Starting phenix.real_space_refine
on Thu Jan 16 03:27:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y92_39067/01_2025/8y92_39067.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y92_39067/01_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_39067/01_2025/8y92_39067.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y92_39067/01_2025/8y92_39067.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y92_39067/01_2025/8y92_39067.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y92_39067/01_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 6.09, per 1000 atoms: 0.67
  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: 2.58
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.82
  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: 2.62

  Time building geometry restraints manager: 2.90 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:             5.950
  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:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.930
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.760
-------------------------------------------------------------------------------
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= 0.212
  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 

*********************** 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  : 1.070 
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: 0.1903
  time to fit residues: 80.5874
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  : 1.118 
-------------------------------------------------------------------------------
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 = 0.196373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.172389 restraints weight = 12797.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.4132 rms_B_bonded: 2.31
r_work: 0.4018 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
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= 0.200
  Angle     :  0.565   7.555  12776  Z= 0.288
  Chirality :  0.039   0.135   1420
  Planarity :  0.004   0.040   1556
  Dihedral  :  7.388 107.710   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 

*********************** 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  : 0.992 
Fit side-chains
REVERT: A  365 LEU cc_start: 0.7690 (mt) cc_final: 0.7296 (mt)
REVERT: A  425 GLU cc_start: 0.7399 (tt0) cc_final: 0.7125 (tt0)
REVERT: B  202 TYR cc_start: 0.5436 (OUTLIER) cc_final: 0.3451 (t80)
REVERT: B  364 ILE cc_start: 0.8492 (mp) cc_final: 0.8248 (mp)
REVERT: B  365 LEU cc_start: 0.7719 (mt) cc_final: 0.7314 (mt)
REVERT: B  601 VAL cc_start: 0.8595 (t) cc_final: 0.8275 (m)
  outliers start: 37
  outliers final: 22
  residues processed: 200
  average time/residue: 0.1642
  time to fit residues: 49.9509
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  : 1.005 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 22 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 24 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.4259 r_free = 0.4259 target = 0.185202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.158627 restraints weight = 13193.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3975 rms_B_bonded: 2.40
r_work: 0.3849 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9366  Z= 0.258
  Angle     :  0.599   7.612  12776  Z= 0.313
  Chirality :  0.041   0.139   1420
  Planarity :  0.004   0.040   1556
  Dihedral  :  5.904  47.958   1251
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 14.39 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.25), residues: 1126
  helix:  0.91 (0.18), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.72 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 128 
 HIS   0.008   0.001   HIS A 199 
 PHE   0.022   0.002   PHE B 409 
 TYR   0.021   0.002   TYR A 111 
 ARG   0.005   0.000   ARG B 216 

*********************** 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
  205 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 156
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8475 (m-80)
REVERT: A  473 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6834 (t0)
REVERT: A  566 MET cc_start: 0.6018 (mtt) cc_final: 0.5703 (mtt)
REVERT: A  588 LEU cc_start: 0.8050 (mt) cc_final: 0.7840 (mt)
REVERT: B  112 MET cc_start: 0.8115 (ttp) cc_final: 0.7881 (ttt)
REVERT: B  133 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8032 (m-80)
REVERT: B  202 TYR cc_start: 0.5445 (OUTLIER) cc_final: 0.3442 (t80)
REVERT: B  481 ILE cc_start: 0.8662 (tp) cc_final: 0.8453 (tp)
  outliers start: 49
  outliers final: 32
  residues processed: 190
  average time/residue: 0.1735
  time to fit residues: 49.3680
Evaluate side-chains
  173 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 137
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
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  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  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  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:    0.2980
   chunk 90 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 95 optimal weight:    0.6980
   chunk 107 optimal weight:    5.9990
   chunk 69 optimal weight:   20.0000
   chunk 45 optimal weight:    0.2980
   chunk 111 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4280 r_free = 0.4280 target = 0.187307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.161269 restraints weight = 12927.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 2.35
r_work: 0.3889 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9366  Z= 0.176
  Angle     :  0.542   6.372  12776  Z= 0.278
  Chirality :  0.039   0.128   1420
  Planarity :  0.004   0.032   1556
  Dihedral  :  5.691  47.699   1251
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 15.97 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.26), residues: 1126
  helix:  1.13 (0.19), residues: 796
  sheet:  None (None), residues: 0
  loop : -0.58 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 128 
 HIS   0.005   0.001   HIS B 222 
 PHE   0.016   0.001   PHE A 359 
 TYR   0.018   0.001   TYR A 111 
 ARG   0.003   0.000   ARG B 216 

*********************** 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
  185 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 139
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
REVERT: A  204 LYS cc_start: 0.6361 (tmmt) cc_final: 0.5542 (mtmt)
REVERT: A  225 SER cc_start: 0.8248 (m) cc_final: 0.7728 (t)
REVERT: A  473 ASP cc_start: 0.6664 (OUTLIER) cc_final: 0.6108 (t0)
REVERT: A  481 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8326 (tp)
REVERT: B  133 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8024 (m-80)
REVERT: B  202 TYR cc_start: 0.5393 (OUTLIER) cc_final: 0.3600 (t80)
REVERT: B  473 ASP cc_start: 0.6623 (OUTLIER) cc_final: 0.6134 (t0)
REVERT: B  481 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8376 (tp)
  outliers start: 46
  outliers final: 33
  residues processed: 172
  average time/residue: 0.1561
  time to fit residues: 41.3819
Evaluate side-chains
  173 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 134
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
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  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  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  509 MET
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  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:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 31 optimal weight:    8.9990
   chunk 54 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.4253 r_free = 0.4253 target = 0.184317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.157822 restraints weight = 13052.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 2.35
r_work: 0.3848 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.3996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9366  Z= 0.221
  Angle     :  0.566   7.836  12776  Z= 0.290
  Chirality :  0.040   0.154   1420
  Planarity :  0.004   0.033   1556
  Dihedral  :  5.649  47.375   1251
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 16.60 %
    Favored  : 77.63 %
  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:  1.01 (0.26), residues: 1126
  helix:  1.18 (0.19), residues: 794
  sheet:  None (None), residues: 0
  loop : -0.44 (0.38), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 128 
 HIS   0.003   0.001   HIS B 222 
 PHE   0.020   0.002   PHE B 275 
 TYR   0.017   0.001   TYR A 111 
 ARG   0.003   0.000   ARG B 216 

*********************** 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
  199 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 144
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A  133 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8502 (m-80)
REVERT: A  225 SER cc_start: 0.8273 (m) cc_final: 0.7768 (t)
REVERT: A  473 ASP cc_start: 0.6883 (OUTLIER) cc_final: 0.6671 (t0)
REVERT: A  481 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8376 (tp)
REVERT: B  133 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8018 (m-80)
REVERT: B  202 TYR cc_start: 0.5331 (OUTLIER) cc_final: 0.3617 (t80)
REVERT: B  473 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6573 (t0)
REVERT: B  481 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8435 (tp)
  outliers start: 55
  outliers final: 38
  residues processed: 184
  average time/residue: 0.1553
  time to fit residues: 43.9370
Evaluate side-chains
  182 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 137
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
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  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  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  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  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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    8.9990
   chunk 3 optimal weight:    0.2980
   chunk 79 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0870
   chunk 70 optimal weight:   20.0000
   chunk 100 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.8560

-------------------------------------------------------------------------------
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 = 0.4263 r_free = 0.4263 target = 0.185232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.159131 restraints weight = 12955.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3990 rms_B_bonded: 2.33
r_work: 0.3866 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.4088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9366  Z= 0.192
  Angle     :  0.548   7.002  12776  Z= 0.279
  Chirality :  0.039   0.134   1420
  Planarity :  0.004   0.034   1556
  Dihedral  :  5.561  47.256   1251
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 18.07 %
    Favored  : 76.68 %
  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:  1.13 (0.26), residues: 1126
  helix:  1.29 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.44 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 404 
 HIS   0.004   0.001   HIS A 222 
 PHE   0.037   0.002   PHE B 408 
 TYR   0.016   0.001   TYR A 111 
 ARG   0.003   0.000   ARG A 216 

*********************** 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
  200 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 150
  time to evaluate  : 0.794 
Fit side-chains
REVERT: A  133 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8487 (m-80)
REVERT: A  225 SER cc_start: 0.8250 (m) cc_final: 0.7748 (t)
REVERT: A  292 ASN cc_start: 0.7899 (m-40) cc_final: 0.7408 (m-40)
REVERT: A  473 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6195 (t0)
REVERT: A  481 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8323 (tp)
REVERT: B  133 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8048 (m-80)
REVERT: B  202 TYR cc_start: 0.5328 (OUTLIER) cc_final: 0.3706 (t80)
REVERT: B  473 ASP cc_start: 0.6707 (OUTLIER) cc_final: 0.6190 (t0)
REVERT: B  515 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8070 (tt)
  outliers start: 50
  outliers final: 39
  residues processed: 188
  average time/residue: 0.1537
  time to fit residues: 45.1091
Evaluate side-chains
  186 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 140
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
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  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  190 LEU
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  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  473 ASP
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:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 75 optimal weight:    0.5980
   chunk 109 optimal weight:    9.9990
   chunk 86 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.184157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.158013 restraints weight = 13017.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 2.34
r_work: 0.3851 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.4229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9366  Z= 0.210
  Angle     :  0.571   8.527  12776  Z= 0.289
  Chirality :  0.040   0.176   1420
  Planarity :  0.004   0.038   1556
  Dihedral  :  5.533  46.957   1251
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 18.70 %
    Favored  : 76.16 %
  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:  1.17 (0.26), residues: 1126
  helix:  1.32 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.42 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 128 
 HIS   0.003   0.001   HIS A 222 
 PHE   0.022   0.002   PHE B 275 
 TYR   0.023   0.001   TYR B 496 
 ARG   0.003   0.000   ARG A 216 

*********************** 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
  192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 143
  time to evaluate  : 1.034 
Fit side-chains
REVERT: A  133 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8495 (m-80)
REVERT: A  292 ASN cc_start: 0.7897 (m-40) cc_final: 0.7404 (m-40)
REVERT: A  473 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6570 (t0)
REVERT: A  481 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8376 (tp)
REVERT: B  133 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8009 (m-80)
REVERT: B  202 TYR cc_start: 0.5380 (OUTLIER) cc_final: 0.3694 (t80)
REVERT: B  473 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.6546 (t0)
REVERT: B  515 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8109 (tt)
REVERT: B  584 LEU cc_start: 0.7289 (mm) cc_final: 0.6752 (pt)
  outliers start: 49
  outliers final: 38
  residues processed: 180
  average time/residue: 0.1689
  time to fit residues: 46.4682
Evaluate side-chains
  184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 139
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
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  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  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  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  473 ASP
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:    0.5980
   chunk 63 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 6 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4275 r_free = 0.4275 target = 0.186323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.160104 restraints weight = 13337.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3997 rms_B_bonded: 2.40
r_work: 0.3874 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.4245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9366  Z= 0.177
  Angle     :  0.553   9.575  12776  Z= 0.278
  Chirality :  0.039   0.222   1420
  Planarity :  0.004   0.041   1556
  Dihedral  :  5.316  46.656   1249
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 18.91 %
    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:  1.29 (0.26), residues: 1126
  helix:  1.40 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.36 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 559 
 HIS   0.004   0.001   HIS A 222 
 PHE   0.022   0.001   PHE A 275 
 TYR   0.017   0.001   TYR B 496 
 ARG   0.003   0.000   ARG A 216 

*********************** 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
  195 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 150
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A  133 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8471 (m-80)
REVERT: A  225 SER cc_start: 0.8258 (m) cc_final: 0.7754 (t)
REVERT: A  292 ASN cc_start: 0.7929 (m-40) cc_final: 0.7457 (m-40)
REVERT: A  473 ASP cc_start: 0.6604 (OUTLIER) cc_final: 0.6014 (t0)
REVERT: A  481 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8331 (tp)
REVERT: B  133 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8033 (m-80)
REVERT: B  202 TYR cc_start: 0.5345 (OUTLIER) cc_final: 0.3633 (t80)
REVERT: B  297 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7858 (mt)
REVERT: B  306 THR cc_start: 0.7619 (p) cc_final: 0.7378 (t)
REVERT: B  473 ASP cc_start: 0.6675 (OUTLIER) cc_final: 0.6173 (t0)
REVERT: B  515 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8073 (tt)
REVERT: B  584 LEU cc_start: 0.7280 (mm) cc_final: 0.6687 (pt)
  outliers start: 45
  outliers final: 34
  residues processed: 182
  average time/residue: 0.1514
  time to fit residues: 42.6903
Evaluate side-chains
  187 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 145
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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  509 MET
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  297 ILE
Chi-restraints excluded: chain B residue  315 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  473 ASP
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:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 110 optimal weight:    4.9990
   chunk 84 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 42 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 = 0.4266 r_free = 0.4266 target = 0.185352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.159428 restraints weight = 13087.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 2.34
r_work: 0.3874 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9366  Z= 0.192
  Angle     :  0.562  11.004  12776  Z= 0.284
  Chirality :  0.040   0.232   1420
  Planarity :  0.004   0.041   1556
  Dihedral  :  5.303  46.739   1249
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 19.43 %
    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:  1.31 (0.26), residues: 1126
  helix:  1.40 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.31 (0.38), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 559 
 HIS   0.004   0.001   HIS A 370 
 PHE   0.016   0.001   PHE B 362 
 TYR   0.014   0.001   TYR B 496 
 ARG   0.003   0.000   ARG B 216 

*********************** 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
  192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 147
  time to evaluate  : 1.006 
Fit side-chains
REVERT: A  133 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8467 (m-80)
REVERT: A  225 SER cc_start: 0.8220 (m) cc_final: 0.7730 (t)
REVERT: A  292 ASN cc_start: 0.7944 (m-40) cc_final: 0.7480 (m-40)
REVERT: A  473 ASP cc_start: 0.6709 (OUTLIER) cc_final: 0.6166 (t0)
REVERT: A  481 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8373 (tp)
REVERT: B  133 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8009 (m-80)
REVERT: B  202 TYR cc_start: 0.5368 (OUTLIER) cc_final: 0.3588 (t80)
REVERT: B  473 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.6317 (t0)
REVERT: B  584 LEU cc_start: 0.7264 (mm) cc_final: 0.6715 (pt)
  outliers start: 45
  outliers final: 36
  residues processed: 178
  average time/residue: 0.1504
  time to fit residues: 41.6943
Evaluate side-chains
  189 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 147
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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  315 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  473 ASP
Chi-restraints excluded: chain B residue  509 MET
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:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 80 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 56 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.4168 r_free = 0.4168 target = 0.178181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.151937 restraints weight = 13271.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 2.37
r_work: 0.3754 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.4472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9366  Z= 0.228
  Angle     :  0.598  11.521  12776  Z= 0.300
  Chirality :  0.041   0.221   1420
  Planarity :  0.004   0.042   1556
  Dihedral  :  5.403  46.734   1249
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 19.75 %
    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:  1.25 (0.26), residues: 1126
  helix:  1.34 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.28 (0.38), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 559 
 HIS   0.004   0.001   HIS A 222 
 PHE   0.022   0.002   PHE A 275 
 TYR   0.014   0.001   TYR A 111 
 ARG   0.003   0.000   ARG B 216 

********************** 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
  184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 142
  time to evaluate  : 1.228 
Fit side-chains
REVERT: A  133 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8551 (m-80)
REVERT: A  225 SER cc_start: 0.8407 (m) cc_final: 0.7820 (t)
REVERT: A  292 ASN cc_start: 0.7862 (m-40) cc_final: 0.7389 (m-40)
REVERT: A  473 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6719 (t0)
REVERT: A  481 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8379 (tp)
REVERT: A  566 MET cc_start: 0.6189 (mtm) cc_final: 0.5934 (mtt)
REVERT: B  133 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8002 (m-80)
REVERT: B  202 TYR cc_start: 0.5320 (OUTLIER) cc_final: 0.3561 (t80)
REVERT: B  292 ASN cc_start: 0.7926 (m-40) cc_final: 0.7446 (m-40)
REVERT: B  584 LEU cc_start: 0.7244 (mm) cc_final: 0.6691 (pt)
  outliers start: 42
  outliers final: 35
  residues processed: 172
  average time/residue: 0.1692
  time to fit residues: 44.1368
Evaluate side-chains
  178 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 138
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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  315 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  509 MET
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:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0370
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.7458

-------------------------------------------------------------------------------
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 = 0.4264 r_free = 0.4264 target = 0.185193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.159125 restraints weight = 13121.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 2.35
r_work: 0.3864 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.4483

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= 0.190
  Angle     :  0.580  11.420  12776  Z= 0.290
  Chirality :  0.040   0.224   1420
  Planarity :  0.005   0.101   1556
  Dihedral  :  5.345  46.839   1249
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.17 %
    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:  1.31 (0.26), residues: 1126
  helix:  1.40 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -0.30 (0.37), residues: 334

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   0.015   0.001   PHE A 362 
 TYR   0.011   0.001   TYR B 496 
 ARG   0.002   0.000   ARG B 216 
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: 3544.29 seconds
wall clock time: 63 minutes 44.56 seconds (3824.56 seconds total)