cc_final: 0.7266 (mttp)
REVERT: B  169 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7409 (mp10)
REVERT: B  349 ASN cc_start: 0.8848 (t0) cc_final: 0.8312 (t0)
REVERT: B  453 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7520 (mm-40)
REVERT: A  164 LYS cc_start: 0.7539 (mppt) cc_final: 0.7271 (mttp)
REVERT: A  199 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7877 (p0)
REVERT: A  349 ASN cc_start: 0.8704 (t0) cc_final: 0.8118 (t0)
  outliers start: 26
  outliers final: 12
  residues processed: 118
  average time/residue: 0.6532
  time to fit residues: 81.0299
Evaluate side-chains
  111 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
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  325 SER
Chi-restraints excluded: chain B residue  378 SER
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain A residue  174 VAL
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0980
   chunk 72 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3712 r_free = 0.3712 target = 0.134095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.104177 restraints weight = 9720.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 2.39
r_work: 0.3112 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
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   0.046   7450  Z= 0.127
  Angle     :  0.524   8.305  10106  Z= 0.274
  Chirality :  0.044   0.141   1024
  Planarity :  0.004   0.037   1304
  Dihedral  :  4.157  17.218    978
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 22.87 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.29), residues: 894
  helix:  0.77 (0.32), residues: 288
  sheet: -0.67 (0.37), residues: 182
  loop :  1.03 (0.33), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 308 
 TYR   0.016   0.001   TYR A 264 
 PHE   0.010   0.001   PHE A 105 
 TRP   0.010   0.001   TRP A  36 
 HIS   0.002   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7450)
  covalent geometry    : angle       0.52369 (10106)
  hydrogen bonds       : bond        0.02973 (  250)
  hydrogen bonds       : angle       5.29586 (  756)

********************** 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
  118 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7721 (pp20)
REVERT: B  169 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7434 (mp10)
REVERT: B  349 ASN cc_start: 0.8837 (t0) cc_final: 0.8301 (t0)
REVERT: B  403 MET cc_start: 0.7921 (tpp) cc_final: 0.7720 (tpt)
REVERT: A  164 LYS cc_start: 0.7540 (mppt) cc_final: 0.7264 (mttp)
REVERT: A  199 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7882 (p0)
REVERT: A  349 ASN cc_start: 0.8683 (t0) cc_final: 0.8092 (t0)
  outliers start: 17
  outliers final: 13
  residues processed: 113
  average time/residue: 0.6041
  time to fit residues: 71.8371
Evaluate side-chains
  115 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
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  325 SER
Chi-restraints excluded: chain B residue  378 SER
Chi-restraints excluded: chain B residue  379 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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 75 optimal weight:    0.3980
   chunk 48 optimal weight:    0.9980
   chunk 37 optimal weight:    0.3980
   chunk 7 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 78 optimal weight:    3.9990
   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  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 = 0.3713 r_free = 0.3713 target = 0.134289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.104430 restraints weight = 9803.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 2.40
r_work: 0.3120 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.2244

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= 0.120
  Angle     :  0.533   9.525  10106  Z= 0.278
  Chirality :  0.044   0.141   1024
  Planarity :  0.004   0.034   1304
  Dihedral  :  4.094  17.118    978
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 23.54 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.29), residues: 894
  helix:  0.79 (0.32), residues: 288
  sheet: -0.70 (0.37), residues: 182
  loop :  1.04 (0.33), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 308 
 TYR   0.015   0.001   TYR A 264 
 PHE   0.008   0.001   PHE B 105 
 TRP   0.010   0.001   TRP A  36 
 HIS   0.002   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7450)
  covalent geometry    : angle       0.53266 (10106)
  hydrogen bonds       : bond        0.02879 (  250)
  hydrogen bonds       : angle       5.27578 (  756)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2865.49 seconds
wall clock time: 49 minutes 37.49 seconds (2977.49 seconds total)