Starting phenix.real_space_refine
on Tue Nov 18 01:25:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6r7y_4747/11_2025/6r7y_4747.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6r7y_4747/11_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_4747/11_2025/6r7y_4747.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6r7y_4747/11_2025/6r7y_4747.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6r7y_4747/11_2025/6r7y_4747.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6r7y_4747/11_2025/6r7y_4747.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'ASP:plan': 3, 'GLU:plan': 8, 'GLN:plan1': 3, 'ARG:plan': 2}
          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: 3.54, per 1000 atoms: 0.35
  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: 0.80
  Conformation dependent library (CDL) restraints added in 325.8 milliseconds
  

  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: 0.26
  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: 1.43

  Time building geometry restraints manager: 1.03 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: 0.01
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:             0.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     10.700
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.000
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.004   0.001   ARG B 543 
 TYR   0.020   0.003   TYR B 243 
 PHE   0.046   0.004   PHE B 337 
 TRP   0.021   0.003   TRP A 186 
 HIS   0.013   0.003   HIS B 399 

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

*********************** 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  : 0.395 
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: 0.1023
  time to fit residues: 47.1281
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  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 123 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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
** 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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.125149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.098954 restraints weight = 15584.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.101466 restraints weight = 10535.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.103223 restraints weight = 8125.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.104414 restraints weight = 6830.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.105034 restraints weight = 6098.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10312  Z= 0.132
  Angle     :  0.545   5.995  14008  Z= 0.285
  Chirality :  0.038   0.142   1588
  Planarity :  0.005   0.042   1742
  Dihedral  :  4.286  21.769   1370
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.32 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.22), residues: 1250
  helix:  0.21 (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
 ARG   0.006   0.001   ARG A  78 
 TYR   0.017   0.001   TYR B 308 
 PHE   0.028   0.002   PHE B 407 
 TRP   0.035   0.002   TRP B 186 
 HIS   0.006   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (10312)
  covalent geometry    : angle       0.54522 (14008)
  hydrogen bonds       : bond        0.04247 (  614)
  hydrogen bonds       : angle       4.16671 ( 1806)

*********************** 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
  262 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8553 (mt) cc_final: 0.8090 (tp)
REVERT: A   91 GLU cc_start: 0.7838 (pm20) cc_final: 0.7599 (pm20)
REVERT: A  121 MET cc_start: 0.7611 (tpp) cc_final: 0.7296 (tpp)
REVERT: A  125 GLN cc_start: 0.8743 (mt0) cc_final: 0.8494 (mt0)
REVERT: A  176 SER cc_start: 0.8614 (p) cc_final: 0.8206 (t)
REVERT: A  183 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7773 (mt-10)
REVERT: A  217 TYR cc_start: 0.8891 (t80) cc_final: 0.8617 (t80)
REVERT: A  373 MET cc_start: 0.8317 (ttp) cc_final: 0.7499 (tpp)
REVERT: A  377 TYR cc_start: 0.8816 (t80) cc_final: 0.8402 (t80)
REVERT: A  521 PHE cc_start: 0.8727 (m-10) cc_final: 0.8463 (m-10)
REVERT: A  528 THR cc_start: 0.9258 (p) cc_final: 0.8863 (t)
REVERT: A  540 VAL cc_start: 0.9251 (t) cc_final: 0.8846 (t)
REVERT: A  576 MET cc_start: 0.7952 (mtt) cc_final: 0.7751 (mtp)
REVERT: A  606 LYS cc_start: 0.9177 (ttmm) cc_final: 0.8976 (ttmt)
REVERT: B   81 LEU cc_start: 0.8735 (mt) cc_final: 0.8222 (tp)
REVERT: B  125 GLN cc_start: 0.8804 (mt0) cc_final: 0.8586 (mt0)
REVERT: B  176 SER cc_start: 0.8642 (p) cc_final: 0.8170 (t)
REVERT: B  187 TYR cc_start: 0.7813 (m-10) cc_final: 0.6901 (m-10)
REVERT: B  217 TYR cc_start: 0.8632 (t80) cc_final: 0.8263 (t80)
REVERT: B  241 ASP cc_start: 0.7722 (p0) cc_final: 0.7503 (p0)
REVERT: B  327 TYR cc_start: 0.7750 (t80) cc_final: 0.7427 (t80)
REVERT: B  373 MET cc_start: 0.8417 (ttp) cc_final: 0.7873 (tpp)
REVERT: B  453 TYR cc_start: 0.8950 (t80) cc_final: 0.8548 (t80)
REVERT: B  504 GLN cc_start: 0.8020 (mt0) cc_final: 0.7763 (tt0)
REVERT: B  528 THR cc_start: 0.9179 (p) cc_final: 0.8599 (t)
REVERT: B  531 ASN cc_start: 0.8534 (m-40) cc_final: 0.7661 (t0)
REVERT: B  579 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8414 (mt0)
REVERT: B  584 PHE cc_start: 0.8765 (m-80) cc_final: 0.8519 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.0762
  time to fit residues: 30.6731
Evaluate side-chains
  175 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 98 optimal weight:    5.9990
   chunk 112 optimal weight:    3.9990
   chunk 113 optimal weight:    5.9990
   chunk 74 optimal weight:    9.9990
   chunk 106 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9980
   overall best weight:    3.9988

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.124020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.098830 restraints weight = 16002.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.100838 restraints weight = 11482.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.102235 restraints weight = 9223.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.103034 restraints weight = 7965.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.103389 restraints weight = 7265.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  10312  Z= 0.243
  Angle     :  0.679   7.583  14008  Z= 0.341
  Chirality :  0.042   0.135   1588
  Planarity :  0.004   0.040   1742
  Dihedral  :  4.309  20.349   1370
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.88 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.23), residues: 1250
  helix:  0.79 (0.18), residues: 794
  sheet:  0.30 (0.74), residues: 40
  loop : -1.06 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 539 
 TYR   0.017   0.002   TYR B 377 
 PHE   0.024   0.002   PHE A 611 
 TRP   0.018   0.002   TRP A 261 
 HIS   0.006   0.002   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 (10312)
  covalent geometry    : angle       0.67921 (14008)
  hydrogen bonds       : bond        0.04517 (  614)
  hydrogen bonds       : angle       4.10993 ( 1806)

*********************** 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
  223 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8471 (mt) cc_final: 0.7997 (tp)
REVERT: A  217 TYR cc_start: 0.8899 (t80) cc_final: 0.8686 (t80)
REVERT: A  270 TYR cc_start: 0.8908 (t80) cc_final: 0.8496 (t80)
REVERT: A  308 TYR cc_start: 0.8224 (p90) cc_final: 0.8000 (p90)
REVERT: A  373 MET cc_start: 0.8244 (ttp) cc_final: 0.7565 (tpp)
REVERT: A  405 LEU cc_start: 0.9512 (tp) cc_final: 0.9186 (tp)
REVERT: A  458 LYS cc_start: 0.8568 (mttt) cc_final: 0.8288 (mttp)
REVERT: A  528 THR cc_start: 0.9253 (p) cc_final: 0.8856 (t)
REVERT: B   81 LEU cc_start: 0.8597 (mt) cc_final: 0.8034 (tp)
REVERT: B   91 GLU cc_start: 0.7658 (pm20) cc_final: 0.7053 (pp20)
REVERT: B   92 CYS cc_start: 0.7229 (t) cc_final: 0.6864 (t)
REVERT: B  125 GLN cc_start: 0.8937 (mt0) cc_final: 0.8726 (mt0)
REVERT: B  176 SER cc_start: 0.8540 (p) cc_final: 0.8083 (t)
REVERT: B  217 TYR cc_start: 0.8835 (t80) cc_final: 0.8555 (t80)
REVERT: B  373 MET cc_start: 0.8397 (ttp) cc_final: 0.7895 (tpp)
REVERT: B  453 TYR cc_start: 0.8946 (t80) cc_final: 0.8680 (t80)
REVERT: B  528 THR cc_start: 0.9279 (p) cc_final: 0.8829 (t)
REVERT: B  579 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8476 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.0734
  time to fit residues: 25.9425
Evaluate side-chains
  161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 89 optimal weight:    9.9990
   chunk 78 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 110 optimal weight:    0.9980
   chunk 113 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 130 HIS
A 390 HIS
A 504 GLN
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 570 ASN ** 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 = 0.3466 r_free = 0.3466 target = 0.130361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.105934 restraints weight = 15479.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.107981 restraints weight = 11168.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.109209 restraints weight = 8992.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.110279 restraints weight = 7799.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.110836 restraints weight = 7085.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10312  Z= 0.118
  Angle     :  0.507   6.437  14008  Z= 0.261
  Chirality :  0.037   0.144   1588
  Planarity :  0.003   0.038   1742
  Dihedral  :  4.014  17.383   1370
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.24 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.24), residues: 1250
  helix:  1.40 (0.18), residues: 788
  sheet:  0.88 (0.76), residues: 40
  loop : -0.76 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 539 
 TYR   0.019   0.001   TYR B 308 
 PHE   0.029   0.001   PHE B 407 
 TRP   0.049   0.002   TRP A 186 
 HIS   0.006   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (10312)
  covalent geometry    : angle       0.50670 (14008)
  hydrogen bonds       : bond        0.03680 (  614)
  hydrogen bonds       : angle       3.87365 ( 1806)

*********************** 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
  230 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8598 (mt) cc_final: 0.8071 (tp)
REVERT: A  187 TYR cc_start: 0.7353 (m-10) cc_final: 0.7009 (m-10)
REVERT: A  217 TYR cc_start: 0.8681 (t80) cc_final: 0.8336 (t80)
REVERT: A  270 TYR cc_start: 0.8774 (t80) cc_final: 0.8415 (t80)
REVERT: A  373 MET cc_start: 0.8162 (ttp) cc_final: 0.7560 (tpp)
REVERT: A  405 LEU cc_start: 0.9379 (tp) cc_final: 0.9151 (tp)
REVERT: A  458 LYS cc_start: 0.8552 (mttt) cc_final: 0.8310 (mttp)
REVERT: A  528 THR cc_start: 0.9025 (p) cc_final: 0.8437 (t)
REVERT: A  531 ASN cc_start: 0.8408 (m-40) cc_final: 0.7537 (t0)
REVERT: A  606 LYS cc_start: 0.9267 (ttmm) cc_final: 0.8877 (ttmt)
REVERT: B   81 LEU cc_start: 0.8601 (mt) cc_final: 0.8039 (tp)
REVERT: B   91 GLU cc_start: 0.7624 (pm20) cc_final: 0.6976 (pp20)
REVERT: B  176 SER cc_start: 0.8561 (p) cc_final: 0.8111 (t)
REVERT: B  217 TYR cc_start: 0.8592 (t80) cc_final: 0.8189 (t80)
REVERT: B  237 TRP cc_start: 0.8457 (m-10) cc_final: 0.7944 (m-90)
REVERT: B  270 TYR cc_start: 0.8919 (t80) cc_final: 0.8491 (t80)
REVERT: B  373 MET cc_start: 0.8343 (ttp) cc_final: 0.7906 (tpp)
REVERT: B  453 TYR cc_start: 0.8894 (t80) cc_final: 0.8593 (t80)
REVERT: B  528 THR cc_start: 0.9221 (p) cc_final: 0.8565 (t)
REVERT: B  579 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8558 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.0728
  time to fit residues: 26.4980
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  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 3 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 110 optimal weight:    0.6980
   chunk 85 optimal weight:    0.6980
   chunk 59 optimal weight:    6.9990
   chunk 95 optimal weight:   30.0000
   overall best weight:    3.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 250 ASN ** 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 = 0.3418 r_free = 0.3418 target = 0.126047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.101967 restraints weight = 15780.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.103909 restraints weight = 11400.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.105025 restraints weight = 9170.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.105933 restraints weight = 7993.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.105933 restraints weight = 7216.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.3660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10312  Z= 0.194
  Angle     :  0.602   8.888  14008  Z= 0.301
  Chirality :  0.040   0.143   1588
  Planarity :  0.004   0.037   1742
  Dihedral  :  4.054  16.770   1370
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.32 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.24), residues: 1250
  helix:  1.47 (0.18), residues: 794
  sheet:  1.09 (0.81), residues: 40
  loop : -0.66 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 539 
 TYR   0.021   0.002   TYR A 187 
 PHE   0.026   0.002   PHE B 611 
 TRP   0.019   0.001   TRP A 186 
 HIS   0.005   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (10312)
  covalent geometry    : angle       0.60163 (14008)
  hydrogen bonds       : bond        0.04011 (  614)
  hydrogen bonds       : angle       3.89781 ( 1806)

*********************** 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
  214 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8506 (mt) cc_final: 0.8000 (tp)
REVERT: A  217 TYR cc_start: 0.8747 (t80) cc_final: 0.8491 (t80)
REVERT: A  235 PHE cc_start: 0.6677 (t80) cc_final: 0.6353 (t80)
REVERT: A  270 TYR cc_start: 0.8867 (t80) cc_final: 0.8508 (t80)
REVERT: A  373 MET cc_start: 0.8227 (ttp) cc_final: 0.7585 (tpp)
REVERT: A  405 LEU cc_start: 0.9503 (tp) cc_final: 0.9259 (tp)
REVERT: A  458 LYS cc_start: 0.8573 (mttt) cc_final: 0.8319 (mttp)
REVERT: A  528 THR cc_start: 0.9179 (p) cc_final: 0.8693 (t)
REVERT: A  627 LEU cc_start: 0.8837 (tp) cc_final: 0.8618 (tt)
REVERT: B   81 LEU cc_start: 0.8567 (mt) cc_final: 0.8005 (tp)
REVERT: B  217 TYR cc_start: 0.8726 (t80) cc_final: 0.8423 (t80)
REVERT: B  237 TRP cc_start: 0.8452 (m-10) cc_final: 0.8154 (m-10)
REVERT: B  270 TYR cc_start: 0.8940 (t80) cc_final: 0.8552 (t80)
REVERT: B  373 MET cc_start: 0.8365 (ttp) cc_final: 0.7941 (tpp)
REVERT: B  453 TYR cc_start: 0.8961 (t80) cc_final: 0.8625 (t80)
REVERT: B  528 THR cc_start: 0.9186 (p) cc_final: 0.8705 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.0739
  time to fit residues: 24.9906
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  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   chunk 43 optimal weight:    0.6980
   chunk 121 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 95 optimal weight:   20.0000
   overall best weight:    3.1388

-------------------------------------------------------------------------------
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**
** 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 = 0.3435 r_free = 0.3435 target = 0.127184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.102562 restraints weight = 15948.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.104495 restraints weight = 11416.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.105887 restraints weight = 9185.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.106880 restraints weight = 7892.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.107612 restraints weight = 7105.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10312  Z= 0.201
  Angle     :  0.622  10.806  14008  Z= 0.314
  Chirality :  0.041   0.296   1588
  Planarity :  0.004   0.038   1742
  Dihedral  :  4.115  15.744   1370
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.56 %
    Favored  : 97.28 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.24), residues: 1250
  helix:  1.58 (0.19), residues: 790
  sheet:  1.06 (0.84), residues: 40
  loop : -0.74 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 539 
 TYR   0.021   0.002   TYR A 187 
 PHE   0.032   0.002   PHE B 407 
 TRP   0.059   0.002   TRP A 186 
 HIS   0.005   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (10312)
  covalent geometry    : angle       0.62202 (14008)
  hydrogen bonds       : bond        0.04138 (  614)
  hydrogen bonds       : angle       3.98141 ( 1806)

*********************** 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
  212 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.394 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8519 (mt) cc_final: 0.8048 (tp)
REVERT: A  217 TYR cc_start: 0.8750 (t80) cc_final: 0.8448 (t80)
REVERT: A  270 TYR cc_start: 0.8842 (t80) cc_final: 0.8464 (t80)
REVERT: A  308 TYR cc_start: 0.8144 (p90) cc_final: 0.7941 (p90)
REVERT: A  373 MET cc_start: 0.8356 (ttm) cc_final: 0.7739 (tpp)
REVERT: A  458 LYS cc_start: 0.8613 (mttt) cc_final: 0.8317 (mttp)
REVERT: A  528 THR cc_start: 0.9185 (p) cc_final: 0.8613 (t)
REVERT: A  531 ASN cc_start: 0.8631 (m-40) cc_final: 0.7793 (t0)
REVERT: B   81 LEU cc_start: 0.8584 (mt) cc_final: 0.8030 (tp)
REVERT: B   91 GLU cc_start: 0.7689 (pm20) cc_final: 0.7088 (pp20)
REVERT: B   92 CYS cc_start: 0.7209 (t) cc_final: 0.6865 (t)
REVERT: B  217 TYR cc_start: 0.8718 (t80) cc_final: 0.8408 (t80)
REVERT: B  270 TYR cc_start: 0.8983 (t80) cc_final: 0.8562 (t80)
REVERT: B  373 MET cc_start: 0.8312 (ttp) cc_final: 0.7899 (tpp)
REVERT: B  453 TYR cc_start: 0.8892 (t80) cc_final: 0.8575 (t80)
REVERT: B  458 LYS cc_start: 0.8609 (mttt) cc_final: 0.8295 (mttp)
REVERT: B  528 THR cc_start: 0.9089 (p) cc_final: 0.8527 (t)
REVERT: B  531 ASN cc_start: 0.8380 (m-40) cc_final: 0.7693 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.0713
  time to fit residues: 24.0801
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  : 0.388 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 62 optimal weight:   10.0000
   chunk 110 optimal weight:    0.7980
   chunk 68 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 121 optimal weight:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 64 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    3.1588

-------------------------------------------------------------------------------
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**
B 130 HIS
** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.117898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.094218 restraints weight = 16308.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.095863 restraints weight = 12114.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.097133 restraints weight = 9910.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.097734 restraints weight = 8668.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.098349 restraints weight = 7999.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10312  Z= 0.198
  Angle     :  0.612   7.580  14008  Z= 0.308
  Chirality :  0.040   0.176   1588
  Planarity :  0.004   0.037   1742
  Dihedral  :  4.102  15.448   1370
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.56 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.24), residues: 1250
  helix:  1.57 (0.18), residues: 792
  sheet:  0.99 (0.86), residues: 40
  loop : -0.73 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 201 
 TYR   0.020   0.002   TYR B 308 
 PHE   0.025   0.002   PHE A 521 
 TRP   0.023   0.002   TRP A 272 
 HIS   0.005   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (10312)
  covalent geometry    : angle       0.61184 (14008)
  hydrogen bonds       : bond        0.04018 (  614)
  hydrogen bonds       : angle       3.95403 ( 1806)

*********************** 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
  210 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8521 (mt) cc_final: 0.8071 (tp)
REVERT: A  217 TYR cc_start: 0.8718 (t80) cc_final: 0.8430 (t80)
REVERT: A  270 TYR cc_start: 0.8859 (t80) cc_final: 0.8411 (t80)
REVERT: A  373 MET cc_start: 0.8362 (ttm) cc_final: 0.7715 (tpp)
REVERT: A  458 LYS cc_start: 0.8669 (mttt) cc_final: 0.8364 (mttp)
REVERT: A  528 THR cc_start: 0.9227 (p) cc_final: 0.8562 (t)
REVERT: A  531 ASN cc_start: 0.8919 (m-40) cc_final: 0.7872 (t0)
REVERT: B  121 MET cc_start: 0.7535 (tpp) cc_final: 0.7249 (tpp)
REVERT: B  217 TYR cc_start: 0.8710 (t80) cc_final: 0.8410 (t80)
REVERT: B  270 TYR cc_start: 0.8973 (t80) cc_final: 0.8548 (t80)
REVERT: B  373 MET cc_start: 0.8384 (ttp) cc_final: 0.7920 (tpp)
REVERT: B  405 LEU cc_start: 0.9489 (tp) cc_final: 0.9253 (tp)
REVERT: B  427 LYS cc_start: 0.8182 (pttt) cc_final: 0.7927 (tptp)
REVERT: B  458 LYS cc_start: 0.8647 (mttt) cc_final: 0.8312 (mttp)
REVERT: B  528 THR cc_start: 0.9204 (p) cc_final: 0.8731 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.0740
  time to fit residues: 24.4719
Evaluate side-chains
  161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 106 optimal weight:    7.9990
   chunk 116 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 82 optimal weight:    3.9990
   chunk 118 optimal weight:    8.9990
   chunk 62 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   chunk 45 optimal weight:    0.1980
   chunk 74 optimal weight:    0.6980
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** B 250 ASN ** 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 = 0.3449 r_free = 0.3449 target = 0.128437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.104166 restraints weight = 15520.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.106234 restraints weight = 11090.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.107642 restraints weight = 8867.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.108404 restraints weight = 7637.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.109224 restraints weight = 6961.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.4153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10312  Z= 0.149
  Angle     :  0.568   7.861  14008  Z= 0.288
  Chirality :  0.039   0.218   1588
  Planarity :  0.003   0.037   1742
  Dihedral  :  3.979  15.871   1370
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.00 %
    Favored  : 97.84 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.24), residues: 1250
  helix:  1.69 (0.18), residues: 792
  sheet:  0.96 (0.85), residues: 40
  loop : -0.72 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 539 
 TYR   0.025   0.001   TYR B 453 
 PHE   0.030   0.002   PHE B 407 
 TRP   0.019   0.001   TRP B 261 
 HIS   0.005   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (10312)
  covalent geometry    : angle       0.56830 (14008)
  hydrogen bonds       : bond        0.03850 (  614)
  hydrogen bonds       : angle       3.91813 ( 1806)

*********************** 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
  201 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8539 (mt) cc_final: 0.8038 (tp)
REVERT: A  217 TYR cc_start: 0.8651 (t80) cc_final: 0.8329 (t80)
REVERT: A  270 TYR cc_start: 0.8799 (t80) cc_final: 0.8402 (t80)
REVERT: A  373 MET cc_start: 0.8315 (ttm) cc_final: 0.7596 (tpp)
REVERT: A  528 THR cc_start: 0.9181 (p) cc_final: 0.8567 (t)
REVERT: B   81 LEU cc_start: 0.8281 (mp) cc_final: 0.7570 (tp)
REVERT: B  217 TYR cc_start: 0.8586 (t80) cc_final: 0.8234 (t80)
REVERT: B  270 TYR cc_start: 0.8941 (t80) cc_final: 0.8489 (t80)
REVERT: B  373 MET cc_start: 0.8319 (ttp) cc_final: 0.7881 (tpp)
REVERT: B  458 LYS cc_start: 0.8659 (mttt) cc_final: 0.8420 (mttp)
REVERT: B  528 THR cc_start: 0.9205 (p) cc_final: 0.8567 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0746
  time to fit residues: 24.2170
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  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 54 optimal weight:    0.3980
   chunk 31 optimal weight:    3.9990
   chunk 94 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0770
   chunk 58 optimal weight:    7.9990
   chunk 121 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 72 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    2.0942

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

Flipped N/Q/H residues before XYZ refinement:
A 390 HIS
A 581 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.127237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.102075 restraints weight = 15788.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.104176 restraints weight = 11193.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.105477 restraints weight = 8879.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.106659 restraints weight = 7652.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.107096 restraints weight = 6886.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.4262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10312  Z= 0.151
  Angle     :  0.564   8.834  14008  Z= 0.285
  Chirality :  0.039   0.181   1588
  Planarity :  0.004   0.036   1742
  Dihedral  :  3.958  15.711   1370
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.48 %
    Favored  : 97.36 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.24), residues: 1250
  helix:  1.79 (0.18), residues: 786
  sheet:  1.04 (0.86), residues: 40
  loop : -0.72 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  78 
 TYR   0.021   0.001   TYR B 453 
 PHE   0.018   0.001   PHE B 611 
 TRP   0.020   0.001   TRP B 342 
 HIS   0.005   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (10312)
  covalent geometry    : angle       0.56445 (14008)
  hydrogen bonds       : bond        0.03750 (  614)
  hydrogen bonds       : angle       3.88442 ( 1806)

*********************** 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
  199 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.424 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8671 (mt) cc_final: 0.8174 (tp)
REVERT: A  217 TYR cc_start: 0.8620 (t80) cc_final: 0.8245 (t80)
REVERT: A  270 TYR cc_start: 0.8839 (t80) cc_final: 0.8358 (t80)
REVERT: A  371 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7555 (tp30)
REVERT: A  373 MET cc_start: 0.8366 (ttm) cc_final: 0.7591 (tpp)
REVERT: A  528 THR cc_start: 0.9276 (p) cc_final: 0.8730 (t)
REVERT: B   81 LEU cc_start: 0.8408 (mp) cc_final: 0.7693 (tp)
REVERT: B  217 TYR cc_start: 0.8547 (t80) cc_final: 0.8160 (t80)
REVERT: B  270 TYR cc_start: 0.8915 (t80) cc_final: 0.8417 (t80)
REVERT: B  371 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7652 (tp30)
REVERT: B  373 MET cc_start: 0.8439 (ttp) cc_final: 0.7793 (tpp)
REVERT: B  528 THR cc_start: 0.9303 (p) cc_final: 0.8745 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.0696
  time to fit residues: 22.3939
Evaluate side-chains
  153 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 65 optimal weight:    0.0270
   chunk 37 optimal weight:    0.6980
   chunk 51 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 62 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   chunk 110 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    1.3242

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.121791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.099369 restraints weight = 15930.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.100888 restraints weight = 12056.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.101936 restraints weight = 10077.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.102560 restraints weight = 8955.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.102771 restraints weight = 8278.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.4393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10312  Z= 0.122
  Angle     :  0.541   9.811  14008  Z= 0.274
  Chirality :  0.038   0.136   1588
  Planarity :  0.003   0.038   1742
  Dihedral  :  3.870  15.228   1370
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.16 %
    Favored  : 97.68 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.24), residues: 1250
  helix:  1.87 (0.18), residues: 788
  sheet:  1.36 (0.86), residues: 40
  loop : -0.62 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.022   0.001   TYR B 308 
 PHE   0.026   0.001   PHE B 407 
 TRP   0.020   0.001   TRP B 261 
 HIS   0.005   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (10312)
  covalent geometry    : angle       0.54121 (14008)
  hydrogen bonds       : bond        0.03601 (  614)
  hydrogen bonds       : angle       3.85181 ( 1806)

********************** 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
  202 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A   70 TYR cc_start: 0.7020 (m-80) cc_final: 0.6605 (m-80)
REVERT: A   81 LEU cc_start: 0.8586 (mt) cc_final: 0.8047 (tp)
REVERT: A  169 GLN cc_start: 0.7759 (pm20) cc_final: 0.7474 (pm20)
REVERT: A  217 TYR cc_start: 0.8563 (t80) cc_final: 0.8219 (t80)
REVERT: A  373 MET cc_start: 0.8260 (ttm) cc_final: 0.7513 (tpp)
REVERT: A  528 THR cc_start: 0.9206 (p) cc_final: 0.8642 (t)
REVERT: B   81 LEU cc_start: 0.8291 (mp) cc_final: 0.7631 (tt)
REVERT: B  217 TYR cc_start: 0.8415 (t80) cc_final: 0.8036 (t80)
REVERT: B  270 TYR cc_start: 0.8846 (t80) cc_final: 0.8421 (t80)
REVERT: B  373 MET cc_start: 0.8331 (ttp) cc_final: 0.7778 (tpp)
REVERT: B  453 TYR cc_start: 0.8976 (t80) cc_final: 0.8631 (t80)
REVERT: B  507 TYR cc_start: 0.9061 (m-80) cc_final: 0.8833 (m-80)
REVERT: B  528 THR cc_start: 0.9260 (p) cc_final: 0.8718 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.0685
  time to fit residues: 22.3795
Evaluate side-chains
  158 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   chunk 108 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 87 optimal weight:    7.9990
   chunk 94 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 104 optimal weight:    5.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 581 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.120487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.096310 restraints weight = 16378.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.098024 restraints weight = 11966.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.099342 restraints weight = 9764.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.100000 restraints weight = 8536.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.100636 restraints weight = 7863.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.4268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.076  10312  Z= 0.353
  Angle     :  0.799   8.484  14008  Z= 0.400
  Chirality :  0.046   0.142   1588
  Planarity :  0.005   0.036   1742
  Dihedral  :  4.506  20.421   1370
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.00 %
    Favored  : 95.84 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.24), residues: 1250
  helix:  1.35 (0.18), residues: 786
  sheet:  1.09 (0.88), residues: 40
  loop : -0.95 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 618 
 TYR   0.024   0.002   TYR B 453 
 PHE   0.028   0.003   PHE A 611 
 TRP   0.014   0.002   TRP A 237 
 HIS   0.007   0.002   HIS B 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00811 (10312)
  covalent geometry    : angle       0.79911 (14008)
  hydrogen bonds       : bond        0.04727 (  614)
  hydrogen bonds       : angle       4.28741 ( 1806)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1488.55 seconds
wall clock time: 26 minutes 34.14 seconds (1594.14 seconds total)