Starting phenix.real_space_refine
on Wed Apr 30 00:03:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y92_39067/04_2025/8y92_39067.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y92_39067/04_2025/8y92_39067.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y92_39067/04_2025/8y92_39067.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y92_39067/04_2025/8y92_39067.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y92_39067/04_2025/8y92_39067.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y92_39067/04_2025/8y92_39067.cif"
  }
  resolution = 3.29
  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=   0.046
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: 6
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     Cl      2      4.86       5
     Na      1      4.78       5
     C    6086      2.51       5
     N    1414      2.21       5
     O    1535      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9078
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4516
          Classifications: {'peptide': 565}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 544}
    Chain: "B"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4516
          Classifications: {'peptide': 565}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 544}
    Chain: "A"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 20
          Unusual residues: {' CL': 1, 'A1LX4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 21
          Unusual residues: {' CL': 1, ' NA': 1, 'A1LX4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.87, per 1000 atoms: 0.65
  Number of scatterers: 9078
  At special positions: 0
  Unit cell: (80.3, 116.8, 89.06, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      2     17.00
     S      40     16.00
     Na      1     11.00
     O    1535      8.00
     N    1414      7.00
     C    6086      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.44
  Conformation dependent library (CDL) restraints added in 982.6 milliseconds
  

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2076

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 0 sheets defined
      80.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 74
      removed outlier: 3.683A  pdb=" N   PHE A  65 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 81
    Processing helix  chain 'A' and resid 81 through 89
    Processing helix  chain 'A' and resid 90 through 93
    Processing helix  chain 'A' and resid 94 through 105
    Processing helix  chain 'A' and resid 105 through 121
    Processing helix  chain 'A' and resid 125 through 134
      removed outlier: 3.707A  pdb=" N   TRP A 128 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ILE A 130 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      Proline residue:  A 132  - end of helix
    Processing helix  chain 'A' and resid 135 through 166
      removed outlier: 3.766A  pdb=" N   TYR A 139 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   TYR A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   VAL A 154 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 175
      removed outlier: 3.835A  pdb=" N   ASP A 175 " --> pdb=" O   PRO A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 3.642A  pdb=" N   TYR A 214 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 224
      removed outlier: 3.627A  pdb=" N   GLU A 223 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   SER A 224 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 220 through 224'
    Processing helix  chain 'A' and resid 234 through 253
    Processing helix  chain 'A' and resid 255 through 283
      removed outlier: 3.575A  pdb=" N   SER A 259 " --> pdb=" O   GLY A 255 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   TRP A 264 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ILE A 265 " --> pdb=" O   LYS A 261 " (cutoff:3.500A)
      Proline residue:  A 270  - end of helix
      removed outlier: 4.074A  pdb=" N   THR A 283 " --> pdb=" O   VAL A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 296
    Processing helix  chain 'A' and resid 298 through 304
      removed outlier: 3.911A  pdb=" N   ARG A 301 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS A 303 " --> pdb=" O   TYR A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 320
      removed outlier: 3.863A  pdb=" N   GLY A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 331
      removed outlier: 4.233A  pdb=" N   ILE A 327 " --> pdb=" O   PHE A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 372
    Processing helix  chain 'A' and resid 375 through 380
      removed outlier: 3.652A  pdb=" N   VAL A 379 " --> pdb=" O   ASN A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 389
    Processing helix  chain 'A' and resid 389 through 398
    Processing helix  chain 'A' and resid 400 through 435
      removed outlier: 3.672A  pdb=" N   TRP A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER A 419 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 441
      removed outlier: 3.705A  pdb=" N   LYS A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 458
    Processing helix  chain 'A' and resid 464 through 494
      removed outlier: 4.527A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 509
      removed outlier: 3.544A  pdb=" N   PHE A 501 " --> pdb=" O   GLY A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 523
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 551 through 580
      removed outlier: 4.166A  pdb=" N   ASN A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      Proline residue:  A 570  - end of helix
      removed outlier: 3.625A  pdb=" N   THR A 580 " --> pdb=" O   LYS A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 593
    Processing helix  chain 'A' and resid 598 through 602
      removed outlier: 3.898A  pdb=" N   ALA A 602 " --> pdb=" O   HIS A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 615
      removed outlier: 3.960A  pdb=" N   TRP A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 74
      removed outlier: 3.674A  pdb=" N   PHE B  65 " --> pdb=" O   LYS B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 81
      removed outlier: 3.696A  pdb=" N   VAL B  79 " --> pdb=" O   ASP B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 89
    Processing helix  chain 'B' and resid 90 through 93
    Processing helix  chain 'B' and resid 94 through 104
      removed outlier: 3.667A  pdb=" N   ILE B 104 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 120
      removed outlier: 3.613A  pdb=" N   MET B 112 " --> pdb=" O   PRO B 108 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   GLU B 113 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 133
      removed outlier: 3.529A  pdb=" N   TRP B 128 " --> pdb=" O   ALA B 125 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LYS B 129 " --> pdb=" O   THR B 126 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   ILE B 130 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
      Proline residue:  B 132  - end of helix
    Processing helix  chain 'B' and resid 134 through 166
      removed outlier: 3.924A  pdb=" N   ILE B 142 " --> pdb=" O   GLY B 138 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TYR B 151 " --> pdb=" O   TYR B 147 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   VAL B 154 " --> pdb=" O   PHE B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 217
      removed outlier: 3.788A  pdb=" N   TYR B 214 " --> pdb=" O   ALA B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 224
      removed outlier: 3.543A  pdb=" N   SER B 224 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 253
    Processing helix  chain 'B' and resid 255 through 283
      removed outlier: 3.645A  pdb=" N   SER B 259 " --> pdb=" O   GLY B 255 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   TRP B 264 " --> pdb=" O   GLY B 260 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ILE B 265 " --> pdb=" O   LYS B 261 " (cutoff:3.500A)
      Proline residue:  B 270  - end of helix
      removed outlier: 4.049A  pdb=" N   THR B 283 " --> pdb=" O   VAL B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 295
    Processing helix  chain 'B' and resid 298 through 303
      removed outlier: 3.578A  pdb=" N   ARG B 301 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LYS B 303 " --> pdb=" O   TYR B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 320
      removed outlier: 4.152A  pdb=" N   TRP B 308 " --> pdb=" O   GLU B 304 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   ALA B 312 " --> pdb=" O   TRP B 308 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLY B 320 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 332
      removed outlier: 4.284A  pdb=" N   ILE B 327 " --> pdb=" O   PHE B 323 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   TYR B 332 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 372
      removed outlier: 3.508A  pdb=" N   ASP B 342 " --> pdb=" O   ASN B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 380
      removed outlier: 3.687A  pdb=" N   VAL B 379 " --> pdb=" O   ASN B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 389
    Processing helix  chain 'B' and resid 389 through 398
    Processing helix  chain 'B' and resid 400 through 435
      removed outlier: 3.606A  pdb=" N   TRP B 404 " --> pdb=" O   GLY B 400 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   SER B 419 " --> pdb=" O   LEU B 415 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASP B 434 " --> pdb=" O   GLY B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 441
      removed outlier: 3.794A  pdb=" N   LYS B 439 " --> pdb=" O   PHE B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 458
    Processing helix  chain 'B' and resid 459 through 461
      No H-bonds generated for 'chain 'B' and resid 459 through 461'
    Processing helix  chain 'B' and resid 465 through 496
    Processing helix  chain 'B' and resid 497 through 509
    Processing helix  chain 'B' and resid 514 through 523
    Processing helix  chain 'B' and resid 523 through 539
    Processing helix  chain 'B' and resid 553 through 580
      Proline residue:  B 570  - end of helix
      removed outlier: 3.506A  pdb=" N   THR B 580 " --> pdb=" O   LYS B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 593
      removed outlier: 3.729A  pdb=" N   TYR B 590 " --> pdb=" O   GLU B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 602
      removed outlier: 3.524A  pdb=" N   VAL B 601 " --> pdb=" O   HIS B 598 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ALA B 602 " --> pdb=" O   HIS B 599 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 598 through 602'
    Processing helix  chain 'B' and resid 610 through 616
      removed outlier: 4.170A  pdb=" N   TRP B 614 " --> pdb=" O   GLN B 610 " (cutoff:3.500A)

    587 hydrogen bonds defined for protein.
    1728 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: 2.54

  Time building geometry restraints manager: 2.65 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1342
        1.32 -     1.44: 2934
        1.44 -     1.56: 5028
        1.56 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 9366
  Sorted by residual:
  bond pdb=" CA  VAL A  74 "
       pdb=" C   VAL A  74 "
    ideal  model  delta    sigma   weight residual
    1.523  1.416  0.107 1.27e-02 6.20e+03 7.13e+01
  bond pdb=" CA  ASP A  75 "
       pdb=" C   ASP A  75 "
    ideal  model  delta    sigma   weight residual
    1.524  1.433  0.091 1.35e-02 5.49e+03 4.57e+01
  bond pdb=" N   ASP A  75 "
       pdb=" CA  ASP A  75 "
    ideal  model  delta    sigma   weight residual
    1.456  1.371  0.084 1.44e-02 4.82e+03 3.44e+01
  bond pdb=" CA  ALA A  77 "
       pdb=" C   ALA A  77 "
    ideal  model  delta    sigma   weight residual
    1.522  1.466  0.056 1.40e-02 5.10e+03 1.62e+01
  bond pdb=" N   ALA A  73 "
       pdb=" CA  ALA A  73 "
    ideal  model  delta    sigma   weight residual
    1.459  1.420  0.039 1.17e-02 7.31e+03 1.12e+01
  ... (remaining 9361 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.80: 12752
        4.80 -     9.60: 23
        9.60 -    14.40: 0
       14.40 -    19.20: 0
       19.20 -    24.00: 1
  Bond angle restraints: 12776
  Sorted by residual:
  angle pdb=" N   ASP A  75 "
        pdb=" CA  ASP A  75 "
        pdb=" C   ASP A  75 "
      ideal   model   delta    sigma   weight residual
     109.18   85.18   24.00 1.42e+00 4.96e-01 2.86e+02
  angle pdb=" CA  ALA A  73 "
        pdb=" C   ALA A  73 "
        pdb=" N   VAL A  74 "
      ideal   model   delta    sigma   weight residual
     116.92  121.89   -4.97 1.16e+00 7.43e-01 1.83e+01
  angle pdb=" N   ASP A  75 "
        pdb=" CA  ASP A  75 "
        pdb=" CB  ASP A  75 "
      ideal   model   delta    sigma   weight residual
     111.22  105.08    6.14 1.58e+00 4.01e-01 1.51e+01
  angle pdb=" CA  ALA A  73 "
        pdb=" C   ALA A  73 "
        pdb=" O   ALA A  73 "
      ideal   model   delta    sigma   weight residual
     121.00  117.29    3.71 1.05e+00 9.07e-01 1.25e+01
  angle pdb=" C   ASN B 198 "
        pdb=" N   HIS B 199 "
        pdb=" CA  HIS B 199 "
      ideal   model   delta    sigma   weight residual
     120.79  125.70   -4.91 1.39e+00 5.18e-01 1.25e+01
  ... (remaining 12771 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.60: 5111
       28.60 -    57.19: 117
       57.19 -    85.79: 9
       85.79 -   114.38: 0
      114.38 -   142.98: 1
  Dihedral angle restraints: 5238
    sinusoidal: 1974
      harmonic: 3264
  Sorted by residual:
  dihedral pdb=" N   ASP A  75 "
           pdb=" C   ASP A  75 "
           pdb=" CA  ASP A  75 "
           pdb=" CB  ASP A  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  104.46   18.34     0      2.50e+00 1.60e-01 5.38e+01
  dihedral pdb=" C10 A1LX4 B 701 "
           pdb=" C11 A1LX4 B 701 "
           pdb=" N12 A1LX4 B 701 "
           pdb=" C13 A1LX4 B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -79.57   63.41 -142.98     1      3.00e+01 1.11e-03 1.92e+01
  dihedral pdb=" C   VAL A  74 "
           pdb=" N   VAL A  74 "
           pdb=" CA  VAL A  74 "
           pdb=" CB  VAL A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.95    8.95     0      2.50e+00 1.60e-01 1.28e+01
  ... (remaining 5235 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1342
       0.070 -    0.139: 75
       0.139 -    0.208: 1
       0.208 -    0.278: 1
       0.278 -    0.347: 1
  Chirality restraints: 1420
  Sorted by residual:
  chirality pdb=" CA  VAL A  74 "
            pdb=" N   VAL A  74 "
            pdb=" C   VAL A  74 "
            pdb=" CB  VAL A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.09    0.35 2.00e-01 2.50e+01 3.02e+00
  chirality pdb=" CA  LEU A  76 "
            pdb=" N   LEU A  76 "
            pdb=" C   LEU A  76 "
            pdb=" CB  LEU A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CA  ALA A  77 "
            pdb=" N   ALA A  77 "
            pdb=" C   ALA A  77 "
            pdb=" CB  ALA A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.32    0.17 2.00e-01 2.50e+01 7.14e-01
  ... (remaining 1417 not shown)

  Planarity restraints: 1556
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  71 "    0.015 2.00e-02 2.50e+03   2.89e-02 8.35e+00
        pdb=" C   GLY A  71 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   GLY A  71 "    0.019 2.00e-02 2.50e+03
        pdb=" N   PHE A  72 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 107 "   -0.028 5.00e-02 4.00e+02   4.16e-02 2.77e+00
        pdb=" N   PRO A 108 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 108 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 108 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 569 "    0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO B 570 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B 570 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 570 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1553 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 65
        2.54 -     3.13: 7267
        3.13 -     3.72: 15084
        3.72 -     4.31: 20518
        4.31 -     4.90: 34248
  Nonbonded interactions: 77182
  Sorted by model distance:
  nonbonded pdb=" N   ASP A  75 "
            pdb=" O   ASP A  75 "
     model   vdw
     1.954 2.496
  nonbonded pdb=" OG  SER B 318 "
            pdb="CL    CL B 703 "
     model   vdw
     2.152 3.190
  nonbonded pdb=" OG  SER A 583 "
            pdb=" OE1 GLU A 586 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OG  SER A 318 "
            pdb="CL    CL A 702 "
     model   vdw
     2.215 3.190
  nonbonded pdb=" O   LEU A 163 "
            pdb=" OG  SER A 166 "
     model   vdw
     2.236 3.040
  ... (remaining 77177 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 53 through 617 or resid 701))
  selection = (chain 'B' and (resid 53 through 617 or resid 701))
}

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:             15.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.960
  Find NCS groups from input model:        0.380
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6458
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   0.107   9366  Z= 0.217
  Angle     :  0.636  24.001  12776  Z= 0.389
  Chirality :  0.037   0.347   1420
  Planarity :  0.004   0.042   1556
  Dihedral  : 11.667 142.975   3162
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  :  7.77 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.23), residues: 1126
  helix: -0.36 (0.17), residues: 766
  sheet:  None (None), residues: 0
  loop : -1.50 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 308 
 HIS   0.001   0.000   HIS B 199 
 PHE   0.012   0.001   PHE B 362 
 TYR   0.006   0.001   TYR B 572 
 ARG   0.002   0.000   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15166 (  587)
  hydrogen bonds       : angle       5.40212 ( 1728)
  covalent geometry    : bond        0.00327 ( 9366)
  covalent geometry    : angle       0.63574 (12776)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 268
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7614 (p)
REVERT: A  306 THR cc_start: 0.7747 (p) cc_final: 0.7434 (t)
REVERT: A  455 LEU cc_start: 0.7424 (mt) cc_final: 0.7219 (mt)
REVERT: B  507 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7593 (tm-30)
REVERT: B  586 GLU cc_start: 0.7668 (mp0) cc_final: 0.7034 (mp0)
  outliers start: 45
  outliers final: 9
  residues processed: 298
  average time/residue: 0.1829
  time to fit residues: 78.1051
Evaluate side-chains
  179 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 168
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain B residue  507 GLN
Chi-restraints excluded: chain B residue  531 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 84 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 87 optimal weight:    7.9990
   chunk 33 optimal weight:    0.5980
   chunk 53 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 101 optimal weight:    0.5980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.196371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.172386 restraints weight = 12796.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.4132 rms_B_bonded: 2.31
r_work: 0.4015 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9366  Z= 0.143
  Angle     :  0.565   7.554  12776  Z= 0.288
  Chirality :  0.039   0.135   1420
  Planarity :  0.004   0.040   1556
  Dihedral  :  7.388 107.697   1265
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 14.71 %
    Favored  : 81.41 %
  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:  0.38 (0.25), residues: 1126
  helix:  0.83 (0.18), residues: 778
  sheet:  None (None), residues: 0
  loop : -0.94 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 128 
 HIS   0.005   0.001   HIS B 280 
 PHE   0.016   0.001   PHE B 316 
 TYR   0.013   0.001   TYR A 111 
 ARG   0.005   0.001   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04448 (  587)
  hydrogen bonds       : angle       4.57405 ( 1728)
  covalent geometry    : bond        0.00317 ( 9366)
  covalent geometry    : angle       0.56512 (12776)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 175
  time to evaluate  : 0.868 
Fit side-chains
REVERT: A  365 LEU cc_start: 0.7707 (mt) cc_final: 0.7315 (mt)
REVERT: A  425 GLU cc_start: 0.7395 (tt0) cc_final: 0.7117 (tt0)
REVERT: B  202 TYR cc_start: 0.5426 (OUTLIER) cc_final: 0.3437 (t80)
REVERT: B  364 ILE cc_start: 0.8494 (mp) cc_final: 0.8251 (mp)
REVERT: B  365 LEU cc_start: 0.7736 (mt) cc_final: 0.7329 (mt)
REVERT: B  601 VAL cc_start: 0.8601 (t) cc_final: 0.8281 (m)
  outliers start: 37
  outliers final: 22
  residues processed: 200
  average time/residue: 0.1507
  time to fit residues: 45.9996
Evaluate side-chains
  163 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  531 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0000
   chunk 24 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0030
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.0000

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.189475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.164008 restraints weight = 13108.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.4035 rms_B_bonded: 2.37
r_work: 0.3913 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9366  Z= 0.150
  Angle     :  0.557   7.970  12776  Z= 0.287
  Chirality :  0.040   0.139   1420
  Planarity :  0.004   0.038   1556
  Dihedral  :  5.744  50.150   1251
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 15.13 %
    Favored  : 80.15 %
  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 (0.25), residues: 1126
  helix:  1.07 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -0.78 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 128 
 HIS   0.006   0.001   HIS A 199 
 PHE   0.021   0.002   PHE B 275 
 TYR   0.018   0.002   TYR A 111 
 ARG   0.004   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04769 (  587)
  hydrogen bonds       : angle       4.61489 ( 1728)
  covalent geometry    : bond        0.00335 ( 9366)
  covalent geometry    : angle       0.55718 (12776)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 156
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
REVERT: A  473 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.5994 (t0)
REVERT: A  566 MET cc_start: 0.5642 (mtt) cc_final: 0.5338 (mtt)
REVERT: B  133 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7991 (m-80)
REVERT: B  202 TYR cc_start: 0.5448 (OUTLIER) cc_final: 0.3420 (t80)
REVERT: B  425 GLU cc_start: 0.7627 (tt0) cc_final: 0.7373 (tt0)
REVERT: B  486 LEU cc_start: 0.7773 (tp) cc_final: 0.7418 (tp)
REVERT: B  566 MET cc_start: 0.5590 (mtt) cc_final: 0.5353 (mtt)
REVERT: B  601 VAL cc_start: 0.8609 (t) cc_final: 0.8292 (m)
  outliers start: 45
  outliers final: 33
  residues processed: 188
  average time/residue: 0.1584
  time to fit residues: 45.3390
Evaluate side-chains
  174 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 138
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  531 PHE
Chi-restraints excluded: chain B residue  615 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 102 optimal weight:    0.0270
   chunk 90 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 107 optimal weight:    0.5980
   chunk 69 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 111 optimal weight:    7.9990
   chunk 85 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6638

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.189576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.164182 restraints weight = 12908.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.4042 rms_B_bonded: 2.33
r_work: 0.3920 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.3485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9366  Z= 0.125
  Angle     :  0.525   6.787  12776  Z= 0.270
  Chirality :  0.038   0.126   1420
  Planarity :  0.004   0.035   1556
  Dihedral  :  5.542  46.381   1251
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 15.02 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.26), residues: 1126
  helix:  1.23 (0.19), residues: 796
  sheet:  None (None), residues: 0
  loop : -0.55 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 128 
 HIS   0.003   0.001   HIS A 370 
 PHE   0.015   0.001   PHE A 359 
 TYR   0.018   0.001   TYR A 111 
 ARG   0.004   0.000   ARG B 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04471 (  587)
  hydrogen bonds       : angle       4.55879 ( 1728)
  covalent geometry    : bond        0.00267 ( 9366)
  covalent geometry    : angle       0.52531 (12776)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 152
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8399 (m-80)
REVERT: A  225 SER cc_start: 0.8190 (m) cc_final: 0.7694 (t)
REVERT: A  473 ASP cc_start: 0.6374 (OUTLIER) cc_final: 0.5722 (t0)
REVERT: A  481 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8286 (tp)
REVERT: A  566 MET cc_start: 0.5658 (mtt) cc_final: 0.5433 (mtt)
REVERT: A  588 LEU cc_start: 0.8118 (mt) cc_final: 0.7885 (mt)
REVERT: B  122 GLU cc_start: 0.8217 (mp0) cc_final: 0.7948 (mp0)
REVERT: B  133 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.8020 (m-80)
REVERT: B  202 TYR cc_start: 0.5365 (OUTLIER) cc_final: 0.3458 (t80)
REVERT: B  473 ASP cc_start: 0.6348 (OUTLIER) cc_final: 0.5656 (t0)
REVERT: B  481 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8305 (tp)
REVERT: B  601 VAL cc_start: 0.8594 (t) cc_final: 0.8284 (m)
  outliers start: 53
  outliers final: 34
  residues processed: 187
  average time/residue: 0.1507
  time to fit residues: 43.4303
Evaluate side-chains
  181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 140
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  318 SER
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  481 ILE
Chi-restraints excluded: chain B residue  531 PHE
Chi-restraints excluded: chain B residue  615 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 31 optimal weight:    6.9990
   chunk 54 optimal weight:    7.9990
   chunk 63 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.1982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.184241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.158123 restraints weight = 13032.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3978 rms_B_bonded: 2.32
r_work: 0.3856 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9366  Z= 0.165
  Angle     :  0.572   8.292  12776  Z= 0.296
  Chirality :  0.040   0.155   1420
  Planarity :  0.004   0.034   1556
  Dihedral  :  5.591  47.189   1251
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 16.60 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.26), residues: 1126
  helix:  1.22 (0.19), residues: 794
  sheet:  None (None), residues: 0
  loop : -0.46 (0.37), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 128 
 HIS   0.004   0.001   HIS A 222 
 PHE   0.023   0.002   PHE B 275 
 TYR   0.018   0.001   TYR A 111 
 ARG   0.004   0.000   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05034 (  587)
  hydrogen bonds       : angle       4.75027 ( 1728)
  covalent geometry    : bond        0.00374 ( 9366)
  covalent geometry    : angle       0.57218 (12776)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 147
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A  133 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8509 (m-80)
REVERT: A  225 SER cc_start: 0.8273 (m) cc_final: 0.7755 (t)
REVERT: A  473 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6672 (t0)
REVERT: A  481 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8352 (tp)
REVERT: B  133 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8060 (m-80)
REVERT: B  202 TYR cc_start: 0.5328 (OUTLIER) cc_final: 0.3619 (t80)
REVERT: B  481 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8390 (tp)
REVERT: B  588 LEU cc_start: 0.8009 (mt) cc_final: 0.7801 (mt)
  outliers start: 51
  outliers final: 35
  residues processed: 186
  average time/residue: 0.1515
  time to fit residues: 43.5046
Evaluate side-chains
  180 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 139
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  481 ILE
Chi-restraints excluded: chain B residue  531 PHE
Chi-restraints excluded: chain B residue  615 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:   10.0000
   chunk 3 optimal weight:    0.8980
   chunk 79 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0970
   chunk 70 optimal weight:   20.0000
   chunk 100 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.184536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.158517 restraints weight = 12998.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3979 rms_B_bonded: 2.33
r_work: 0.3855 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.4011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9366  Z= 0.145
  Angle     :  0.559   6.829  12776  Z= 0.286
  Chirality :  0.039   0.134   1420
  Planarity :  0.004   0.033   1556
  Dihedral  :  5.543  47.054   1251
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 18.17 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.26), residues: 1126
  helix:  1.32 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.46 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 128 
 HIS   0.004   0.001   HIS B 222 
 PHE   0.020   0.001   PHE A 495 
 TYR   0.015   0.001   TYR A 111 
 ARG   0.003   0.000   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04894 (  587)
  hydrogen bonds       : angle       4.70847 ( 1728)
  covalent geometry    : bond        0.00323 ( 9366)
  covalent geometry    : angle       0.55862 (12776)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 148
  time to evaluate  : 1.003 
Fit side-chains
REVERT: A  133 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8501 (m-80)
REVERT: A  292 ASN cc_start: 0.7894 (m-40) cc_final: 0.7405 (m-40)
REVERT: A  473 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.6568 (t0)
REVERT: A  481 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8339 (tp)
REVERT: A  566 MET cc_start: 0.6153 (mtm) cc_final: 0.5948 (mtt)
REVERT: B  133 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8097 (m-80)
REVERT: B  202 TYR cc_start: 0.5335 (OUTLIER) cc_final: 0.3712 (t80)
REVERT: B  481 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8384 (tp)
REVERT: B  515 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8055 (tt)
  outliers start: 46
  outliers final: 35
  residues processed: 179
  average time/residue: 0.1513
  time to fit residues: 41.7973
Evaluate side-chains
  182 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 140
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  236 GLN
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  481 ILE
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  531 PHE
Chi-restraints excluded: chain B residue  615 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 109 optimal weight:    9.9990
   chunk 86 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   overall best weight:    1.2986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.177367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.150950 restraints weight = 13238.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 2.36
r_work: 0.3769 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.4257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9366  Z= 0.171
  Angle     :  0.589   7.870  12776  Z= 0.302
  Chirality :  0.041   0.187   1420
  Planarity :  0.004   0.035   1556
  Dihedral  :  5.609  47.478   1251
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 17.75 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.26), residues: 1126
  helix:  1.25 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.40 (0.38), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 128 
 HIS   0.005   0.001   HIS A 222 
 PHE   0.023   0.002   PHE A 275 
 TYR   0.017   0.001   TYR A 111 
 ARG   0.003   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05287 (  587)
  hydrogen bonds       : angle       4.82072 ( 1728)
  covalent geometry    : bond        0.00392 ( 9366)
  covalent geometry    : angle       0.58862 (12776)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 146
  time to evaluate  : 1.011 
Fit side-chains
REVERT: A  133 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8593 (m-80)
REVERT: A  292 ASN cc_start: 0.7835 (m-40) cc_final: 0.7366 (m-40)
REVERT: A  481 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8376 (tp)
REVERT: B  133 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8093 (m-80)
REVERT: B  202 TYR cc_start: 0.5427 (OUTLIER) cc_final: 0.3735 (t80)
REVERT: B  515 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8095 (tt)
REVERT: B  588 LEU cc_start: 0.7980 (mt) cc_final: 0.7770 (mt)
  outliers start: 50
  outliers final: 37
  residues processed: 181
  average time/residue: 0.1701
  time to fit residues: 47.1148
Evaluate side-chains
  179 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 137
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  236 GLN
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  296 HIS
Chi-restraints excluded: chain B residue  315 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  615 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 3 optimal weight:    0.4980
   chunk 63 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 97 optimal weight:    0.7980
   chunk 17 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.179892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.153911 restraints weight = 13401.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3908 rms_B_bonded: 2.39
r_work: 0.3785 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.4280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9366  Z= 0.137
  Angle     :  0.561   8.499  12776  Z= 0.286
  Chirality :  0.039   0.185   1420
  Planarity :  0.004   0.035   1556
  Dihedral  :  5.368  47.026   1249
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 18.70 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.26), residues: 1126
  helix:  1.38 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.38 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 180 
 HIS   0.004   0.001   HIS A 222 
 PHE   0.033   0.001   PHE B 408 
 TYR   0.012   0.001   TYR A 111 
 ARG   0.002   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04824 (  587)
  hydrogen bonds       : angle       4.70473 ( 1728)
  covalent geometry    : bond        0.00298 ( 9366)
  covalent geometry    : angle       0.56113 (12776)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 147
  time to evaluate  : 0.965 
Fit side-chains
REVERT: A  133 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8473 (m-80)
REVERT: A  292 ASN cc_start: 0.7903 (m-40) cc_final: 0.7438 (m-40)
REVERT: A  481 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8310 (tp)
REVERT: B  133 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8087 (m-80)
REVERT: B  202 TYR cc_start: 0.5359 (OUTLIER) cc_final: 0.3627 (t80)
REVERT: B  515 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8022 (tt)
REVERT: B  584 LEU cc_start: 0.7315 (mm) cc_final: 0.6574 (pt)
REVERT: B  588 LEU cc_start: 0.7961 (mt) cc_final: 0.7753 (mt)
  outliers start: 45
  outliers final: 36
  residues processed: 179
  average time/residue: 0.1952
  time to fit residues: 54.6110
Evaluate side-chains
  184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 143
  time to evaluate  : 1.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  236 GLN
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  296 HIS
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  615 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 89 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 110 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.185098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.159466 restraints weight = 13142.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3985 rms_B_bonded: 2.32
r_work: 0.3861 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.4334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9366  Z= 0.139
  Angle     :  0.569  10.024  12776  Z= 0.289
  Chirality :  0.040   0.219   1420
  Planarity :  0.004   0.036   1556
  Dihedral  :  5.338  46.696   1249
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 19.22 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.26), residues: 1126
  helix:  1.37 (0.19), residues: 784
  sheet:  None (None), residues: 0
  loop : -0.31 (0.37), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 559 
 HIS   0.004   0.001   HIS A 370 
 PHE   0.061   0.002   PHE B 408 
 TYR   0.013   0.001   TYR A 590 
 ARG   0.002   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04826 (  587)
  hydrogen bonds       : angle       4.71029 ( 1728)
  covalent geometry    : bond        0.00305 ( 9366)
  covalent geometry    : angle       0.56890 (12776)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 146
  time to evaluate  : 0.869 
Fit side-chains
REVERT: A  133 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8477 (m-80)
REVERT: A  292 ASN cc_start: 0.7920 (m-40) cc_final: 0.7454 (m-40)
REVERT: A  481 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8359 (tp)
REVERT: B  112 MET cc_start: 0.8075 (ttp) cc_final: 0.7827 (ttt)
REVERT: B  133 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8069 (m-80)
REVERT: B  202 TYR cc_start: 0.5355 (OUTLIER) cc_final: 0.3573 (t80)
REVERT: B  280 HIS cc_start: 0.5810 (t70) cc_final: 0.5417 (m-70)
REVERT: B  584 LEU cc_start: 0.7335 (mm) cc_final: 0.6583 (pt)
REVERT: B  588 LEU cc_start: 0.7993 (mt) cc_final: 0.7792 (mt)
  outliers start: 42
  outliers final: 34
  residues processed: 176
  average time/residue: 0.1431
  time to fit residues: 39.2898
Evaluate side-chains
  181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 143
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  236 GLN
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  296 HIS
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  615 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 80 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 56 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9980
   chunk 106 optimal weight:    4.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.187227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.160957 restraints weight = 13165.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 2.34
r_work: 0.3891 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.4427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9366  Z= 0.144
  Angle     :  0.589  11.645  12776  Z= 0.297
  Chirality :  0.040   0.222   1420
  Planarity :  0.004   0.038   1556
  Dihedral  :  5.252  46.301   1247
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 19.85 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.26), residues: 1126
  helix:  1.35 (0.19), residues: 784
  sheet:  None (None), residues: 0
  loop : -0.31 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 559 
 HIS   0.004   0.001   HIS A 370 
 PHE   0.027   0.001   PHE B 408 
 TYR   0.011   0.001   TYR A 111 
 ARG   0.002   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04904 (  587)
  hydrogen bonds       : angle       4.72246 ( 1728)
  covalent geometry    : bond        0.00321 ( 9366)
  covalent geometry    : angle       0.58911 (12776)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 147
  time to evaluate  : 0.876 
Fit side-chains
REVERT: A  133 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8563 (m-80)
REVERT: A  225 SER cc_start: 0.8179 (m) cc_final: 0.7693 (t)
REVERT: A  292 ASN cc_start: 0.7941 (m-40) cc_final: 0.7469 (m-40)
REVERT: A  481 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8372 (tp)
REVERT: B  133 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8088 (m-80)
REVERT: B  202 TYR cc_start: 0.5364 (OUTLIER) cc_final: 0.3570 (t80)
REVERT: B  292 ASN cc_start: 0.7953 (m-40) cc_final: 0.7473 (m-40)
REVERT: B  486 LEU cc_start: 0.7808 (tp) cc_final: 0.7399 (tp)
REVERT: B  584 LEU cc_start: 0.7354 (mm) cc_final: 0.6590 (pt)
  outliers start: 39
  outliers final: 34
  residues processed: 174
  average time/residue: 0.1504
  time to fit residues: 40.4182
Evaluate side-chains
  181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 143
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  236 GLN
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  296 HIS
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  615 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0070
   chunk 83 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.8802

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.187074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.160816 restraints weight = 13168.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 2.34
r_work: 0.3893 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.4474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9366  Z= 0.146
  Angle     :  0.593  11.423  12776  Z= 0.297
  Chirality :  0.040   0.224   1420
  Planarity :  0.005   0.095   1556
  Dihedral  :  5.271  46.349   1247
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 19.96 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.26), residues: 1126
  helix:  1.34 (0.19), residues: 784
  sheet:  None (None), residues: 0
  loop : -0.30 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 559 
 HIS   0.004   0.001   HIS A 370 
 PHE   0.024   0.002   PHE B 408 
 TYR   0.011   0.001   TYR A 111 
 ARG   0.002   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04925 (  587)
  hydrogen bonds       : angle       4.73230 ( 1728)
  covalent geometry    : bond        0.00326 ( 9366)
  covalent geometry    : angle       0.59315 (12776)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

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Job complete
usr+sys time: 4047.35 seconds
wall clock time: 71 minutes 53.75 seconds (4313.75 seconds total)