Starting phenix.real_space_refine
on Mon Jul 28 00:15:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6r7y_4747/07_2025/6r7y_4747.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6r7y_4747/07_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_4747/07_2025/6r7y_4747.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6r7y_4747/07_2025/6r7y_4747.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6r7y_4747/07_2025/6r7y_4747.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6r7y_4747/07_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 9.37, per 1000 atoms: 0.93
  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: 2.37
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.91
  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: 2.73

  Time building geometry restraints manager: 2.85 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:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.880
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.140
-------------------------------------------------------------------------------
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= 0.456
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19555 (  614)
  hydrogen bonds       : angle       6.58939 ( 1806)
  covalent geometry    : bond        0.01027 (10312)
  covalent geometry    : angle       1.06885 (14008)

*********************** 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  : 1.187 
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: 0.2413
  time to fit residues: 109.5377
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  : 1.214 
-------------------------------------------------------------------------------
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 = 0.3068 r_free = 0.3068 target = 0.098794 restraints weight = 15541.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.101207 restraints weight = 10652.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.102910 restraints weight = 8287.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
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= 0.128
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04276 (  614)
  hydrogen bonds       : angle       4.17514 ( 1806)
  covalent geometry    : bond        0.00279 (10312)
  covalent geometry    : angle       0.53999 (14008)

*********************** 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  : 1.186 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8559 (mt) cc_final: 0.8095 (tp)
REVERT: A   91 GLU cc_start: 0.7845 (pm20) cc_final: 0.7583 (pm20)
REVERT: A  121 MET cc_start: 0.7601 (tpp) cc_final: 0.7304 (tpp)
REVERT: A  125 GLN cc_start: 0.8754 (mt0) cc_final: 0.8518 (mt0)
REVERT: A  176 SER cc_start: 0.8623 (p) cc_final: 0.8207 (t)
REVERT: A  183 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7763 (mt-10)
REVERT: A  217 TYR cc_start: 0.8884 (t80) cc_final: 0.8608 (t80)
REVERT: A  373 MET cc_start: 0.8307 (ttp) cc_final: 0.7468 (tpp)
REVERT: A  377 TYR cc_start: 0.8799 (t80) cc_final: 0.8388 (t80)
REVERT: A  521 PHE cc_start: 0.8722 (m-10) cc_final: 0.8480 (m-10)
REVERT: A  528 THR cc_start: 0.9256 (p) cc_final: 0.8864 (t)
REVERT: A  540 VAL cc_start: 0.9238 (t) cc_final: 0.8850 (t)
REVERT: A  576 MET cc_start: 0.7948 (mtt) cc_final: 0.7738 (mtp)
REVERT: B   81 LEU cc_start: 0.8741 (mt) cc_final: 0.8229 (tp)
REVERT: B  125 GLN cc_start: 0.8819 (mt0) cc_final: 0.8598 (mt0)
REVERT: B  176 SER cc_start: 0.8646 (p) cc_final: 0.8172 (t)
REVERT: B  187 TYR cc_start: 0.7816 (m-10) cc_final: 0.6963 (m-10)
REVERT: B  217 TYR cc_start: 0.8628 (t80) cc_final: 0.8262 (t80)
REVERT: B  327 TYR cc_start: 0.7744 (t80) cc_final: 0.7422 (t80)
REVERT: B  373 MET cc_start: 0.8408 (ttp) cc_final: 0.7876 (tpp)
REVERT: B  453 TYR cc_start: 0.8946 (t80) cc_final: 0.8541 (t80)
REVERT: B  504 GLN cc_start: 0.8013 (mt0) cc_final: 0.7734 (tt0)
REVERT: B  528 THR cc_start: 0.9173 (p) cc_final: 0.8587 (t)
REVERT: B  531 ASN cc_start: 0.8546 (m-40) cc_final: 0.7687 (t0)
REVERT: B  584 PHE cc_start: 0.8775 (m-80) cc_final: 0.8530 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 264
  average time/residue: 0.1722
  time to fit residues: 67.8953
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  : 1.071 
-------------------------------------------------------------------------------
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:    7.9990
   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:    0.9980
   chunk 2 optimal weight:    9.9990
   chunk 71 optimal weight:    0.9980
   chunk 93 optimal weight:    6.9990
   overall best weight:    2.1584

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.128732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.103245 restraints weight = 15778.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.105496 restraints weight = 11027.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.106721 restraints weight = 8684.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.3088

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= 0.151
  Angle     :  0.557   6.996  14008  Z= 0.282
  Chirality :  0.038   0.135   1588
  Planarity :  0.004   0.039   1742
  Dihedral  :  4.082  20.178   1370
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.24 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  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:  0.48 (0.23), residues: 1250
  helix:  1.01 (0.18), residues: 782
  sheet:  0.03 (0.74), residues: 44
  loop : -0.88 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 261 
 HIS   0.005   0.001   HIS A 390 
 PHE   0.021   0.001   PHE A 611 
 TYR   0.019   0.001   TYR B 187 
 ARG   0.005   0.000   ARG A 539 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03993 (  614)
  hydrogen bonds       : angle       3.92434 ( 1806)
  covalent geometry    : bond        0.00336 (10312)
  covalent geometry    : angle       0.55653 (14008)

*********************** 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
  229 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8503 (mt) cc_final: 0.7984 (tp)
REVERT: A  121 MET cc_start: 0.7736 (tpp) cc_final: 0.7194 (tpp)
REVERT: A  125 GLN cc_start: 0.8936 (mt0) cc_final: 0.8528 (mt0)
REVERT: A  176 SER cc_start: 0.8419 (p) cc_final: 0.8176 (t)
REVERT: A  183 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7759 (mt-10)
REVERT: A  217 TYR cc_start: 0.8732 (t80) cc_final: 0.8453 (t80)
REVERT: A  237 TRP cc_start: 0.8291 (m-10) cc_final: 0.8080 (m-10)
REVERT: A  373 MET cc_start: 0.8161 (ttp) cc_final: 0.7513 (tpp)
REVERT: A  377 TYR cc_start: 0.9010 (t80) cc_final: 0.8755 (t80)
REVERT: A  405 LEU cc_start: 0.9449 (tp) cc_final: 0.9208 (tp)
REVERT: A  528 THR cc_start: 0.9215 (p) cc_final: 0.8819 (t)
REVERT: A  581 ASN cc_start: 0.8767 (m110) cc_final: 0.8387 (p0)
REVERT: A  608 ILE cc_start: 0.9267 (mt) cc_final: 0.9003 (mm)
REVERT: B   81 LEU cc_start: 0.8601 (mt) cc_final: 0.8099 (tp)
REVERT: B   91 GLU cc_start: 0.7451 (pm20) cc_final: 0.7001 (pp20)
REVERT: B  176 SER cc_start: 0.8520 (p) cc_final: 0.8117 (t)
REVERT: B  217 TYR cc_start: 0.8639 (t80) cc_final: 0.8337 (t80)
REVERT: B  241 ASP cc_start: 0.7206 (p0) cc_final: 0.6996 (p0)
REVERT: B  373 MET cc_start: 0.8368 (ttp) cc_final: 0.7904 (tpp)
REVERT: B  453 TYR cc_start: 0.8871 (t80) cc_final: 0.8584 (t80)
REVERT: B  528 THR cc_start: 0.9192 (p) cc_final: 0.8735 (t)
REVERT: B  579 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8396 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1672
  time to fit residues: 59.0306
Evaluate side-chains
  167 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.225 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 35 optimal weight:    3.9990
   chunk 17 optimal weight:    9.9990
   chunk 57 optimal weight:   10.0000
   chunk 85 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 107 optimal weight:    7.9990
   chunk 82 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    1.5382

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

Flipped N/Q/H residues before XYZ refinement:
B 125 GLN
** B 441 GLN ** 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 = 0.3465 r_free = 0.3465 target = 0.130030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.105271 restraints weight = 15476.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.107451 restraints weight = 10780.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.109085 restraints weight = 8525.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.3408

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= 0.124
  Angle     :  0.512   7.353  14008  Z= 0.260
  Chirality :  0.037   0.141   1588
  Planarity :  0.003   0.036   1742
  Dihedral  :  3.921  17.381   1370
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.32 %
    Favored  : 97.52 %
  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:  1.07 (0.24), residues: 1250
  helix:  1.47 (0.18), residues: 782
  sheet:  0.27 (0.74), residues: 44
  loop : -0.62 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 261 
 HIS   0.004   0.001   HIS B 459 
 PHE   0.034   0.002   PHE B 407 
 TYR   0.019   0.001   TYR B 308 
 ARG   0.004   0.000   ARG A 539 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03706 (  614)
  hydrogen bonds       : angle       3.79851 ( 1806)
  covalent geometry    : bond        0.00273 (10312)
  covalent geometry    : angle       0.51237 (14008)

*********************** 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
  229 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 1.209 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8507 (mt) cc_final: 0.8013 (tp)
REVERT: A  176 SER cc_start: 0.8423 (p) cc_final: 0.8103 (t)
REVERT: A  183 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7697 (mt-10)
REVERT: A  217 TYR cc_start: 0.8633 (t80) cc_final: 0.8338 (t80)
REVERT: A  270 TYR cc_start: 0.8790 (t80) cc_final: 0.8322 (t80)
REVERT: A  308 TYR cc_start: 0.8237 (p90) cc_final: 0.7961 (p90)
REVERT: A  373 MET cc_start: 0.8141 (ttp) cc_final: 0.7554 (tpp)
REVERT: A  528 THR cc_start: 0.9239 (p) cc_final: 0.8702 (t)
REVERT: A  581 ASN cc_start: 0.8696 (m110) cc_final: 0.8403 (p0)
REVERT: A  608 ILE cc_start: 0.9247 (mt) cc_final: 0.9023 (mm)
REVERT: B   81 LEU cc_start: 0.8605 (mt) cc_final: 0.8019 (tp)
REVERT: B   91 GLU cc_start: 0.7532 (pm20) cc_final: 0.6951 (pp20)
REVERT: B  217 TYR cc_start: 0.8571 (t80) cc_final: 0.8217 (t80)
REVERT: B  241 ASP cc_start: 0.7292 (p0) cc_final: 0.7000 (p0)
REVERT: B  270 TYR cc_start: 0.8950 (t80) cc_final: 0.8557 (t80)
REVERT: B  373 MET cc_start: 0.8332 (ttp) cc_final: 0.7898 (tpp)
REVERT: B  528 THR cc_start: 0.9207 (p) cc_final: 0.8525 (t)
REVERT: B  579 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8462 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1713
  time to fit residues: 59.3877
Evaluate side-chains
  174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 55 optimal weight:    6.9990
   chunk 114 optimal weight:    3.9990
   chunk 95 optimal weight:   20.0000
   chunk 24 optimal weight:    0.8980
   chunk 83 optimal weight:    6.9990
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 441 GLN ** 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 = 0.3377 r_free = 0.3377 target = 0.122756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.098441 restraints weight = 16128.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.100229 restraints weight = 11987.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.101229 restraints weight = 9765.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  10312  Z= 0.282
  Angle     :  0.713   7.395  14008  Z= 0.355
  Chirality :  0.043   0.147   1588
  Planarity :  0.004   0.038   1742
  Dihedral  :  4.291  16.963   1370
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.88 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  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:  0.79 (0.24), residues: 1250
  helix:  1.19 (0.18), residues: 794
  sheet:  0.91 (0.81), residues: 40
  loop : -0.73 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 261 
 HIS   0.005   0.002   HIS B 459 
 PHE   0.026   0.002   PHE B 611 
 TYR   0.021   0.002   TYR B 377 
 ARG   0.003   0.001   ARG B 618 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04533 (  614)
  hydrogen bonds       : angle       4.09203 ( 1806)
  covalent geometry    : bond        0.00640 (10312)
  covalent geometry    : angle       0.71311 (14008)

*********************** 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
  215 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 MET cc_start: 0.7678 (mmm) cc_final: 0.7379 (mmt)
REVERT: A   81 LEU cc_start: 0.8595 (mt) cc_final: 0.8096 (tp)
REVERT: A  176 SER cc_start: 0.8574 (p) cc_final: 0.8276 (t)
REVERT: A  237 TRP cc_start: 0.8412 (m-10) cc_final: 0.8058 (m-10)
REVERT: A  270 TYR cc_start: 0.8925 (t80) cc_final: 0.8489 (t80)
REVERT: A  373 MET cc_start: 0.8304 (ttp) cc_final: 0.7623 (tpp)
REVERT: A  458 LYS cc_start: 0.8624 (mttt) cc_final: 0.8350 (mttp)
REVERT: A  528 THR cc_start: 0.9277 (p) cc_final: 0.8852 (t)
REVERT: A  627 LEU cc_start: 0.8790 (tp) cc_final: 0.8543 (tt)
REVERT: B   81 LEU cc_start: 0.8646 (mt) cc_final: 0.8033 (tt)
REVERT: B  217 TYR cc_start: 0.8867 (t80) cc_final: 0.8637 (t80)
REVERT: B  373 MET cc_start: 0.8431 (ttp) cc_final: 0.7962 (tpp)
REVERT: B  405 LEU cc_start: 0.9543 (tp) cc_final: 0.9264 (tp)
REVERT: B  528 THR cc_start: 0.9259 (p) cc_final: 0.8824 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1953
  time to fit residues: 65.7896
Evaluate side-chains
  160 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 41 optimal weight:    8.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3407 r_free = 0.3407 target = 0.125108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.100684 restraints weight = 15932.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.102742 restraints weight = 11397.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.104101 restraints weight = 9066.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.3761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  10312  Z= 0.204
  Angle     :  0.611   6.658  14008  Z= 0.310
  Chirality :  0.040   0.138   1588
  Planarity :  0.004   0.038   1742
  Dihedral  :  4.203  15.875   1370
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.72 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  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:  0.99 (0.24), residues: 1250
  helix:  1.39 (0.18), residues: 794
  sheet:  0.99 (0.82), residues: 40
  loop : -0.76 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.003   TRP A 186 
 HIS   0.005   0.001   HIS B 459 
 PHE   0.036   0.002   PHE A 407 
 TYR   0.021   0.002   TYR B 308 
 ARG   0.002   0.000   ARG A 539 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04159 (  614)
  hydrogen bonds       : angle       4.00130 ( 1806)
  covalent geometry    : bond        0.00467 (10312)
  covalent geometry    : angle       0.61053 (14008)

*********************** 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
  218 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8543 (mt) cc_final: 0.8045 (tp)
REVERT: A  217 TYR cc_start: 0.8787 (t80) cc_final: 0.8559 (t80)
REVERT: A  235 PHE cc_start: 0.7445 (m-10) cc_final: 0.7170 (m-10)
REVERT: A  237 TRP cc_start: 0.8304 (m-10) cc_final: 0.7972 (m-10)
REVERT: A  259 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7807 (mm-30)
REVERT: A  270 TYR cc_start: 0.8888 (t80) cc_final: 0.8468 (t80)
REVERT: A  373 MET cc_start: 0.8226 (ttp) cc_final: 0.7594 (tpp)
REVERT: A  458 LYS cc_start: 0.8617 (mttt) cc_final: 0.8367 (mttp)
REVERT: A  528 THR cc_start: 0.9266 (p) cc_final: 0.8721 (t)
REVERT: A  531 ASN cc_start: 0.9062 (m-40) cc_final: 0.7957 (t0)
REVERT: B   81 LEU cc_start: 0.8581 (mt) cc_final: 0.8024 (tp)
REVERT: B  217 TYR cc_start: 0.8751 (t80) cc_final: 0.8424 (t80)
REVERT: B  270 TYR cc_start: 0.8976 (t80) cc_final: 0.8487 (t80)
REVERT: B  373 MET cc_start: 0.8318 (ttp) cc_final: 0.7907 (tpp)
REVERT: B  454 TRP cc_start: 0.8869 (t60) cc_final: 0.8386 (t60)
REVERT: B  458 LYS cc_start: 0.8521 (mttt) cc_final: 0.8278 (mttp)
REVERT: B  528 THR cc_start: 0.9064 (p) cc_final: 0.8509 (t)
REVERT: B  531 ASN cc_start: 0.8457 (m-40) cc_final: 0.7659 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.2095
  time to fit residues: 71.0254
Evaluate side-chains
  166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.955 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 107 optimal weight:    0.1980
   chunk 46 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 95 optimal weight:   20.0000
   chunk 97 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 130 HIS
B 130 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.128315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.103839 restraints weight = 15891.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.105877 restraints weight = 11425.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.107304 restraints weight = 9159.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.3972

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= 0.126
  Angle     :  0.527   7.176  14008  Z= 0.267
  Chirality :  0.038   0.141   1588
  Planarity :  0.003   0.037   1742
  Dihedral  :  3.972  15.323   1370
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.08 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  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:  1.33 (0.24), residues: 1250
  helix:  1.63 (0.18), residues: 794
  sheet:  0.96 (0.84), residues: 40
  loop : -0.56 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 186 
 HIS   0.005   0.001   HIS B 459 
 PHE   0.022   0.001   PHE A 611 
 TYR   0.017   0.001   TYR B 377 
 ARG   0.004   0.000   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03693 (  614)
  hydrogen bonds       : angle       3.87442 ( 1806)
  covalent geometry    : bond        0.00284 (10312)
  covalent geometry    : angle       0.52669 (14008)

*********************** 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
  214 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 1.213 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8598 (mt) cc_final: 0.8087 (tp)
REVERT: A  185 THR cc_start: 0.8292 (p) cc_final: 0.8064 (t)
REVERT: A  217 TYR cc_start: 0.8560 (t80) cc_final: 0.8313 (t80)
REVERT: A  237 TRP cc_start: 0.8085 (m-10) cc_final: 0.7786 (m-10)
REVERT: A  259 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7711 (mm-30)
REVERT: A  270 TYR cc_start: 0.8773 (t80) cc_final: 0.8390 (t80)
REVERT: A  373 MET cc_start: 0.8288 (ttm) cc_final: 0.7661 (tpp)
REVERT: A  405 LEU cc_start: 0.9451 (tp) cc_final: 0.9235 (tp)
REVERT: A  458 LYS cc_start: 0.8609 (mttt) cc_final: 0.8353 (mttp)
REVERT: A  478 LEU cc_start: 0.8601 (tt) cc_final: 0.8380 (mm)
REVERT: A  528 THR cc_start: 0.9235 (p) cc_final: 0.8766 (t)
REVERT: A  633 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8237 (mm-30)
REVERT: B  121 MET cc_start: 0.7606 (tpp) cc_final: 0.7169 (tpp)
REVERT: B  217 TYR cc_start: 0.8576 (t80) cc_final: 0.8209 (t80)
REVERT: B  270 TYR cc_start: 0.8941 (t80) cc_final: 0.8478 (t80)
REVERT: B  373 MET cc_start: 0.8348 (ttp) cc_final: 0.7864 (tpp)
REVERT: B  528 THR cc_start: 0.9103 (p) cc_final: 0.8453 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.2312
  time to fit residues: 75.8963
Evaluate side-chains
  173 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 2.405 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 117 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 118 optimal weight:    6.9990
   chunk 88 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 63 optimal weight:   10.0000
   chunk 21 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.3464 r_free = 0.3464 target = 0.129369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.105256 restraints weight = 15552.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.107226 restraints weight = 11139.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.108626 restraints weight = 8907.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.4167

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= 0.125
  Angle     :  0.539   7.783  14008  Z= 0.274
  Chirality :  0.038   0.195   1588
  Planarity :  0.003   0.036   1742
  Dihedral  :  3.860  14.944   1370
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.08 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  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:  1.44 (0.24), residues: 1250
  helix:  1.74 (0.18), residues: 794
  sheet:  1.00 (0.85), residues: 40
  loop : -0.55 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 186 
 HIS   0.005   0.001   HIS B 459 
 PHE   0.032   0.001   PHE B 407 
 TYR   0.014   0.001   TYR A 377 
 ARG   0.005   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03638 (  614)
  hydrogen bonds       : angle       3.81302 ( 1806)
  covalent geometry    : bond        0.00285 (10312)
  covalent geometry    : angle       0.53897 (14008)

*********************** 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  : 1.826 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8552 (mt) cc_final: 0.8093 (tp)
REVERT: A  185 THR cc_start: 0.8346 (p) cc_final: 0.8102 (t)
REVERT: A  237 TRP cc_start: 0.8096 (m-10) cc_final: 0.7782 (m-10)
REVERT: A  259 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7757 (mm-30)
REVERT: A  371 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7732 (tp30)
REVERT: A  373 MET cc_start: 0.8285 (ttm) cc_final: 0.7651 (tpp)
REVERT: A  405 LEU cc_start: 0.9439 (tp) cc_final: 0.9234 (tp)
REVERT: A  458 LYS cc_start: 0.8633 (mttt) cc_final: 0.8396 (mttp)
REVERT: A  528 THR cc_start: 0.9225 (p) cc_final: 0.8776 (t)
REVERT: B   81 LEU cc_start: 0.8309 (mp) cc_final: 0.7635 (tp)
REVERT: B  121 MET cc_start: 0.7523 (tpp) cc_final: 0.7074 (tpp)
REVERT: B  217 TYR cc_start: 0.8493 (t80) cc_final: 0.8119 (t80)
REVERT: B  270 TYR cc_start: 0.8880 (t80) cc_final: 0.8381 (t80)
REVERT: B  371 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7716 (tp30)
REVERT: B  373 MET cc_start: 0.8301 (ttp) cc_final: 0.7771 (tpp)
REVERT: B  510 LEU cc_start: 0.9203 (mt) cc_final: 0.8861 (mt)
REVERT: B  521 PHE cc_start: 0.7969 (m-80) cc_final: 0.7737 (m-80)
REVERT: B  528 THR cc_start: 0.9150 (p) cc_final: 0.8538 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.1712
  time to fit residues: 56.5130
Evaluate side-chains
  174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 60 optimal weight:    0.0980
   chunk 34 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 87 optimal weight:    8.9990
   chunk 94 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 61 optimal weight:    8.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    2.0184

-------------------------------------------------------------------------------
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 = 0.3362 r_free = 0.3362 target = 0.120035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.095570 restraints weight = 16245.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.097246 restraints weight = 12003.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.098590 restraints weight = 9846.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.4251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10312  Z= 0.147
  Angle     :  0.561   8.212  14008  Z= 0.282
  Chirality :  0.038   0.135   1588
  Planarity :  0.004   0.036   1742
  Dihedral  :  3.843  14.348   1370
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.48 %
    Favored  : 97.36 %
  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 (0.24), residues: 1250
  helix:  1.79 (0.18), residues: 794
  sheet:  1.07 (0.85), residues: 40
  loop : -0.51 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 186 
 HIS   0.005   0.001   HIS B 459 
 PHE   0.022   0.002   PHE B 611 
 TYR   0.024   0.001   TYR B 377 
 ARG   0.005   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03694 (  614)
  hydrogen bonds       : angle       3.79245 ( 1806)
  covalent geometry    : bond        0.00337 (10312)
  covalent geometry    : angle       0.56142 (14008)

*********************** 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
  202 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 1.176 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8520 (mt) cc_final: 0.8006 (tp)
REVERT: A  185 THR cc_start: 0.8402 (p) cc_final: 0.8157 (t)
REVERT: A  237 TRP cc_start: 0.7954 (m-10) cc_final: 0.7631 (m-10)
REVERT: A  259 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7802 (mm-30)
REVERT: A  270 TYR cc_start: 0.8788 (t80) cc_final: 0.8386 (t80)
REVERT: A  373 MET cc_start: 0.8296 (ttm) cc_final: 0.7675 (tpp)
REVERT: A  405 LEU cc_start: 0.9495 (tp) cc_final: 0.9250 (tp)
REVERT: A  458 LYS cc_start: 0.8693 (mttt) cc_final: 0.8431 (mttp)
REVERT: A  528 THR cc_start: 0.9230 (p) cc_final: 0.8715 (t)
REVERT: A  581 ASN cc_start: 0.8772 (m110) cc_final: 0.8300 (p0)
REVERT: B   81 LEU cc_start: 0.8270 (mp) cc_final: 0.7597 (tp)
REVERT: B  217 TYR cc_start: 0.8533 (t80) cc_final: 0.8182 (t80)
REVERT: B  373 MET cc_start: 0.8352 (ttp) cc_final: 0.7838 (tpp)
REVERT: B  458 LYS cc_start: 0.8569 (mttt) cc_final: 0.8294 (mttp)
REVERT: B  528 THR cc_start: 0.9210 (p) cc_final: 0.8604 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.1808
  time to fit residues: 57.0847
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  : 1.183 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 120 optimal weight:    7.9990
   chunk 118 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 96 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 10 optimal weight:    9.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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 = 0.3432 r_free = 0.3432 target = 0.126892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.102435 restraints weight = 15688.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.104444 restraints weight = 11216.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.105510 restraints weight = 8980.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.4266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10312  Z= 0.183
  Angle     :  0.608   8.396  14008  Z= 0.308
  Chirality :  0.040   0.139   1588
  Planarity :  0.004   0.036   1742
  Dihedral  :  3.961  15.661   1370
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.64 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.24), residues: 1250
  helix:  1.68 (0.18), residues: 794
  sheet:  0.98 (0.86), residues: 40
  loop : -0.59 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 186 
 HIS   0.005   0.001   HIS B 459 
 PHE   0.025   0.002   PHE B 611 
 TYR   0.023   0.002   TYR B 187 
 ARG   0.005   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 (  614)
  hydrogen bonds       : angle       3.88221 ( 1806)
  covalent geometry    : bond        0.00422 (10312)
  covalent geometry    : angle       0.60825 (14008)

********************** 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
  203 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8451 (mt) cc_final: 0.7993 (tp)
REVERT: A  185 THR cc_start: 0.8491 (p) cc_final: 0.8230 (t)
REVERT: A  187 TYR cc_start: 0.8693 (m-10) cc_final: 0.8430 (m-80)
REVERT: A  237 TRP cc_start: 0.8020 (m-10) cc_final: 0.7620 (m-10)
REVERT: A  259 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7856 (mm-30)
REVERT: A  270 TYR cc_start: 0.8852 (t80) cc_final: 0.8445 (t80)
REVERT: A  373 MET cc_start: 0.8290 (ttm) cc_final: 0.7574 (tpp)
REVERT: A  405 LEU cc_start: 0.9557 (tp) cc_final: 0.9301 (tp)
REVERT: A  458 LYS cc_start: 0.8730 (mttt) cc_final: 0.8475 (mttp)
REVERT: A  528 THR cc_start: 0.9229 (p) cc_final: 0.8717 (t)
REVERT: A  581 ASN cc_start: 0.8747 (m110) cc_final: 0.8275 (p0)
REVERT: B   70 TYR cc_start: 0.7211 (m-10) cc_final: 0.7007 (m-80)
REVERT: B   81 LEU cc_start: 0.8376 (mp) cc_final: 0.7668 (tt)
REVERT: B  121 MET cc_start: 0.7655 (tpp) cc_final: 0.7372 (tpp)
REVERT: B  217 TYR cc_start: 0.8627 (t80) cc_final: 0.8298 (t80)
REVERT: B  270 TYR cc_start: 0.8900 (t80) cc_final: 0.8486 (t80)
REVERT: B  373 MET cc_start: 0.8340 (ttp) cc_final: 0.7787 (tpp)
REVERT: B  458 LYS cc_start: 0.8618 (mttt) cc_final: 0.8343 (mttp)
REVERT: B  528 THR cc_start: 0.9207 (p) cc_final: 0.8558 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.1632
  time to fit residues: 51.3675
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  : 1.162 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 77 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 7 optimal weight:    9.9990
   chunk 56 optimal weight:    9.9990
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    9.9990
   chunk 99 optimal weight:    0.3980
   chunk 8 optimal weight:    9.9990
   chunk 108 optimal weight:    7.9990
   chunk 123 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 390 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.132211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.107873 restraints weight = 15226.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.109954 restraints weight = 10737.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.111428 restraints weight = 8509.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.4551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10312  Z= 0.107
  Angle     :  0.519   8.451  14008  Z= 0.263
  Chirality :  0.037   0.138   1588
  Planarity :  0.003   0.036   1742
  Dihedral  :  3.733  14.566   1370
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.16 %
    Favored  : 97.76 %
  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:  1.61 (0.24), residues: 1250
  helix:  1.85 (0.18), residues: 794
  sheet:  0.99 (0.87), residues: 40
  loop : -0.42 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 237 
 HIS   0.005   0.001   HIS B 459 
 PHE   0.032   0.001   PHE B 611 
 TYR   0.023   0.001   TYR B 308 
 ARG   0.004   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03413 (  614)
  hydrogen bonds       : angle       3.79154 ( 1806)
  covalent geometry    : bond        0.00235 (10312)
  covalent geometry    : angle       0.51880 (14008)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3131.45 seconds
wall clock time: 57 minutes 40.17 seconds (3460.17 seconds total)