Starting phenix.real_space_refine
on Mon Jul 28 15:21:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s9a_24930/07_2025/7s9a_24930.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s9a_24930/07_2025/7s9a_24930.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s9a_24930/07_2025/7s9a_24930.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s9a_24930/07_2025/7s9a_24930.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s9a_24930/07_2025/7s9a_24930.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s9a_24930/07_2025/7s9a_24930.cif"
  }
  resolution = 3.8
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    6832      2.51       5
     N    1674      2.21       5
     O    1864      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10420
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 675, 5200
          Classifications: {'peptide': 675}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 32, 'TRANS': 642}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 5200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 675, 5200
          Classifications: {'peptide': 675}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 32, 'TRANS': 642}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 12
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'SAL': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'SAL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.75, per 1000 atoms: 0.65
  Number of scatterers: 10420
  At special positions: 0
  Unit cell: (117.993, 109.489, 116.93, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1864      8.00
     N    1674      7.00
     C    6832      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: 2.88
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2492

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 4 sheets defined
      64.9% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 32
    Processing helix  chain 'A' and resid 44 through 49
      removed outlier: 3.963A  pdb=" N   GLN A  48 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 65
    Processing helix  chain 'A' and resid 65 through 70
      removed outlier: 4.266A  pdb=" N   LYS A  69 " --> pdb=" O   LEU A  65 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   TRP A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 65 through 70'
    Processing helix  chain 'A' and resid 78 through 105
      Proline residue:  A  96  - end of helix
      removed outlier: 3.615A  pdb=" N   ALA A 105 " --> pdb=" O   PHE A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 126
      removed outlier: 3.975A  pdb=" N   GLY A 112 " --> pdb=" O   PRO A 108 " (cutoff:3.500A)
      Proline residue:  A 119  - end of helix
      removed outlier: 3.803A  pdb=" N   MET A 122 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 152
    Processing helix  chain 'A' and resid 169 through 196
    Processing helix  chain 'A' and resid 197 through 201
      removed outlier: 3.938A  pdb=" N   PHE A 200 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL A 201 " --> pdb=" O   PHE A 198 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 197 through 201'
    Processing helix  chain 'A' and resid 206 through 231
      removed outlier: 4.243A  pdb=" N   LYS A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   TYR A 228 " --> pdb=" O   SER A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 253
    Processing helix  chain 'A' and resid 258 through 282
    Processing helix  chain 'A' and resid 291 through 308
    Processing helix  chain 'A' and resid 308 through 313
      removed outlier: 3.537A  pdb=" N   TYR A 313 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 363
      removed outlier: 3.679A  pdb=" N   ALA A 343 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 388
    Processing helix  chain 'A' and resid 396 through 405
    Processing helix  chain 'A' and resid 411 through 428
    Processing helix  chain 'A' and resid 436 through 448
      removed outlier: 4.137A  pdb=" N   LEU A 440 " --> pdb=" O   PRO A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 453
    Processing helix  chain 'A' and resid 456 through 465
      removed outlier: 4.121A  pdb=" N   PHE A 460 " --> pdb=" O   SER A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 481
      removed outlier: 3.577A  pdb=" N   LEU A 469 " --> pdb=" O   SER A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 505
      removed outlier: 4.093A  pdb=" N   VAL A 499 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ILE A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 526
      No H-bonds generated for 'chain 'A' and resid 524 through 526'
    Processing helix  chain 'A' and resid 549 through 560
      removed outlier: 3.668A  pdb=" N   THR A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 579
    Processing helix  chain 'A' and resid 653 through 671
    Processing helix  chain 'A' and resid 680 through 690
    Processing helix  chain 'A' and resid 697 through 700
    Processing helix  chain 'A' and resid 705 through 720
    Processing helix  chain 'B' and resid 25 through 32
    Processing helix  chain 'B' and resid 44 through 49
      removed outlier: 3.963A  pdb=" N   GLN B  48 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 65
    Processing helix  chain 'B' and resid 65 through 70
      removed outlier: 4.265A  pdb=" N   LYS B  69 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   TRP B  70 " --> pdb=" O   PRO B  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 65 through 70'
    Processing helix  chain 'B' and resid 78 through 105
      Proline residue:  B  96  - end of helix
      removed outlier: 3.615A  pdb=" N   ALA B 105 " --> pdb=" O   PHE B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 126
      removed outlier: 3.975A  pdb=" N   GLY B 112 " --> pdb=" O   PRO B 108 " (cutoff:3.500A)
      Proline residue:  B 119  - end of helix
      removed outlier: 3.803A  pdb=" N   MET B 122 " --> pdb=" O   TYR B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 152
    Processing helix  chain 'B' and resid 169 through 196
    Processing helix  chain 'B' and resid 197 through 201
      removed outlier: 3.938A  pdb=" N   PHE B 200 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL B 201 " --> pdb=" O   PHE B 198 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 197 through 201'
    Processing helix  chain 'B' and resid 206 through 231
      removed outlier: 4.244A  pdb=" N   LYS B 227 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   TYR B 228 " --> pdb=" O   SER B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 253
    Processing helix  chain 'B' and resid 258 through 282
    Processing helix  chain 'B' and resid 291 through 308
    Processing helix  chain 'B' and resid 308 through 313
      removed outlier: 3.537A  pdb=" N   TYR B 313 " --> pdb=" O   LEU B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 363
      removed outlier: 3.678A  pdb=" N   ALA B 343 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 388
    Processing helix  chain 'B' and resid 396 through 405
    Processing helix  chain 'B' and resid 411 through 428
    Processing helix  chain 'B' and resid 436 through 448
      removed outlier: 4.137A  pdb=" N   LEU B 440 " --> pdb=" O   PRO B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 453
    Processing helix  chain 'B' and resid 456 through 465
      removed outlier: 4.121A  pdb=" N   PHE B 460 " --> pdb=" O   SER B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 481
      removed outlier: 3.577A  pdb=" N   LEU B 469 " --> pdb=" O   SER B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 505
      removed outlier: 4.596A  pdb=" N   VAL B 499 " --> pdb=" O   ALA B 495 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ILE B 500 " --> pdb=" O   LEU B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 524 through 526
      No H-bonds generated for 'chain 'B' and resid 524 through 526'
    Processing helix  chain 'B' and resid 549 through 560
      removed outlier: 3.667A  pdb=" N   THR B 560 " --> pdb=" O   LEU B 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 563 through 579
    Processing helix  chain 'B' and resid 653 through 671
    Processing helix  chain 'B' and resid 680 through 690
    Processing helix  chain 'B' and resid 697 through 700
    Processing helix  chain 'B' and resid 705 through 720
    Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135
    Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522
      removed outlier: 4.715A  pdb=" N   ILE A 537 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   GLN A 513 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 11.952A  pdb=" N   ILE A 535 " --> pdb=" O   GLN A 513 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   LYS A 536 " --> pdb=" O   ILE A 643 " (cutoff:3.500A)
      removed outlier: 7.650A  pdb=" N   ASP A 645 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   PHE A 538 " --> pdb=" O   ASP A 645 " (cutoff:3.500A)
      removed outlier: 8.495A  pdb=" N   PHE A 703 " --> pdb=" O   VAL A 674 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU A 676 " --> pdb=" O   PHE A 703 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 135
    Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522
      removed outlier: 4.716A  pdb=" N   ILE B 537 " --> pdb=" O   LEU B 511 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   GLN B 513 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 11.952A  pdb=" N   ILE B 535 " --> pdb=" O   GLN B 513 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   LYS B 536 " --> pdb=" O   ILE B 643 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   ASP B 645 " --> pdb=" O   LYS B 536 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   PHE B 538 " --> pdb=" O   ASP B 645 " (cutoff:3.500A)
      removed outlier: 8.495A  pdb=" N   PHE B 703 " --> pdb=" O   VAL B 674 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU B 676 " --> pdb=" O   PHE B 703 " (cutoff:3.500A)

    618 hydrogen bonds defined for protein.
    1824 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: 3.44

  Time building geometry restraints manager: 3.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3206
        1.34 -     1.46: 1644
        1.46 -     1.58: 5720
        1.58 -     1.70: 0
        1.70 -     1.81: 82
  Bond restraints: 10652
  Sorted by residual:
  bond pdb=" N   VAL B 139 "
       pdb=" CA  VAL B 139 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.30e+00
  bond pdb=" N   ILE A 494 "
       pdb=" CA  ILE A 494 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.035 1.21e-02 6.83e+03 8.24e+00
  bond pdb=" N   VAL A 139 "
       pdb=" CA  VAL A 139 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.20e+00
  bond pdb=" N   ILE B 494 "
       pdb=" CA  ILE B 494 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.035 1.21e-02 6.83e+03 8.16e+00
  bond pdb=" N   VAL B 499 "
       pdb=" CA  VAL B 499 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.19e-02 7.06e+03 7.39e+00
  ... (remaining 10647 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 14145
        1.63 -     3.26: 253
        3.26 -     4.88: 52
        4.88 -     6.51: 20
        6.51 -     8.14: 6
  Bond angle restraints: 14476
  Sorted by residual:
  angle pdb=" O   GLY A 135 "
        pdb=" C   GLY A 135 "
        pdb=" N   PRO A 136 "
      ideal   model   delta    sigma   weight residual
     121.77  118.21    3.56 1.00e+00 1.00e+00 1.26e+01
  angle pdb=" C   GLU A 694 "
        pdb=" N   ASN A 695 "
        pdb=" CA  ASN A 695 "
      ideal   model   delta    sigma   weight residual
     122.83  126.60   -3.77 1.08e+00 8.57e-01 1.22e+01
  angle pdb=" C   GLU B 694 "
        pdb=" N   ASN B 695 "
        pdb=" CA  ASN B 695 "
      ideal   model   delta    sigma   weight residual
     122.83  126.56   -3.73 1.08e+00 8.57e-01 1.19e+01
  angle pdb=" N   GLY B 366 "
        pdb=" CA  GLY B 366 "
        pdb=" C   GLY B 366 "
      ideal   model   delta    sigma   weight residual
     113.18  121.32   -8.14 2.37e+00 1.78e-01 1.18e+01
  angle pdb=" N   GLY A 366 "
        pdb=" CA  GLY A 366 "
        pdb=" C   GLY A 366 "
      ideal   model   delta    sigma   weight residual
     113.18  121.32   -8.14 2.37e+00 1.78e-01 1.18e+01
  ... (remaining 14471 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.62: 5709
       16.62 -    33.24: 487
       33.24 -    49.86: 86
       49.86 -    66.48: 8
       66.48 -    83.10: 6
  Dihedral angle restraints: 6296
    sinusoidal: 2404
      harmonic: 3892
  Sorted by residual:
  dihedral pdb=" CA  ASN B 695 "
           pdb=" C   ASN B 695 "
           pdb=" N   PRO B 696 "
           pdb=" CA  PRO B 696 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.04   24.96     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  ASN A 695 "
           pdb=" C   ASN A 695 "
           pdb=" N   PRO A 696 "
           pdb=" CA  PRO A 696 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.04   24.96     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  GLY B 366 "
           pdb=" C   GLY B 366 "
           pdb=" N   TYR B 367 "
           pdb=" CA  TYR B 367 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.06  -17.94     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 6293 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1138
       0.039 -    0.077: 415
       0.077 -    0.116: 148
       0.116 -    0.154: 18
       0.154 -    0.192: 3
  Chirality restraints: 1722
  Sorted by residual:
  chirality pdb=" CA  ILE A 140 "
            pdb=" N   ILE A 140 "
            pdb=" C   ILE A 140 "
            pdb=" CB  ILE A 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.26e-01
  chirality pdb=" CA  VAL A 139 "
            pdb=" N   VAL A 139 "
            pdb=" C   VAL A 139 "
            pdb=" CB  VAL A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 7.81e-01
  chirality pdb=" CA  VAL B 139 "
            pdb=" N   VAL B 139 "
            pdb=" C   VAL B 139 "
            pdb=" CB  VAL B 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.56e-01
  ... (remaining 1719 not shown)

  Planarity restraints: 1802
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  65 "    0.058 5.00e-02 4.00e+02   8.73e-02 1.22e+01
        pdb=" N   PRO B  66 "   -0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO B  66 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO B  66 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  65 "    0.058 5.00e-02 4.00e+02   8.72e-02 1.22e+01
        pdb=" N   PRO A  66 "   -0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO A  66 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A  66 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 290 "   -0.040 5.00e-02 4.00e+02   6.05e-02 5.86e+00
        pdb=" N   PRO A 291 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 291 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 291 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 1799 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2826
        2.81 -     3.33: 10410
        3.33 -     3.86: 16489
        3.86 -     4.38: 17707
        4.38 -     4.90: 31907
  Nonbonded interactions: 79339
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 239 "
            pdb=" OG  SER A 242 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   GLY B 239 "
            pdb=" OG  SER B 242 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   SER A 505 "
            pdb=" OG  SER A 505 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O   SER B 505 "
            pdb=" OG  SER B 505 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O   ALA A 495 "
            pdb=" CG2 THR A 498 "
     model   vdw
     2.355 3.460
  ... (remaining 79334 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     27.730
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
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   0.052  10652  Z= 0.166
  Angle     :  0.598   8.139  14476  Z= 0.326
  Chirality :  0.044   0.192   1722
  Planarity :  0.005   0.087   1802
  Dihedral  : 12.628  83.104   3804
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.56 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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:  1.38 (0.24), residues: 1342
  helix:  1.98 (0.19), residues: 860
  sheet:  3.56 (0.78), residues: 36
  loop : -1.53 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 472 
 HIS   0.002   0.000   HIS A 220 
 PHE   0.027   0.001   PHE B 282 
 TYR   0.010   0.001   TYR A 545 
 ARG   0.005   0.000   ARG A 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13325 (  618)
  hydrogen bonds       : angle       4.82288 ( 1824)
  covalent geometry    : bond        0.00308 (10652)
  covalent geometry    : angle       0.59831 (14476)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.181 
Fit side-chains
REVERT: B  291 PRO cc_start: 0.8667 (Cg_exo) cc_final: 0.8376 (Cg_endo)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.1927
  time to fit residues: 42.6143
Evaluate side-chains
  123 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    3.9990
   chunk 101 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 68 optimal weight:    0.4980
   chunk 54 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 78 optimal weight:    7.9990
   chunk 121 optimal weight:    0.8980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3556 r_free = 0.3556 target = 0.129574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.097845 restraints weight = 17055.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.096866 restraints weight = 15696.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.098539 restraints weight = 15452.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.0834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10652  Z= 0.128
  Angle     :  0.583   7.850  14476  Z= 0.290
  Chirality :  0.043   0.155   1722
  Planarity :  0.005   0.062   1802
  Dihedral  :  4.123  36.827   1444
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.96 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  6.67 %
    Favored  : 92.02 %
  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:  1.64 (0.25), residues: 1342
  helix:  2.18 (0.19), residues: 862
  sheet:  3.72 (0.82), residues: 36
  loop : -1.46 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 472 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.025   0.001   PHE B 388 
 TYR   0.011   0.001   TYR A 545 
 ARG   0.003   0.000   ARG A 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04341 (  618)
  hydrogen bonds       : angle       3.80013 ( 1824)
  covalent geometry    : bond        0.00291 (10652)
  covalent geometry    : angle       0.58294 (14476)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 1.130 
Fit side-chains
REVERT: A  434 SER cc_start: 0.7814 (m) cc_final: 0.7402 (p)
REVERT: A  548 ASN cc_start: 0.7693 (t0) cc_final: 0.7358 (p0)
REVERT: B  434 SER cc_start: 0.7750 (m) cc_final: 0.7308 (p)
REVERT: B  548 ASN cc_start: 0.7749 (t0) cc_final: 0.7427 (p0)
  outliers start: 15
  outliers final: 13
  residues processed: 142
  average time/residue: 0.1942
  time to fit residues: 41.6150
Evaluate side-chains
  136 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  192 CYS
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  619 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 22 optimal weight:    8.9990
   chunk 71 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 81 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   chunk 87 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 130 optimal weight:    2.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.3531 r_free = 0.3531 target = 0.127758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.096577 restraints weight = 17268.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.095582 restraints weight = 15138.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.096775 restraints weight = 14026.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.1025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10652  Z= 0.141
  Angle     :  0.557   7.986  14476  Z= 0.284
  Chirality :  0.043   0.157   1722
  Planarity :  0.004   0.053   1802
  Dihedral  :  4.194  39.592   1444
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.96 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  8.60 %
    Favored  : 90.18 %
  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:  1.66 (0.25), residues: 1342
  helix:  2.21 (0.19), residues: 862
  sheet:  3.50 (0.80), residues: 36
  loop : -1.46 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 472 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.030   0.002   PHE B 388 
 TYR   0.009   0.001   TYR A 123 
 ARG   0.002   0.000   ARG A 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04251 (  618)
  hydrogen bonds       : angle       3.64146 ( 1824)
  covalent geometry    : bond        0.00332 (10652)
  covalent geometry    : angle       0.55739 (14476)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 1.224 
Fit side-chains
REVERT: B  548 ASN cc_start: 0.7982 (t0) cc_final: 0.7765 (p0)
  outliers start: 14
  outliers final: 14
  residues processed: 135
  average time/residue: 0.1974
  time to fit residues: 39.6196
Evaluate side-chains
  134 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  619 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0770
   chunk 33 optimal weight:    5.9990
   chunk 109 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 117 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.7542

-------------------------------------------------------------------------------
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 = 0.3555 r_free = 0.3555 target = 0.129606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.098426 restraints weight = 17003.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.096775 restraints weight = 15992.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.097952 restraints weight = 16448.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10652  Z= 0.109
  Angle     :  0.538   7.870  14476  Z= 0.270
  Chirality :  0.042   0.151   1722
  Planarity :  0.004   0.046   1802
  Dihedral  :  4.128  39.478   1444
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.11 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 11.05 %
    Favored  : 87.72 %
  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:  1.73 (0.25), residues: 1342
  helix:  2.26 (0.19), residues: 862
  sheet:  3.30 (0.78), residues: 36
  loop : -1.41 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 472 
 HIS   0.001   0.000   HIS B 365 
 PHE   0.027   0.001   PHE B 278 
 TYR   0.008   0.001   TYR B 340 
 ARG   0.002   0.000   ARG A 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03546 (  618)
  hydrogen bonds       : angle       3.47949 ( 1824)
  covalent geometry    : bond        0.00239 (10652)
  covalent geometry    : angle       0.53800 (14476)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 1.123 
Fit side-chains
REVERT: A  423 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8547 (tp)
REVERT: B  422 LEU cc_start: 0.9357 (tp) cc_final: 0.9132 (tt)
REVERT: B  423 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8501 (tp)
  outliers start: 14
  outliers final: 10
  residues processed: 136
  average time/residue: 0.2004
  time to fit residues: 40.2607
Evaluate side-chains
  131 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  619 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 130 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 97 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3506 r_free = 0.3506 target = 0.126017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.095127 restraints weight = 17202.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.093944 restraints weight = 15830.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.094800 restraints weight = 15452.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10652  Z= 0.161
  Angle     :  0.576   8.162  14476  Z= 0.292
  Chirality :  0.043   0.155   1722
  Planarity :  0.004   0.044   1802
  Dihedral  :  4.244  42.390   1444
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.74 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 11.75 %
    Favored  : 86.75 %
  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:  1.68 (0.25), residues: 1342
  helix:  2.25 (0.19), residues: 864
  sheet:  2.98 (0.77), residues: 36
  loop : -1.47 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 472 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.027   0.002   PHE B 278 
 TYR   0.013   0.001   TYR A 545 
 ARG   0.002   0.000   ARG A 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04319 (  618)
  hydrogen bonds       : angle       3.56258 ( 1824)
  covalent geometry    : bond        0.00386 (10652)
  covalent geometry    : angle       0.57598 (14476)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 1.220 
Fit side-chains
REVERT: A  387 LEU cc_start: 0.8406 (tt) cc_final: 0.8049 (tp)
REVERT: B  387 LEU cc_start: 0.8426 (tt) cc_final: 0.8125 (tp)
  outliers start: 17
  outliers final: 15
  residues processed: 133
  average time/residue: 0.2036
  time to fit residues: 39.9474
Evaluate side-chains
  138 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  192 CYS
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  619 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 99 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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 = 0.3512 r_free = 0.3512 target = 0.126491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.095897 restraints weight = 17330.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.094927 restraints weight = 15261.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.095729 restraints weight = 17646.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10652  Z= 0.137
  Angle     :  0.555   8.039  14476  Z= 0.281
  Chirality :  0.043   0.152   1722
  Planarity :  0.004   0.043   1802
  Dihedral  :  4.262  43.331   1444
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.81 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.54 %
    Favored  : 85.88 %
  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:  1.63 (0.25), residues: 1342
  helix:  2.23 (0.19), residues: 864
  sheet:  2.63 (0.77), residues: 38
  loop : -1.52 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 472 
 HIS   0.002   0.001   HIS B 337 
 PHE   0.025   0.001   PHE B 278 
 TYR   0.012   0.001   TYR B 545 
 ARG   0.002   0.000   ARG B 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04031 (  618)
  hydrogen bonds       : angle       3.52519 ( 1824)
  covalent geometry    : bond        0.00323 (10652)
  covalent geometry    : angle       0.55492 (14476)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 1.293 
Fit side-chains
REVERT: A  186 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8953 (p)
REVERT: A  387 LEU cc_start: 0.8409 (tt) cc_final: 0.8204 (tp)
REVERT: A  388 PHE cc_start: 0.6444 (m-80) cc_final: 0.6187 (m-80)
REVERT: A  423 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8534 (tp)
REVERT: B  387 LEU cc_start: 0.8398 (tt) cc_final: 0.8115 (tp)
REVERT: B  423 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8526 (tp)
  outliers start: 18
  outliers final: 15
  residues processed: 136
  average time/residue: 0.2056
  time to fit residues: 41.5277
Evaluate side-chains
  135 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  192 CYS
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  619 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 64 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9990
   chunk 86 optimal weight:    0.0980
   chunk 15 optimal weight:    0.0980
   chunk 110 optimal weight:    3.9990
   chunk 97 optimal weight:   10.0000
   chunk 69 optimal weight:    9.9990
   chunk 54 optimal weight:    0.0980
   chunk 38 optimal weight:    0.8980
   chunk 95 optimal weight:    6.9990
   overall best weight:    0.3380

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

Flipped N/Q/H residues before XYZ refinement:
B 256 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.129974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.098954 restraints weight = 17269.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.097949 restraints weight = 15312.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.098901 restraints weight = 15281.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10652  Z= 0.102
  Angle     :  0.543   9.322  14476  Z= 0.267
  Chirality :  0.042   0.152   1722
  Planarity :  0.004   0.040   1802
  Dihedral  :  4.099  40.513   1444
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.37 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 15.18 %
    Favored  : 84.12 %
  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:  1.78 (0.25), residues: 1342
  helix:  2.26 (0.19), residues: 866
  sheet:  2.87 (0.75), residues: 38
  loop : -1.29 (0.32), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 472 
 HIS   0.001   0.000   HIS B 337 
 PHE   0.030   0.001   PHE A 278 
 TYR   0.010   0.001   TYR A 545 
 ARG   0.003   0.000   ARG A 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03156 (  618)
  hydrogen bonds       : angle       3.40000 ( 1824)
  covalent geometry    : bond        0.00218 (10652)
  covalent geometry    : angle       0.54285 (14476)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 1.595 
Fit side-chains
REVERT: A  387 LEU cc_start: 0.8382 (tt) cc_final: 0.8083 (tp)
REVERT: A  423 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8429 (tp)
REVERT: B  387 LEU cc_start: 0.8392 (tt) cc_final: 0.8103 (tp)
REVERT: B  423 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8411 (tp)
  outliers start: 8
  outliers final: 6
  residues processed: 131
  average time/residue: 0.2142
  time to fit residues: 41.5184
Evaluate side-chains
  129 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  423 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 114 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 118 optimal weight:    7.9990
   chunk 91 optimal weight:    0.0270
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.2046

-------------------------------------------------------------------------------
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 = 0.3528 r_free = 0.3528 target = 0.127651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.097559 restraints weight = 17223.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.096639 restraints weight = 16269.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.097442 restraints weight = 17583.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10652  Z= 0.121
  Angle     :  0.542   8.572  14476  Z= 0.270
  Chirality :  0.042   0.146   1722
  Planarity :  0.004   0.042   1802
  Dihedral  :  4.084  40.933   1444
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.04 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.44 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.25), residues: 1342
  helix:  2.31 (0.19), residues: 864
  sheet:  2.75 (0.75), residues: 38
  loop : -1.32 (0.32), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 472 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.026   0.001   PHE A 278 
 TYR   0.012   0.001   TYR A 545 
 ARG   0.001   0.000   ARG A 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03598 (  618)
  hydrogen bonds       : angle       3.38363 ( 1824)
  covalent geometry    : bond        0.00281 (10652)
  covalent geometry    : angle       0.54189 (14476)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 1.212 
Fit side-chains
REVERT: A  225 MET cc_start: 0.8078 (ttt) cc_final: 0.7531 (ttm)
REVERT: A  423 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8353 (tp)
REVERT: B  225 MET cc_start: 0.8035 (ttt) cc_final: 0.7439 (ttm)
REVERT: B  303 ILE cc_start: 0.8324 (mm) cc_final: 0.8034 (mt)
REVERT: B  423 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8406 (tp)
  outliers start: 14
  outliers final: 11
  residues processed: 125
  average time/residue: 0.2119
  time to fit residues: 38.9013
Evaluate side-chains
  130 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  619 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 120 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 34 optimal weight:    0.8980
   chunk 97 optimal weight:   10.0000
   chunk 18 optimal weight:    0.2980
   chunk 130 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3533 r_free = 0.3533 target = 0.128015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.097559 restraints weight = 17416.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.096080 restraints weight = 16189.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.097033 restraints weight = 18942.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10652  Z= 0.114
  Angle     :  0.544   8.707  14476  Z= 0.269
  Chirality :  0.042   0.145   1722
  Planarity :  0.004   0.041   1802
  Dihedral  :  4.081  40.927   1444
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.81 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.35 %
    Favored  : 83.25 %
  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:  1.83 (0.25), residues: 1342
  helix:  2.32 (0.19), residues: 864
  sheet:  2.74 (0.75), residues: 38
  loop : -1.29 (0.32), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 472 
 HIS   0.002   0.000   HIS A 220 
 PHE   0.026   0.001   PHE A 278 
 TYR   0.011   0.001   TYR B 545 
 ARG   0.001   0.000   ARG A 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03543 (  618)
  hydrogen bonds       : angle       3.36971 ( 1824)
  covalent geometry    : bond        0.00262 (10652)
  covalent geometry    : angle       0.54397 (14476)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 1.105 
Fit side-chains
REVERT: A  110 VAL cc_start: 0.6939 (OUTLIER) cc_final: 0.6603 (p)
REVERT: A  225 MET cc_start: 0.7982 (ttt) cc_final: 0.7470 (ttm)
REVERT: A  423 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8410 (tp)
REVERT: B  110 VAL cc_start: 0.6979 (OUTLIER) cc_final: 0.6674 (p)
REVERT: B  225 MET cc_start: 0.7994 (ttt) cc_final: 0.7441 (ttm)
REVERT: B  303 ILE cc_start: 0.8317 (mm) cc_final: 0.8034 (mt)
REVERT: B  423 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8385 (tp)
  outliers start: 16
  outliers final: 10
  residues processed: 128
  average time/residue: 0.2049
  time to fit residues: 38.5106
Evaluate side-chains
  132 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  423 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 91 optimal weight:    0.0070
   chunk 40 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 90 optimal weight:    5.9990
   overall best weight:    1.1602

-------------------------------------------------------------------------------
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 = 0.3528 r_free = 0.3528 target = 0.127623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.097233 restraints weight = 17389.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.095575 restraints weight = 16165.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.096581 restraints weight = 18828.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10652  Z= 0.120
  Angle     :  0.554   8.810  14476  Z= 0.274
  Chirality :  0.042   0.145   1722
  Planarity :  0.004   0.041   1802
  Dihedral  :  4.102  41.193   1444
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.04 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.82 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.25), residues: 1342
  helix:  2.31 (0.19), residues: 864
  sheet:  2.71 (0.75), residues: 38
  loop : -1.30 (0.32), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 472 
 HIS   0.002   0.001   HIS B 220 
 PHE   0.031   0.001   PHE B 278 
 TYR   0.011   0.001   TYR B 545 
 ARG   0.001   0.000   ARG B 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03658 (  618)
  hydrogen bonds       : angle       3.38594 ( 1824)
  covalent geometry    : bond        0.00278 (10652)
  covalent geometry    : angle       0.55382 (14476)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 1.335 
Fit side-chains
REVERT: A  110 VAL cc_start: 0.6957 (OUTLIER) cc_final: 0.6620 (p)
REVERT: A  225 MET cc_start: 0.7907 (ttt) cc_final: 0.7377 (ttm)
REVERT: A  423 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8407 (tp)
REVERT: B  110 VAL cc_start: 0.7052 (OUTLIER) cc_final: 0.6737 (p)
REVERT: B  225 MET cc_start: 0.7940 (ttt) cc_final: 0.7410 (ttm)
REVERT: B  303 ILE cc_start: 0.8318 (mm) cc_final: 0.8043 (mt)
REVERT: B  423 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8302 (tp)
  outliers start: 18
  outliers final: 13
  residues processed: 131
  average time/residue: 0.2128
  time to fit residues: 41.1196
Evaluate side-chains
  133 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  423 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 111 optimal weight:    0.0970
   chunk 77 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 80 optimal weight:    7.9990
   chunk 88 optimal weight:    0.5980
   chunk 86 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 98 optimal weight:    5.9990
   chunk 129 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 13 optimal weight:    7.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3535 r_free = 0.3535 target = 0.128156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.098013 restraints weight = 17014.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.096957 restraints weight = 15769.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.097589 restraints weight = 18047.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10652  Z= 0.111
  Angle     :  0.544   8.652  14476  Z= 0.269
  Chirality :  0.042   0.146   1722
  Planarity :  0.004   0.041   1802
  Dihedral  :  4.071  40.989   1444
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.96 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 15.18 %
    Favored  : 83.51 %
  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:  1.84 (0.25), residues: 1342
  helix:  2.33 (0.19), residues: 864
  sheet:  2.76 (0.75), residues: 38
  loop : -1.28 (0.32), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 472 
 HIS   0.002   0.000   HIS B 220 
 PHE   0.029   0.001   PHE B 278 
 TYR   0.011   0.001   TYR A 545 
 ARG   0.001   0.000   ARG B 571 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03500 (  618)
  hydrogen bonds       : angle       3.35937 ( 1824)
  covalent geometry    : bond        0.00252 (10652)
  covalent geometry    : angle       0.54362 (14476)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3298.49 seconds
wall clock time: 58 minutes 58.45 seconds (3538.45 seconds total)