Starting phenix.real_space_refine
on Fri Feb 14 06:04:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6r7y_4747/02_2025/6r7y_4747.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6r7y_4747/02_2025/6r7y_4747.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6r7y_4747/02_2025/6r7y_4747.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6r7y_4747/02_2025/6r7y_4747.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6r7y_4747/02_2025/6r7y_4747.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6r7y_4747/02_2025/6r7y_4747.cif"
  }
  resolution = 4.2
  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: 5
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     S      54      5.16       5
     C    6640      2.51       5
     N    1618      2.21       5
     O    1744      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10062
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5028
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 627, 5028
          Classifications: {'peptide': 627}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 23, 'TRANS': 603}
          Unresolved non-hydrogen bonds: 105
          Unresolved non-hydrogen angles: 122
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 61
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.45, per 1000 atoms: 0.94
  Number of scatterers: 10062
  At special positions: 0
  Unit cell: (84.666, 132.342, 98.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      6     19.99
     S      54     16.00
     O    1744      8.00
     N    1618      7.00
     C    6640      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 1.2 seconds
  

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2400

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 6 sheets defined
      67.6% alpha, 4.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 41
      removed outlier: 3.746A  pdb=" N   ALA A  41 " --> pdb=" O   ASN A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 67
      removed outlier: 3.639A  pdb=" N   GLN A  67 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 87
    Processing helix  chain 'A' and resid 104 through 108
      removed outlier: 3.854A  pdb=" N   PHE A 108 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 134
    Processing helix  chain 'A' and resid 156 through 164
      removed outlier: 3.563A  pdb=" N   ARG A 160 " --> pdb=" O   SER A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 184
    Processing helix  chain 'A' and resid 196 through 205
    Processing helix  chain 'A' and resid 206 through 220
      removed outlier: 3.545A  pdb=" N   PHE A 220 " --> pdb=" O   GLU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 230
    Processing helix  chain 'A' and resid 230 through 235
    Processing helix  chain 'A' and resid 236 through 240
      removed outlier: 4.178A  pdb=" N   ASP A 239 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 273
      removed outlier: 3.810A  pdb=" N   ALA A 247 " --> pdb=" O   TYR A 243 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   THR A 255 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   LYS A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 316
      removed outlier: 3.643A  pdb=" N   ARG A 310 " --> pdb=" O   PRO A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 350
    Processing helix  chain 'A' and resid 352 through 355
      removed outlier: 3.721A  pdb=" N   THR A 355 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 352 through 355'
    Processing helix  chain 'A' and resid 356 through 387
      removed outlier: 3.907A  pdb=" N   TYR A 360 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
      Proline residue:  A 362  - end of helix
      removed outlier: 3.924A  pdb=" N   ARG A 375 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 422
      removed outlier: 3.696A  pdb=" N   TYR A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   SER A 415 " --> pdb=" O   ASN A 411 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   LEU A 416 " --> pdb=" O   CYS A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 449
      removed outlier: 3.636A  pdb=" N   SER A 449 " --> pdb=" O   GLN A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 469
      removed outlier: 3.760A  pdb=" N   ALA A 469 " --> pdb=" O   ARG A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 487
      removed outlier: 3.673A  pdb=" N   TYR A 479 " --> pdb=" O   ASP A 475 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   GLN A 481 " --> pdb=" O   THR A 477 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLU A 487 " --> pdb=" O   ILE A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 510
      removed outlier: 4.020A  pdb=" N   LEU A 501 " --> pdb=" O   ASP A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 539
      removed outlier: 3.825A  pdb=" N   ASN A 525 " --> pdb=" O   PHE A 521 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   THR A 528 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   ASN A 531 " --> pdb=" O   PHE A 527 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA A 534 " --> pdb=" O   VAL A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 575
      removed outlier: 3.906A  pdb=" N   VAL A 567 " --> pdb=" O   SER A 563 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL A 568 " --> pdb=" O   VAL A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 613
      removed outlier: 3.941A  pdb=" N   LEU A 593 " --> pdb=" O   ALA A 589 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE A 613 " --> pdb=" O   LEU A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 640
    Processing helix  chain 'B' and resid 28 through 41
      removed outlier: 3.746A  pdb=" N   ALA B  41 " --> pdb=" O   ASN B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 67
      removed outlier: 3.639A  pdb=" N   GLN B  67 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 87
    Processing helix  chain 'B' and resid 104 through 108
      removed outlier: 3.854A  pdb=" N   PHE B 108 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 134
    Processing helix  chain 'B' and resid 156 through 164
      removed outlier: 3.563A  pdb=" N   ARG B 160 " --> pdb=" O   SER B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 184
    Processing helix  chain 'B' and resid 196 through 205
    Processing helix  chain 'B' and resid 206 through 220
      removed outlier: 3.546A  pdb=" N   PHE B 220 " --> pdb=" O   GLU B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 230
    Processing helix  chain 'B' and resid 230 through 235
    Processing helix  chain 'B' and resid 236 through 240
      removed outlier: 4.177A  pdb=" N   ASP B 239 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 273
      removed outlier: 3.810A  pdb=" N   ALA B 247 " --> pdb=" O   TYR B 243 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   THR B 255 " --> pdb=" O   LEU B 251 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   LYS B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 316
      removed outlier: 3.643A  pdb=" N   ARG B 310 " --> pdb=" O   PRO B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 350
    Processing helix  chain 'B' and resid 352 through 355
      removed outlier: 3.722A  pdb=" N   THR B 355 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 352 through 355'
    Processing helix  chain 'B' and resid 356 through 387
      removed outlier: 3.908A  pdb=" N   TYR B 360 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL B 361 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)
      Proline residue:  B 362  - end of helix
      removed outlier: 3.924A  pdb=" N   ARG B 375 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 422
      removed outlier: 3.696A  pdb=" N   TYR B 396 " --> pdb=" O   LEU B 392 " (cutoff:3.500A)
      removed outlier: 5.278A  pdb=" N   SER B 415 " --> pdb=" O   ASN B 411 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   LEU B 416 " --> pdb=" O   CYS B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 449
      removed outlier: 3.636A  pdb=" N   SER B 449 " --> pdb=" O   GLN B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 469
      removed outlier: 3.762A  pdb=" N   ALA B 469 " --> pdb=" O   ARG B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 487
      removed outlier: 3.674A  pdb=" N   TYR B 479 " --> pdb=" O   ASP B 475 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   GLN B 481 " --> pdb=" O   THR B 477 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLU B 487 " --> pdb=" O   ILE B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 510
      removed outlier: 4.019A  pdb=" N   LEU B 501 " --> pdb=" O   ASP B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 539
      removed outlier: 3.825A  pdb=" N   ASN B 525 " --> pdb=" O   PHE B 521 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   THR B 528 " --> pdb=" O   LEU B 524 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   ASN B 531 " --> pdb=" O   PHE B 527 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA B 534 " --> pdb=" O   VAL B 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 575
      removed outlier: 3.906A  pdb=" N   VAL B 567 " --> pdb=" O   SER B 563 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL B 568 " --> pdb=" O   VAL B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 589 through 613
      removed outlier: 3.940A  pdb=" N   LEU B 593 " --> pdb=" O   ALA B 589 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE B 613 " --> pdb=" O   LEU B 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 617 through 640
    Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54
      removed outlier: 3.734A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91
    Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 294
    Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 54
      removed outlier: 3.734A  pdb=" N   GLN B 169 " --> pdb=" O   GLU B  22 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 91
    Processing sheet with id=AA6, first strand: chain 'B' and resid 291 through 294

    614 hydrogen bonds defined for protein.
    1806 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: 2.89

  Time building geometry restraints manager: 2.99 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: 3073
        1.34 -     1.45: 1893
        1.45 -     1.57: 5256
        1.57 -     1.69: 0
        1.69 -     1.80: 90
  Bond restraints: 10312
  Sorted by residual:
  bond pdb=" CB  PHE B 218 "
       pdb=" CG  PHE B 218 "
    ideal  model  delta    sigma   weight residual
    1.502  1.457  0.045 2.30e-02 1.89e+03 3.74e+00
  bond pdb=" CB  PHE A 218 "
       pdb=" CG  PHE A 218 "
    ideal  model  delta    sigma   weight residual
    1.502  1.458  0.044 2.30e-02 1.89e+03 3.74e+00
  bond pdb=" CG  GLN B 556 "
       pdb=" CD  GLN B 556 "
    ideal  model  delta    sigma   weight residual
    1.516  1.469  0.047 2.50e-02 1.60e+03 3.56e+00
  bond pdb=" CB  GLN A 556 "
       pdb=" CG  GLN A 556 "
    ideal  model  delta    sigma   weight residual
    1.520  1.464  0.056 3.00e-02 1.11e+03 3.46e+00
  bond pdb=" CG  GLN A 556 "
       pdb=" CD  GLN A 556 "
    ideal  model  delta    sigma   weight residual
    1.516  1.470  0.046 2.50e-02 1.60e+03 3.41e+00
  ... (remaining 10307 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 12944
        1.81 -     3.63: 893
        3.63 -     5.44: 121
        5.44 -     7.26: 34
        7.26 -     9.07: 16
  Bond angle restraints: 14008
  Sorted by residual:
  angle pdb=" N   SER A 352 "
        pdb=" CA  SER A 352 "
        pdb=" C   SER A 352 "
      ideal   model   delta    sigma   weight residual
     113.43  106.65    6.78 1.26e+00 6.30e-01 2.90e+01
  angle pdb=" N   SER B 352 "
        pdb=" CA  SER B 352 "
        pdb=" C   SER B 352 "
      ideal   model   delta    sigma   weight residual
     113.43  106.67    6.76 1.26e+00 6.30e-01 2.88e+01
  angle pdb=" CA  VAL B 236 "
        pdb=" CB  VAL B 236 "
        pdb=" CG1 VAL B 236 "
      ideal   model   delta    sigma   weight residual
     110.40  116.68   -6.28 1.70e+00 3.46e-01 1.37e+01
  angle pdb=" CA  VAL A 236 "
        pdb=" CB  VAL A 236 "
        pdb=" CG1 VAL A 236 "
      ideal   model   delta    sigma   weight residual
     110.40  116.67   -6.27 1.70e+00 3.46e-01 1.36e+01
  angle pdb=" N   SER A 350 "
        pdb=" CA  SER A 350 "
        pdb=" C   SER A 350 "
      ideal   model   delta    sigma   weight residual
     111.24  115.96   -4.72 1.29e+00 6.01e-01 1.34e+01
  ... (remaining 14003 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 5356
       16.01 -    32.02: 602
       32.02 -    48.04: 104
       48.04 -    64.05: 22
       64.05 -    80.06: 4
  Dihedral angle restraints: 6088
    sinusoidal: 2370
      harmonic: 3718
  Sorted by residual:
  dihedral pdb=" CA  ASN A 349 "
           pdb=" C   ASN A 349 "
           pdb=" N   SER A 350 "
           pdb=" CA  SER A 350 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.57  -22.43     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  ASN B 349 "
           pdb=" C   ASN B 349 "
           pdb=" N   SER B 350 "
           pdb=" CA  SER B 350 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.58  -22.42     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" C   VAL A 236 "
           pdb=" N   VAL A 236 "
           pdb=" CA  VAL A 236 "
           pdb=" CB  VAL A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.39    8.39     0      2.50e+00 1.60e-01 1.13e+01
  ... (remaining 6085 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 918
       0.048 -    0.096: 486
       0.096 -    0.144: 155
       0.144 -    0.192: 25
       0.192 -    0.240: 4
  Chirality restraints: 1588
  Sorted by residual:
  chirality pdb=" CB  VAL B 236 "
            pdb=" CA  VAL B 236 "
            pdb=" CG1 VAL B 236 "
            pdb=" CG2 VAL B 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CB  VAL A 236 "
            pdb=" CA  VAL A 236 "
            pdb=" CG1 VAL A 236 "
            pdb=" CG2 VAL A 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  HIS A 399 "
            pdb=" N   HIS A 399 "
            pdb=" C   HIS A 399 "
            pdb=" CB  HIS A 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 1585 not shown)

  Planarity restraints: 1742
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 337 "   -0.026 2.00e-02 2.50e+03   2.03e-02 7.19e+00
        pdb=" CG  PHE B 337 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 337 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 337 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 337 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 337 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 337 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 337 "    0.026 2.00e-02 2.50e+03   2.02e-02 7.11e+00
        pdb=" CG  PHE A 337 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 337 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 337 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 337 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 337 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 337 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 355 "   -0.013 2.00e-02 2.50e+03   2.57e-02 6.61e+00
        pdb=" C   THR B 355 "    0.044 2.00e-02 2.50e+03
        pdb=" O   THR B 355 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   SER B 356 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1739 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 1077
        2.73 -     3.27: 9444
        3.27 -     3.82: 16186
        3.82 -     4.36: 18685
        4.36 -     4.90: 32430
  Nonbonded interactions: 77822
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 500 "
            pdb="CA    CA A 701 "
     model   vdw
     2.188 2.510
  nonbonded pdb=" OE2 GLU B 500 "
            pdb="CA    CA B 701 "
     model   vdw
     2.188 2.510
  nonbonded pdb=" OE2 GLU A 448 "
            pdb="CA    CA A 702 "
     model   vdw
     2.233 2.510
  nonbonded pdb=" OE2 GLU B 448 "
            pdb="CA    CA B 702 "
     model   vdw
     2.234 2.510
  nonbonded pdb=" N   ASN B  57 "
            pdb=" OD1 ASN B  57 "
     model   vdw
     2.297 3.120
  ... (remaining 77817 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: 0.05
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:                  0.010
  Normalize map: mean=0, sd=1:             0.880
  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:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     28.100
  Find NCS groups from input model:        0.180
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
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      :  0.010   0.073  10312  Z= 0.656
  Angle     :  1.069   9.070  14008  Z= 0.597
  Chirality :  0.061   0.240   1588
  Planarity :  0.007   0.056   1742
  Dihedral  : 13.583  80.059   3688
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.56 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  4.29 %
    Favored  : 94.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.18), residues: 1250
  helix: -2.09 (0.13), residues: 758
  sheet: -0.85 (0.67), residues: 44
  loop : -1.88 (0.26), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A 186 
 HIS   0.013   0.003   HIS B 399 
 PHE   0.046   0.004   PHE B 337 
 TYR   0.020   0.003   TYR B 243 
 ARG   0.004   0.001   ARG B 543 

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 312
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 GLU cc_start: 0.7666 (tt0) cc_final: 0.7377 (tt0)
REVERT: A   70 TYR cc_start: 0.7259 (m-80) cc_final: 0.6987 (m-80)
REVERT: A  125 GLN cc_start: 0.9075 (mt0) cc_final: 0.8811 (mt0)
REVERT: A  158 LEU cc_start: 0.9190 (tp) cc_final: 0.8984 (tp)
REVERT: A  176 SER cc_start: 0.8699 (p) cc_final: 0.8320 (t)
REVERT: A  236 VAL cc_start: 0.9089 (p) cc_final: 0.8156 (m)
REVERT: A  308 TYR cc_start: 0.8504 (p90) cc_final: 0.8089 (p90)
REVERT: A  334 MET cc_start: 0.7969 (mmm) cc_final: 0.7548 (mmt)
REVERT: A  370 ILE cc_start: 0.9353 (mt) cc_final: 0.9138 (pt)
REVERT: A  459 HIS cc_start: 0.8586 (t70) cc_final: 0.8326 (t70)
REVERT: A  514 VAL cc_start: 0.9060 (m) cc_final: 0.8804 (p)
REVERT: A  531 ASN cc_start: 0.8825 (m-40) cc_final: 0.8321 (t0)
REVERT: A  576 MET cc_start: 0.7967 (mtt) cc_final: 0.7652 (mtp)
REVERT: A  599 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8905 (tm-30)
REVERT: A  611 PHE cc_start: 0.8353 (t80) cc_final: 0.8081 (t80)
REVERT: A  627 LEU cc_start: 0.8933 (tp) cc_final: 0.8676 (tt)
REVERT: B   22 GLU cc_start: 0.7636 (tt0) cc_final: 0.7395 (tt0)
REVERT: B   40 ILE cc_start: 0.7943 (mt) cc_final: 0.7500 (mt)
REVERT: B   81 LEU cc_start: 0.8636 (mt) cc_final: 0.8084 (tp)
REVERT: B  125 GLN cc_start: 0.9165 (mt0) cc_final: 0.8745 (mt0)
REVERT: B  176 SER cc_start: 0.8623 (p) cc_final: 0.8397 (t)
REVERT: B  183 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7746 (mt-10)
REVERT: B  270 TYR cc_start: 0.9063 (t80) cc_final: 0.8672 (t80)
REVERT: B  334 MET cc_start: 0.7929 (mmm) cc_final: 0.7674 (mmt)
REVERT: B  373 MET cc_start: 0.8512 (ttp) cc_final: 0.7786 (tpp)
REVERT: B  431 GLN cc_start: 0.7993 (mt0) cc_final: 0.7790 (tm-30)
REVERT: B  453 TYR cc_start: 0.9147 (t80) cc_final: 0.8806 (t80)
REVERT: B  454 TRP cc_start: 0.8996 (t60) cc_final: 0.8551 (t-100)
REVERT: B  504 GLN cc_start: 0.8449 (mt0) cc_final: 0.8222 (mm110)
REVERT: B  531 ASN cc_start: 0.8866 (m-40) cc_final: 0.8243 (t0)
REVERT: B  576 MET cc_start: 0.7916 (mtt) cc_final: 0.7613 (mtp)
  outliers start: 18
  outliers final: 8
  residues processed: 329
  average time/residue: 0.2358
  time to fit residues: 107.2374
Evaluate side-chains
  193 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 185
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 112 optimal weight:    0.7980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 399 HIS
A 504 GLN
A 525 ASN
** B  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 399 HIS
B 504 GLN
B 525 ASN
B 579 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.124641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.098793 restraints weight = 15541.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.101176 restraints weight = 10652.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.102654 restraints weight = 8309.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10312  Z= 0.179
  Angle     :  0.540   6.018  14008  Z= 0.282
  Chirality :  0.038   0.141   1588
  Planarity :  0.005   0.042   1742
  Dihedral  :  4.278  21.786   1370
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.32 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  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: -0.60 (0.22), residues: 1250
  helix:  0.18 (0.17), residues: 782
  sheet: -0.05 (0.72), residues: 44
  loop : -1.40 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP B 186 
 HIS   0.005   0.001   HIS B 459 
 PHE   0.027   0.002   PHE B 407 
 TYR   0.016   0.001   TYR B 308 
 ARG   0.005   0.001   ARG A  78 

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8559 (mt) cc_final: 0.8094 (tp)
REVERT: A   91 GLU cc_start: 0.7846 (pm20) cc_final: 0.7582 (pm20)
REVERT: A  121 MET cc_start: 0.7595 (tpp) cc_final: 0.7300 (tpp)
REVERT: A  125 GLN cc_start: 0.8757 (mt0) cc_final: 0.8518 (mt0)
REVERT: A  176 SER cc_start: 0.8627 (p) cc_final: 0.8214 (t)
REVERT: A  183 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7771 (mt-10)
REVERT: A  217 TYR cc_start: 0.8884 (t80) cc_final: 0.8608 (t80)
REVERT: A  373 MET cc_start: 0.8306 (ttp) cc_final: 0.7469 (tpp)
REVERT: A  377 TYR cc_start: 0.8798 (t80) cc_final: 0.8389 (t80)
REVERT: A  521 PHE cc_start: 0.8723 (m-10) cc_final: 0.8481 (m-10)
REVERT: A  528 THR cc_start: 0.9255 (p) cc_final: 0.8864 (t)
REVERT: A  540 VAL cc_start: 0.9236 (t) cc_final: 0.8847 (t)
REVERT: A  576 MET cc_start: 0.7949 (mtt) cc_final: 0.7745 (mtp)
REVERT: B   81 LEU cc_start: 0.8738 (mt) cc_final: 0.8226 (tp)
REVERT: B  125 GLN cc_start: 0.8822 (mt0) cc_final: 0.8599 (mt0)
REVERT: B  176 SER cc_start: 0.8646 (p) cc_final: 0.8170 (t)
REVERT: B  187 TYR cc_start: 0.7819 (m-10) cc_final: 0.6963 (m-10)
REVERT: B  217 TYR cc_start: 0.8629 (t80) cc_final: 0.8264 (t80)
REVERT: B  327 TYR cc_start: 0.7745 (t80) cc_final: 0.7424 (t80)
REVERT: B  373 MET cc_start: 0.8406 (ttp) cc_final: 0.7878 (tpp)
REVERT: B  453 TYR cc_start: 0.8948 (t80) cc_final: 0.8542 (t80)
REVERT: B  504 GLN cc_start: 0.8014 (mt0) cc_final: 0.7735 (tt0)
REVERT: B  528 THR cc_start: 0.9176 (p) cc_final: 0.8590 (t)
REVERT: B  531 ASN cc_start: 0.8544 (m-40) cc_final: 0.7690 (t0)
REVERT: B  584 PHE cc_start: 0.8789 (m-80) cc_final: 0.8546 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 264
  average time/residue: 0.1797
  time to fit residues: 70.9733
Evaluate side-chains
  176 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 82 optimal weight:    3.9990
   chunk 81 optimal weight:    0.7980
   chunk 70 optimal weight:   10.0000
   chunk 55 optimal weight:    7.9990
   chunk 101 optimal weight:    3.9990
   chunk 106 optimal weight:    7.9990
   chunk 96 optimal weight:    0.0010
   chunk 2 optimal weight:    9.9990
   chunk 71 optimal weight:    0.9990
   chunk 93 optimal weight:    6.9990
   overall best weight:    1.9592

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

Flipped N/Q/H residues before XYZ refinement:
** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 504 GLN
B 250 ASN
** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.129241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.103870 restraints weight = 15763.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.106060 restraints weight = 10975.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.107686 restraints weight = 8659.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10312  Z= 0.205
  Angle     :  0.549   7.762  14008  Z= 0.279
  Chirality :  0.038   0.135   1588
  Planarity :  0.004   0.039   1742
  Dihedral  :  4.060  20.288   1370
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.08 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  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:  0.50 (0.23), residues: 1250
  helix:  1.02 (0.18), residues: 782
  sheet:  0.07 (0.75), residues: 44
  loop : -0.86 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 261 
 HIS   0.005   0.001   HIS B 459 
 PHE   0.020   0.001   PHE A 611 
 TYR   0.019   0.001   TYR B 187 
 ARG   0.005   0.001   ARG A 539 

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8543 (mt) cc_final: 0.8042 (tp)
REVERT: A  121 MET cc_start: 0.7754 (tpp) cc_final: 0.7416 (tpp)
REVERT: A  125 GLN cc_start: 0.8914 (mt0) cc_final: 0.8699 (mt0)
REVERT: A  176 SER cc_start: 0.8427 (p) cc_final: 0.8195 (t)
REVERT: A  183 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7803 (mt-10)
REVERT: A  217 TYR cc_start: 0.8721 (t80) cc_final: 0.8429 (t80)
REVERT: A  237 TRP cc_start: 0.8339 (m-10) cc_final: 0.8091 (m-10)
REVERT: A  373 MET cc_start: 0.8206 (ttp) cc_final: 0.7556 (tpp)
REVERT: A  377 TYR cc_start: 0.8977 (t80) cc_final: 0.8644 (t80)
REVERT: A  405 LEU cc_start: 0.9355 (tp) cc_final: 0.9136 (tp)
REVERT: A  528 THR cc_start: 0.9235 (p) cc_final: 0.8878 (t)
REVERT: A  581 ASN cc_start: 0.8791 (m110) cc_final: 0.8398 (p0)
REVERT: B   81 LEU cc_start: 0.8653 (mt) cc_final: 0.8158 (tp)
REVERT: B   91 GLU cc_start: 0.7428 (pm20) cc_final: 0.6964 (pp20)
REVERT: B  176 SER cc_start: 0.8553 (p) cc_final: 0.8132 (t)
REVERT: B  217 TYR cc_start: 0.8611 (t80) cc_final: 0.8309 (t80)
REVERT: B  241 ASP cc_start: 0.7232 (p0) cc_final: 0.7016 (p0)
REVERT: B  373 MET cc_start: 0.8399 (ttp) cc_final: 0.7884 (tpp)
REVERT: B  453 TYR cc_start: 0.8872 (t80) cc_final: 0.8592 (t80)
REVERT: B  528 THR cc_start: 0.9199 (p) cc_final: 0.8739 (t)
REVERT: B  579 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8460 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 227
  average time/residue: 0.1701
  time to fit residues: 58.9131
Evaluate side-chains
  168 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 60 optimal weight:    0.1980
   chunk 35 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 57 optimal weight:   10.0000
   chunk 85 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 107 optimal weight:    8.9990
   chunk 82 optimal weight:    2.9990
   chunk 92 optimal weight:    9.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
B 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.128506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.103747 restraints weight = 15548.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.105860 restraints weight = 10949.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.107070 restraints weight = 8684.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.3361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10312  Z= 0.216
  Angle     :  0.542   5.935  14008  Z= 0.276
  Chirality :  0.038   0.140   1588
  Planarity :  0.004   0.037   1742
  Dihedral  :  3.974  17.393   1370
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.32 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.24), residues: 1250
  helix:  1.33 (0.18), residues: 794
  sheet:  0.80 (0.76), residues: 40
  loop : -0.70 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 261 
 HIS   0.005   0.001   HIS B 459 
 PHE   0.032   0.002   PHE B 407 
 TYR   0.019   0.001   TYR B 308 
 ARG   0.005   0.000   ARG B 539 

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 1.080 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8492 (mt) cc_final: 0.7984 (tp)
REVERT: A  121 MET cc_start: 0.7790 (tpp) cc_final: 0.7537 (tpt)
REVERT: A  176 SER cc_start: 0.8426 (p) cc_final: 0.8125 (t)
REVERT: A  183 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7716 (mt-10)
REVERT: A  217 TYR cc_start: 0.8665 (t80) cc_final: 0.8398 (t80)
REVERT: A  270 TYR cc_start: 0.8785 (t80) cc_final: 0.8375 (t80)
REVERT: A  373 MET cc_start: 0.8168 (ttp) cc_final: 0.7553 (tpp)
REVERT: A  528 THR cc_start: 0.9234 (p) cc_final: 0.8696 (t)
REVERT: A  608 ILE cc_start: 0.9272 (mt) cc_final: 0.9051 (mm)
REVERT: B   81 LEU cc_start: 0.8570 (mt) cc_final: 0.7965 (tp)
REVERT: B   91 GLU cc_start: 0.7590 (pm20) cc_final: 0.7011 (pp20)
REVERT: B  176 SER cc_start: 0.8348 (p) cc_final: 0.8142 (t)
REVERT: B  217 TYR cc_start: 0.8616 (t80) cc_final: 0.8269 (t80)
REVERT: B  241 ASP cc_start: 0.7375 (p0) cc_final: 0.7087 (p0)
REVERT: B  270 TYR cc_start: 0.8943 (t80) cc_final: 0.8720 (t80)
REVERT: B  373 MET cc_start: 0.8345 (ttp) cc_final: 0.7934 (tpp)
REVERT: B  528 THR cc_start: 0.9213 (p) cc_final: 0.8527 (t)
REVERT: B  579 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8449 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 226
  average time/residue: 0.1725
  time to fit residues: 58.7119
Evaluate side-chains
  168 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 63 optimal weight:    7.9990
   chunk 12 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    0.5980
   chunk 55 optimal weight:    6.9990
   chunk 114 optimal weight:    4.9990
   chunk 95 optimal weight:   20.0000
   chunk 24 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   overall best weight:    3.0986

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

Flipped N/Q/H residues before XYZ refinement:
** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.126663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.102160 restraints weight = 15726.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.104281 restraints weight = 11207.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.105786 restraints weight = 8899.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.3569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10312  Z= 0.288
  Angle     :  0.599   6.297  14008  Z= 0.302
  Chirality :  0.040   0.136   1588
  Planarity :  0.004   0.037   1742
  Dihedral  :  4.055  16.674   1370
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.64 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  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:  1.08 (0.24), residues: 1250
  helix:  1.46 (0.18), residues: 790
  sheet:  1.06 (0.79), residues: 40
  loop : -0.72 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 186 
 HIS   0.004   0.001   HIS B 459 
 PHE   0.023   0.002   PHE A 611 
 TYR   0.017   0.001   TYR A 187 
 ARG   0.004   0.000   ARG B 539 

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8486 (mt) cc_final: 0.7992 (tp)
REVERT: A  176 SER cc_start: 0.8487 (p) cc_final: 0.8162 (t)
REVERT: A  183 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7763 (mm-30)
REVERT: A  187 TYR cc_start: 0.7826 (m-10) cc_final: 0.6980 (m-10)
REVERT: A  217 TYR cc_start: 0.8713 (t80) cc_final: 0.8482 (t80)
REVERT: A  237 TRP cc_start: 0.8201 (m-10) cc_final: 0.7851 (m-10)
REVERT: A  270 TYR cc_start: 0.8838 (t80) cc_final: 0.8463 (t80)
REVERT: A  373 MET cc_start: 0.8227 (ttp) cc_final: 0.7573 (tpp)
REVERT: A  405 LEU cc_start: 0.9476 (tp) cc_final: 0.9252 (tp)
REVERT: A  458 LYS cc_start: 0.8612 (mttt) cc_final: 0.8352 (mttp)
REVERT: A  531 ASN cc_start: 0.8352 (m-40) cc_final: 0.7902 (t0)
REVERT: A  608 ILE cc_start: 0.9291 (mt) cc_final: 0.9044 (mm)
REVERT: B   81 LEU cc_start: 0.8568 (mt) cc_final: 0.7982 (tp)
REVERT: B  176 SER cc_start: 0.8360 (p) cc_final: 0.8157 (t)
REVERT: B  217 TYR cc_start: 0.8715 (t80) cc_final: 0.8408 (t80)
REVERT: B  237 TRP cc_start: 0.8403 (m-10) cc_final: 0.8116 (m-10)
REVERT: B  270 TYR cc_start: 0.8898 (t80) cc_final: 0.8596 (t80)
REVERT: B  373 MET cc_start: 0.8371 (ttp) cc_final: 0.7951 (tpp)
REVERT: B  405 LEU cc_start: 0.9515 (tp) cc_final: 0.9282 (tp)
REVERT: B  528 THR cc_start: 0.9202 (p) cc_final: 0.8757 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1612
  time to fit residues: 53.9085
Evaluate side-chains
  170 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   chunk 62 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0040
   chunk 54 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 57 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   chunk 3 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   overall best weight:    2.2000

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 130 HIS
** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.128620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.104509 restraints weight = 15703.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.106493 restraints weight = 11150.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.108039 restraints weight = 8846.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.3791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  10312  Z= 0.228
  Angle     :  0.557   5.912  14008  Z= 0.286
  Chirality :  0.038   0.138   1588
  Planarity :  0.004   0.036   1742
  Dihedral  :  4.021  16.466   1370
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.56 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  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 (0.24), residues: 1250
  helix:  1.65 (0.18), residues: 790
  sheet:  1.14 (0.82), residues: 40
  loop : -0.68 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.067   0.002   TRP A 186 
 HIS   0.004   0.001   HIS B 130 
 PHE   0.033   0.002   PHE A 407 
 TYR   0.028   0.001   TYR B 187 
 ARG   0.003   0.000   ARG B 539 

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 1.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8540 (mt) cc_final: 0.8054 (tp)
REVERT: A  217 TYR cc_start: 0.8659 (t80) cc_final: 0.8350 (t80)
REVERT: A  237 TRP cc_start: 0.8146 (m-10) cc_final: 0.7807 (m-10)
REVERT: A  270 TYR cc_start: 0.8789 (t80) cc_final: 0.8418 (t80)
REVERT: A  373 MET cc_start: 0.8231 (ttp) cc_final: 0.7596 (tpp)
REVERT: A  405 LEU cc_start: 0.9485 (tp) cc_final: 0.9227 (tp)
REVERT: A  531 ASN cc_start: 0.8298 (m-40) cc_final: 0.7712 (t0)
REVERT: A  608 ILE cc_start: 0.9276 (mt) cc_final: 0.9062 (mm)
REVERT: A  627 LEU cc_start: 0.8797 (tp) cc_final: 0.8596 (tt)
REVERT: B   81 LEU cc_start: 0.8578 (mt) cc_final: 0.8002 (tp)
REVERT: B   91 GLU cc_start: 0.7725 (pm20) cc_final: 0.7108 (pp20)
REVERT: B  176 SER cc_start: 0.8477 (p) cc_final: 0.8238 (t)
REVERT: B  217 TYR cc_start: 0.8627 (t80) cc_final: 0.8292 (t80)
REVERT: B  237 TRP cc_start: 0.8377 (m-10) cc_final: 0.8093 (m-10)
REVERT: B  270 TYR cc_start: 0.8869 (t80) cc_final: 0.8533 (t80)
REVERT: B  373 MET cc_start: 0.8303 (ttp) cc_final: 0.7902 (tpp)
REVERT: B  454 TRP cc_start: 0.8815 (t60) cc_final: 0.8521 (t60)
REVERT: B  528 THR cc_start: 0.9108 (p) cc_final: 0.8556 (t)
REVERT: B  531 ASN cc_start: 0.8480 (m-40) cc_final: 0.7720 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1667
  time to fit residues: 57.4438
Evaluate side-chains
  170 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 84 optimal weight:   10.0000
   chunk 107 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 95 optimal weight:   20.0000
   chunk 97 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.124334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.100232 restraints weight = 16115.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.101960 restraints weight = 11618.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.103504 restraints weight = 9401.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  10312  Z= 0.354
  Angle     :  0.669  10.854  14008  Z= 0.337
  Chirality :  0.042   0.185   1588
  Planarity :  0.004   0.037   1742
  Dihedral  :  4.227  18.290   1370
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.96 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  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 (0.24), residues: 1250
  helix:  1.62 (0.18), residues: 784
  sheet:  1.02 (0.86), residues: 40
  loop : -0.83 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP A 186 
 HIS   0.004   0.002   HIS B 459 
 PHE   0.026   0.002   PHE A 611 
 TYR   0.020   0.002   TYR B 377 
 ARG   0.003   0.001   ARG B 539 

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8615 (mt) cc_final: 0.8114 (tp)
REVERT: A  217 TYR cc_start: 0.8740 (t80) cc_final: 0.8536 (t80)
REVERT: A  237 TRP cc_start: 0.8157 (m-10) cc_final: 0.7917 (m-10)
REVERT: A  259 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7961 (mm-30)
REVERT: A  270 TYR cc_start: 0.8911 (t80) cc_final: 0.8518 (t80)
REVERT: A  373 MET cc_start: 0.8293 (ttp) cc_final: 0.7630 (tpp)
REVERT: A  405 LEU cc_start: 0.9534 (tp) cc_final: 0.9261 (tp)
REVERT: A  531 ASN cc_start: 0.8359 (m-40) cc_final: 0.7928 (t0)
REVERT: B   81 LEU cc_start: 0.8580 (mt) cc_final: 0.8017 (tt)
REVERT: B  217 TYR cc_start: 0.8736 (t80) cc_final: 0.8479 (t80)
REVERT: B  237 TRP cc_start: 0.8429 (m-10) cc_final: 0.8172 (m-10)
REVERT: B  373 MET cc_start: 0.8395 (ttp) cc_final: 0.7841 (tpp)
REVERT: B  521 PHE cc_start: 0.8302 (m-80) cc_final: 0.8099 (m-80)
REVERT: B  528 THR cc_start: 0.9250 (p) cc_final: 0.8802 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1870
  time to fit residues: 57.7581
Evaluate side-chains
  162 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 117 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   chunk 118 optimal weight:    7.9990
   chunk 88 optimal weight:    9.9990
   chunk 73 optimal weight:    0.8980
   chunk 63 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   chunk 77 optimal weight:    0.4980
   chunk 44 optimal weight:    6.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.128184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.104596 restraints weight = 15578.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.106353 restraints weight = 11081.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.107887 restraints weight = 8898.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.4076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10312  Z= 0.204
  Angle     :  0.549   7.266  14008  Z= 0.282
  Chirality :  0.038   0.156   1588
  Planarity :  0.004   0.037   1742
  Dihedral  :  4.027  21.529   1370
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.40 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  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:  1.41 (0.24), residues: 1250
  helix:  1.80 (0.19), residues: 788
  sheet:  1.09 (0.86), residues: 40
  loop : -0.74 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.071   0.002   TRP A 186 
 HIS   0.005   0.001   HIS B 459 
 PHE   0.030   0.002   PHE B 407 
 TYR   0.023   0.001   TYR A 308 
 ARG   0.004   0.000   ARG B 539 

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 1.183 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8510 (mt) cc_final: 0.7993 (tp)
REVERT: A  217 TYR cc_start: 0.8514 (t80) cc_final: 0.8296 (t80)
REVERT: A  237 TRP cc_start: 0.8022 (m-10) cc_final: 0.7767 (m-10)
REVERT: A  259 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7867 (mm-30)
REVERT: A  270 TYR cc_start: 0.8821 (t80) cc_final: 0.8426 (t80)
REVERT: A  373 MET cc_start: 0.8230 (ttm) cc_final: 0.7603 (tpp)
REVERT: A  531 ASN cc_start: 0.8126 (m-40) cc_final: 0.7498 (t0)
REVERT: A  608 ILE cc_start: 0.9272 (mt) cc_final: 0.9029 (mm)
REVERT: B  217 TYR cc_start: 0.8570 (t80) cc_final: 0.8238 (t80)
REVERT: B  237 TRP cc_start: 0.8305 (m-10) cc_final: 0.8091 (m-10)
REVERT: B  270 TYR cc_start: 0.8971 (t80) cc_final: 0.8477 (t80)
REVERT: B  371 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7368 (tp30)
REVERT: B  373 MET cc_start: 0.8242 (ttp) cc_final: 0.7806 (tpp)
REVERT: B  458 LYS cc_start: 0.8546 (mttt) cc_final: 0.8320 (mttp)
REVERT: B  521 PHE cc_start: 0.8303 (m-80) cc_final: 0.8025 (m-80)
REVERT: B  528 THR cc_start: 0.9206 (p) cc_final: 0.8654 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.1752
  time to fit residues: 57.3139
Evaluate side-chains
  171 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 115 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 79 optimal weight:    0.4980
   chunk 56 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 94 optimal weight:    9.9990
   chunk 9 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 74 optimal weight:    9.9990
   overall best weight:    1.6382

-------------------------------------------------------------------------------
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 = 0.3456 r_free = 0.3456 target = 0.128946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.104968 restraints weight = 15515.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.107081 restraints weight = 11005.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.108284 restraints weight = 8760.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.4188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10312  Z= 0.193
  Angle     :  0.544   7.991  14008  Z= 0.277
  Chirality :  0.039   0.189   1588
  Planarity :  0.004   0.036   1742
  Dihedral  :  3.881  16.199   1370
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.92 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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:  1.51 (0.25), residues: 1250
  helix:  1.84 (0.19), residues: 788
  sheet:  1.11 (0.87), residues: 40
  loop : -0.59 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 272 
 HIS   0.005   0.001   HIS B 459 
 PHE   0.023   0.001   PHE A 611 
 TYR   0.023   0.001   TYR A 377 
 ARG   0.006   0.000   ARG A 201 

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8558 (mt) cc_final: 0.8036 (tp)
REVERT: A  217 TYR cc_start: 0.8459 (t80) cc_final: 0.8172 (t80)
REVERT: A  259 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7857 (mm-30)
REVERT: A  263 ARG cc_start: 0.9024 (mmm-85) cc_final: 0.8623 (ttm110)
REVERT: A  371 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7722 (tp30)
REVERT: A  373 MET cc_start: 0.8291 (ttm) cc_final: 0.7651 (tpp)
REVERT: A  405 LEU cc_start: 0.9448 (tp) cc_final: 0.9214 (tp)
REVERT: A  531 ASN cc_start: 0.8725 (m-40) cc_final: 0.7828 (t0)
REVERT: A  608 ILE cc_start: 0.9253 (mt) cc_final: 0.8991 (mm)
REVERT: B   81 LEU cc_start: 0.8267 (mp) cc_final: 0.7546 (tp)
REVERT: B  217 TYR cc_start: 0.8528 (t80) cc_final: 0.8179 (t80)
REVERT: B  237 TRP cc_start: 0.8313 (m-10) cc_final: 0.8019 (m-10)
REVERT: B  270 TYR cc_start: 0.8935 (t80) cc_final: 0.8429 (t80)
REVERT: B  373 MET cc_start: 0.8312 (ttp) cc_final: 0.7750 (tpp)
REVERT: B  458 LYS cc_start: 0.8531 (mttt) cc_final: 0.8263 (mttp)
REVERT: B  521 PHE cc_start: 0.8313 (m-80) cc_final: 0.7999 (m-80)
REVERT: B  528 THR cc_start: 0.9284 (p) cc_final: 0.8732 (t)
REVERT: B  608 ILE cc_start: 0.9316 (mt) cc_final: 0.9087 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.1761
  time to fit residues: 55.8045
Evaluate side-chains
  162 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 117 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9990
   chunk 120 optimal weight:    8.9990
   chunk 118 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9980
   chunk 96 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 = 0.3462 r_free = 0.3462 target = 0.129356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.105379 restraints weight = 15554.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.107439 restraints weight = 11150.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.108522 restraints weight = 8922.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10312  Z= 0.189
  Angle     :  0.544   8.293  14008  Z= 0.275
  Chirality :  0.038   0.180   1588
  Planarity :  0.004   0.036   1742
  Dihedral  :  3.786  15.571   1370
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.40 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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:  1.59 (0.24), residues: 1250
  helix:  1.90 (0.18), residues: 788
  sheet:  1.42 (0.87), residues: 40
  loop : -0.59 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 272 
 HIS   0.005   0.001   HIS B 459 
 PHE   0.030   0.002   PHE B 407 
 TYR   0.021   0.001   TYR A 377 
 ARG   0.003   0.000   ARG B 539 

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8551 (mt) cc_final: 0.8031 (tp)
REVERT: A  217 TYR cc_start: 0.8440 (t80) cc_final: 0.8207 (t80)
REVERT: A  237 TRP cc_start: 0.7802 (m-10) cc_final: 0.7438 (m-10)
REVERT: A  259 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7862 (mm-30)
REVERT: A  263 ARG cc_start: 0.9014 (mmm-85) cc_final: 0.8642 (ttm110)
REVERT: A  373 MET cc_start: 0.8335 (ttm) cc_final: 0.7640 (tpp)
REVERT: A  528 THR cc_start: 0.9148 (p) cc_final: 0.8462 (t)
REVERT: A  608 ILE cc_start: 0.9252 (mt) cc_final: 0.9006 (mm)
REVERT: B   81 LEU cc_start: 0.8313 (mp) cc_final: 0.7589 (tt)
REVERT: B  217 TYR cc_start: 0.8484 (t80) cc_final: 0.8112 (t80)
REVERT: B  237 TRP cc_start: 0.8169 (m-10) cc_final: 0.7916 (m-90)
REVERT: B  270 TYR cc_start: 0.8930 (t80) cc_final: 0.8410 (t80)
REVERT: B  373 MET cc_start: 0.8332 (ttp) cc_final: 0.7773 (tpp)
REVERT: B  458 LYS cc_start: 0.8526 (mttt) cc_final: 0.8266 (mttp)
REVERT: B  528 THR cc_start: 0.9306 (p) cc_final: 0.8758 (t)
REVERT: B  562 MET cc_start: 0.8421 (mtp) cc_final: 0.8150 (tpp)
REVERT: B  608 ILE cc_start: 0.9355 (mt) cc_final: 0.9109 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.1795
  time to fit residues: 57.3721
Evaluate side-chains
  165 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 1.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 14 optimal weight:    0.1980
   chunk 7 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 16 optimal weight:    9.9990
   chunk 99 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 108 optimal weight:    0.7980
   chunk 123 optimal weight:    9.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.130698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.107010 restraints weight = 15293.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.109087 restraints weight = 10931.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.110302 restraints weight = 8676.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.4437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10312  Z= 0.161
  Angle     :  0.543  11.598  14008  Z= 0.272
  Chirality :  0.037   0.143   1588
  Planarity :  0.004   0.036   1742
  Dihedral  :  3.716  15.097   1370
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.00 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  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:  1.72 (0.25), residues: 1250
  helix:  1.97 (0.18), residues: 788
  sheet:  1.46 (0.87), residues: 40
  loop : -0.49 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 272 
 HIS   0.005   0.001   HIS B 459 
 PHE   0.031   0.001   PHE B 235 
 TYR   0.020   0.001   TYR A 377 
 ARG   0.003   0.000   ARG B 539 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2680.66 seconds
wall clock time: 49 minutes 7.08 seconds (2947.08 seconds total)