Starting phenix.real_space_refine
on Fri Sep 11 14:32:39 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6r7y_4747/09_2026/6r7y_4747.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6r7y_4747/09_2026/6r7y_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6r7y_4747/09_2026/6r7y_4747.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6r7y_4747/09_2026/6r7y_4747.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6r7y_4747/09_2026/6r7y_4747.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6r7y_4747/09_2026/6r7y_4747.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6r7y_4747/09_2026/6r7y_4747.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6r7y_4747/09_2026/6r7y_4747.map"
  }
  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-2.2.1-6174/lib/python3.11/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: 4.79, per 1000 atoms: 0.48
  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: 0.53
  Conformation dependent library (CDL) restraints added in 229.5 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: 0.18
  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: 1.54

  Time building geometry restraints manager: 0.72 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: 0.02
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:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.490
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
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/Z
  covalent geometry    : bond        0.01027 /  0.46 (10312)
  covalent geometry    : angle       1.06885 /  0.60 (14008)
  hydrogen bonds       : bond        0.19555 / 12.66 (  614)
  hydrogen bonds       : angle       6.58939 /  4.55 ( 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  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 GLU cc_start: 0.7665 (tt0) cc_final: 0.7376 (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: 0.8157 (m)
REVERT: A  308 TYR cc_start: 0.8504 (p90) cc_final: 0.8090 (p90)
REVERT: A  334 MET cc_start: 0.7969 (mmm) cc_final: 0.7549 (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: 0.8320 (t0)
REVERT: A  576 MET cc_start: 0.7968 (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: 0.7637 (tt0) cc_final: 0.7396 (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: 0.8746 (mt0)
REVERT: B  176 SER cc_start: 0.8624 (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: 0.7673 (mmt)
REVERT: B  373 MET cc_start: 0.8512 (ttp) cc_final: 0.7785 (tpp)
REVERT: B  431 GLN cc_start: 0.7993 (mt0) cc_final: 0.7791 (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: 0.0924
  time to fit residues: 43.1632
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  : 0.316 
-------------------------------------------------------------------------------
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...
** 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: 0.8432
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/Z
  covalent geometry    : bond        0.00282 /  0.13 (10312)
  covalent geometry    : angle       0.54522 /  0.28 (14008)
  hydrogen bonds       : bond        0.04247 /  2.72 (  614)
  hydrogen bonds       : angle       4.16671 /  2.90 ( 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  : 0.427 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8553 (mt) cc_final: 0.8096 (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: 0.7297 (tpp)
REVERT: A  125 GLN cc_start: 0.8741 (mt0) cc_final: 0.8495 (mt0)
REVERT: A  176 SER cc_start: 0.8613 (p) cc_final: 0.8205 (t)
REVERT: A  183 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7772 (mt-10)
REVERT: A  217 TYR cc_start: 0.8891 (t80) cc_final: 0.8616 (t80)
REVERT: A  373 MET cc_start: 0.8317 (ttp) cc_final: 0.7499 (tpp)
REVERT: A  377 TYR cc_start: 0.8815 (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: 0.8223 (tp)
REVERT: B  125 GLN cc_start: 0.8804 (mt0) cc_final: 0.8585 (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: 0.8633 (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: 0.7426 (t80)
REVERT: B  373 MET cc_start: 0.8417 (ttp) cc_final: 0.7874 (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: 0.0633
  time to fit residues: 25.6935
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  : 0.436 
-------------------------------------------------------------------------------
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...
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 = 0.3380 r_free = 0.3380 target = 0.123189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.097261 restraints weight = 16142.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.099499 restraints weight = 11313.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.100978 restraints weight = 8945.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.101799 restraints weight = 7679.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.102548 restraints weight = 6954.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  10312  Z= 0.243
  Angle     :  0.676   7.448  14008  Z= 0.339
  Chirality :  0.042   0.136   1588
  Planarity :  0.004   0.040   1742
  Dihedral  :  4.281  20.343   1370
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.80 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  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:  0.22 (0.23), residues: 1250
  helix:  0.80 (0.18), residues: 794
  sheet:  0.32 (0.75), residues: 40
  loop : -1.05 (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   0.005   0.002   HIS B 459 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00550 /  0.24 (10312)
  covalent geometry    : angle       0.67558 /  0.34 (14008)
  hydrogen bonds       : bond        0.04499 /  2.90 (  614)
  hydrogen bonds       : angle       4.09793 /  2.86 ( 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
  221 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8611 (mt) cc_final: 0.8124 (tp)
REVERT: A  121 MET cc_start: 0.7991 (tpp) cc_final: 0.7781 (tpp)
REVERT: A  217 TYR cc_start: 0.8884 (t80) cc_final: 0.8638 (t80)
REVERT: A  270 TYR cc_start: 0.8946 (t80) cc_final: 0.8466 (t80)
REVERT: A  373 MET cc_start: 0.8361 (ttp) cc_final: 0.7598 (tpp)
REVERT: A  405 LEU cc_start: 0.9367 (tp) cc_final: 0.9046 (tp)
REVERT: A  458 LYS cc_start: 0.8480 (mttt) cc_final: 0.8202 (mttp)
REVERT: A  528 THR cc_start: 0.9322 (p) cc_final: 0.8939 (t)
REVERT: A  576 MET cc_start: 0.7983 (mtt) cc_final: 0.7783 (mtp)
REVERT: B   81 LEU cc_start: 0.8742 (mt) cc_final: 0.8214 (tp)
REVERT: B   91 GLU cc_start: 0.7740 (pm20) cc_final: 0.7124 (pp20)
REVERT: B   92 CYS cc_start: 0.7408 (t) cc_final: 0.7111 (m)
REVERT: B  121 MET cc_start: 0.8029 (tpp) cc_final: 0.7762 (tpp)
REVERT: B  176 SER cc_start: 0.8665 (p) cc_final: 0.8207 (t)
REVERT: B  217 TYR cc_start: 0.8800 (t80) cc_final: 0.8501 (t80)
REVERT: B  373 MET cc_start: 0.8540 (ttp) cc_final: 0.7895 (tpp)
REVERT: B  405 LEU cc_start: 0.9363 (tp) cc_final: 0.9084 (tp)
REVERT: B  453 TYR cc_start: 0.8978 (t80) cc_final: 0.8706 (t80)
REVERT: B  579 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8471 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.0650
  time to fit residues: 22.9792
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  : 0.370 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 89 optimal weight:    9.9990
   chunk 78 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 110 optimal weight:    0.5980
   chunk 113 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.130251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.105732 restraints weight = 15473.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.108017 restraints weight = 10862.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.109574 restraints weight = 8554.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.110515 restraints weight = 7267.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.111052 restraints weight = 6545.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.3462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10312  Z= 0.117
  Angle     :  0.511   7.367  14008  Z= 0.264
  Chirality :  0.037   0.143   1588
  Planarity :  0.004   0.038   1742
  Dihedral  :  4.027  17.485   1370
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.16 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  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:  0.88 (0.24), residues: 1250
  helix:  1.33 (0.18), residues: 790
  sheet:  0.85 (0.76), residues: 40
  loop : -0.82 (0.30), residues: 420

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   0.030   0.001   PHE B 407 
 TRP   0.042   0.002   TRP A 186 
 HIS   0.006   0.001   HIS B 459 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 (10312)
  covalent geometry    : angle       0.51134 /  0.26 (14008)
  hydrogen bonds       : bond        0.03752 /  2.40 (  614)
  hydrogen bonds       : angle       3.89457 /  2.73 ( 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  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8521 (mt) cc_final: 0.7998 (tp)
REVERT: A  187 TYR cc_start: 0.7471 (m-10) cc_final: 0.7135 (m-10)
REVERT: A  217 TYR cc_start: 0.8688 (t80) cc_final: 0.8352 (t80)
REVERT: A  270 TYR cc_start: 0.8782 (t80) cc_final: 0.8436 (t80)
REVERT: A  373 MET cc_start: 0.8132 (ttp) cc_final: 0.7529 (tpp)
REVERT: A  458 LYS cc_start: 0.8562 (mttt) cc_final: 0.8361 (mttp)
REVERT: A  528 THR cc_start: 0.9016 (p) cc_final: 0.8456 (t)
REVERT: A  531 ASN cc_start: 0.8402 (m-40) cc_final: 0.7554 (t0)
REVERT: A  576 MET cc_start: 0.7688 (mtt) cc_final: 0.7477 (mtp)
REVERT: A  606 LYS cc_start: 0.9265 (ttmm) cc_final: 0.8903 (ttmt)
REVERT: B   81 LEU cc_start: 0.8536 (mt) cc_final: 0.7987 (tp)
REVERT: B   91 GLU cc_start: 0.7518 (pm20) cc_final: 0.6891 (pp20)
REVERT: B  121 MET cc_start: 0.7697 (tpp) cc_final: 0.7464 (tpp)
REVERT: B  176 SER cc_start: 0.8537 (p) cc_final: 0.8077 (t)
REVERT: B  217 TYR cc_start: 0.8586 (t80) cc_final: 0.8226 (t80)
REVERT: B  237 TRP cc_start: 0.8423 (m-10) cc_final: 0.7943 (m-90)
REVERT: B  241 ASP cc_start: 0.7420 (p0) cc_final: 0.7185 (p0)
REVERT: B  270 TYR cc_start: 0.8932 (t80) cc_final: 0.8535 (t80)
REVERT: B  373 MET cc_start: 0.8301 (ttp) cc_final: 0.7875 (tpp)
REVERT: B  453 TYR cc_start: 0.8878 (t80) cc_final: 0.8592 (t80)
REVERT: B  528 THR cc_start: 0.9199 (p) cc_final: 0.8538 (t)
REVERT: B  579 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8470 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.0684
  time to fit residues: 24.7570
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  : 0.390 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 39 optimal weight:    0.8980
   chunk 22 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 3 optimal weight:    0.0770
   chunk 53 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 110 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 95 optimal weight:   20.0000
   overall best weight:    1.7944

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 130 HIS
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.128866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.104603 restraints weight = 15558.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.106669 restraints weight = 11090.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.107945 restraints weight = 8810.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.109069 restraints weight = 7598.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.109509 restraints weight = 6856.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.3623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10312  Z= 0.135
  Angle     :  0.534   8.694  14008  Z= 0.269
  Chirality :  0.038   0.142   1588
  Planarity :  0.003   0.036   1742
  Dihedral  :  3.907  16.772   1370
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.32 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  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:  1.19 (0.24), residues: 1250
  helix:  1.50 (0.18), residues: 796
  sheet:  1.09 (0.81), residues: 40
  loop : -0.57 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 539 
 TYR   0.020   0.001   TYR B 377 
 PHE   0.024   0.001   PHE B 611 
 TRP   0.015   0.001   TRP A 261 
 HIS   0.005   0.001   HIS B 459 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.13 (10312)
  covalent geometry    : angle       0.53409 /  0.27 (14008)
  hydrogen bonds       : bond        0.03710 /  2.38 (  614)
  hydrogen bonds       : angle       3.82237 /  2.68 ( 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
  220 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8533 (mt) cc_final: 0.7995 (tp)
REVERT: A  217 TYR cc_start: 0.8665 (t80) cc_final: 0.8379 (t80)
REVERT: A  235 PHE cc_start: 0.6554 (t80) cc_final: 0.6326 (t80)
REVERT: A  270 TYR cc_start: 0.8744 (t80) cc_final: 0.8447 (t80)
REVERT: A  373 MET cc_start: 0.8187 (ttp) cc_final: 0.7500 (tpp)
REVERT: A  458 LYS cc_start: 0.8571 (mttt) cc_final: 0.8364 (mttp)
REVERT: A  528 THR cc_start: 0.9127 (p) cc_final: 0.8677 (t)
REVERT: B   81 LEU cc_start: 0.8537 (mt) cc_final: 0.7950 (tp)
REVERT: B   91 GLU cc_start: 0.7522 (pm20) cc_final: 0.6957 (pp20)
REVERT: B  121 MET cc_start: 0.7718 (tpp) cc_final: 0.7350 (tpp)
REVERT: B  125 GLN cc_start: 0.8537 (mt0) cc_final: 0.7852 (mt0)
REVERT: B  217 TYR cc_start: 0.8581 (t80) cc_final: 0.8217 (t80)
REVERT: B  237 TRP cc_start: 0.8395 (m-10) cc_final: 0.7977 (m-10)
REVERT: B  241 ASP cc_start: 0.7437 (p0) cc_final: 0.7156 (p0)
REVERT: B  270 TYR cc_start: 0.8885 (t80) cc_final: 0.8561 (t80)
REVERT: B  373 MET cc_start: 0.8317 (ttp) cc_final: 0.7876 (tpp)
REVERT: B  453 TYR cc_start: 0.8914 (t80) cc_final: 0.8583 (t80)
REVERT: B  528 THR cc_start: 0.9180 (p) cc_final: 0.8549 (t)
REVERT: B  579 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8504 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0652
  time to fit residues: 23.0576
Evaluate side-chains
  169 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 57 optimal weight:    0.6980
   chunk 82 optimal weight:    5.9990
   chunk 81 optimal weight:    0.6980
   chunk 1 optimal weight:    6.9990
   chunk 91 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 121 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 95 optimal weight:   20.0000
   overall best weight:    1.2384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 441 GLN
** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.131537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.107446 restraints weight = 15512.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.109669 restraints weight = 10881.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.111226 restraints weight = 8526.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.112004 restraints weight = 7263.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.112871 restraints weight = 6558.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.3908

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= 0.118
  Angle     :  0.512   8.496  14008  Z= 0.261
  Chirality :  0.037   0.136   1588
  Planarity :  0.003   0.035   1742
  Dihedral  :  3.813  15.679   1370
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.00 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  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:  1.49 (0.24), residues: 1250
  helix:  1.76 (0.18), residues: 790
  sheet:  1.25 (0.83), residues: 40
  loop : -0.50 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 539 
 TYR   0.023   0.001   TYR A 187 
 PHE   0.031   0.002   PHE A 407 
 TRP   0.049   0.001   TRP A 186 
 HIS   0.005   0.001   HIS B 459 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 (10312)
  covalent geometry    : angle       0.51231 /  0.26 (14008)
  hydrogen bonds       : bond        0.03591 /  2.30 (  614)
  hydrogen bonds       : angle       3.78016 /  2.64 ( 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
  221 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8623 (mt) cc_final: 0.8098 (tp)
REVERT: A  125 GLN cc_start: 0.8762 (mt0) cc_final: 0.8380 (mt0)
REVERT: A  217 TYR cc_start: 0.8512 (t80) cc_final: 0.8131 (t80)
REVERT: A  373 MET cc_start: 0.8283 (ttp) cc_final: 0.7540 (tpp)
REVERT: A  458 LYS cc_start: 0.8559 (mttt) cc_final: 0.8321 (mttp)
REVERT: A  528 THR cc_start: 0.9179 (p) cc_final: 0.8444 (t)
REVERT: A  531 ASN cc_start: 0.8674 (m-40) cc_final: 0.7764 (t0)
REVERT: A  606 LYS cc_start: 0.9205 (ttmm) cc_final: 0.8853 (ttmt)
REVERT: A  633 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8191 (mm-30)
REVERT: B   81 LEU cc_start: 0.8619 (mt) cc_final: 0.8070 (tp)
REVERT: B   91 GLU cc_start: 0.7561 (pm20) cc_final: 0.6922 (pp20)
REVERT: B  121 MET cc_start: 0.7806 (tpp) cc_final: 0.7483 (tpp)
REVERT: B  217 TYR cc_start: 0.8431 (t80) cc_final: 0.8090 (t80)
REVERT: B  237 TRP cc_start: 0.8207 (m-10) cc_final: 0.7814 (m-10)
REVERT: B  241 ASP cc_start: 0.7469 (p0) cc_final: 0.7174 (p0)
REVERT: B  270 TYR cc_start: 0.8906 (t80) cc_final: 0.8555 (t80)
REVERT: B  373 MET cc_start: 0.8380 (ttp) cc_final: 0.7847 (tpp)
REVERT: B  528 THR cc_start: 0.9292 (p) cc_final: 0.8713 (t)
REVERT: B  579 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8585 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.0705
  time to fit residues: 24.6837
Evaluate side-chains
  167 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 5 optimal weight:    0.5980
   chunk 62 optimal weight:   10.0000
   chunk 110 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 121 optimal weight:    0.7980
   chunk 46 optimal weight:   10.0000
   chunk 64 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    2.0784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 130 HIS
** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.128787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.104302 restraints weight = 15584.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.106219 restraints weight = 11276.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.107677 restraints weight = 9111.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.108171 restraints weight = 7881.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.108878 restraints weight = 7327.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.3990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10312  Z= 0.147
  Angle     :  0.554   7.127  14008  Z= 0.278
  Chirality :  0.039   0.185   1588
  Planarity :  0.003   0.035   1742
  Dihedral  :  3.845  15.408   1370
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.24 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  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:  1.52 (0.24), residues: 1250
  helix:  1.76 (0.18), residues: 796
  sheet:  1.23 (0.85), residues: 40
  loop : -0.45 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 539 
 TYR   0.021   0.001   TYR B 377 
 PHE   0.023   0.002   PHE A 611 
 TRP   0.015   0.001   TRP A 186 
 HIS   0.005   0.001   HIS B 459 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.15 (10312)
  covalent geometry    : angle       0.55450 /  0.28 (14008)
  hydrogen bonds       : bond        0.03704 /  2.38 (  614)
  hydrogen bonds       : angle       3.75745 /  2.63 ( 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
  211 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8478 (mt) cc_final: 0.7983 (tp)
REVERT: A  121 MET cc_start: 0.7599 (tpp) cc_final: 0.7316 (tpp)
REVERT: A  217 TYR cc_start: 0.8572 (t80) cc_final: 0.8277 (t80)
REVERT: A  259 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7727 (mm-30)
REVERT: A  270 TYR cc_start: 0.8752 (t80) cc_final: 0.8444 (t80)
REVERT: A  373 MET cc_start: 0.8230 (ttp) cc_final: 0.7608 (tpp)
REVERT: A  528 THR cc_start: 0.9140 (p) cc_final: 0.8427 (t)
REVERT: A  531 ASN cc_start: 0.8917 (m-40) cc_final: 0.7768 (t0)
REVERT: B   81 LEU cc_start: 0.8533 (mt) cc_final: 0.7977 (tt)
REVERT: B   91 GLU cc_start: 0.7623 (pm20) cc_final: 0.7083 (pp20)
REVERT: B  217 TYR cc_start: 0.8547 (t80) cc_final: 0.8201 (t80)
REVERT: B  270 TYR cc_start: 0.8910 (t80) cc_final: 0.8549 (t80)
REVERT: B  371 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7663 (tp30)
REVERT: B  373 MET cc_start: 0.8313 (ttp) cc_final: 0.7859 (tpp)
REVERT: B  458 LYS cc_start: 0.8601 (mttt) cc_final: 0.8313 (mttp)
REVERT: B  528 THR cc_start: 0.9245 (p) cc_final: 0.8668 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.0692
  time to fit residues: 23.4267
Evaluate side-chains
  166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 106 optimal weight:    7.9990
   chunk 116 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   chunk 118 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 45 optimal weight:   20.0000
   chunk 74 optimal weight:   10.0000
   overall best weight:    3.5990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.125111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.100812 restraints weight = 15890.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.102712 restraints weight = 11565.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.103742 restraints weight = 9409.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.104706 restraints weight = 8289.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.105072 restraints weight = 7595.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  10312  Z= 0.222
  Angle     :  0.645   7.813  14008  Z= 0.324
  Chirality :  0.041   0.156   1588
  Planarity :  0.004   0.036   1742
  Dihedral  :  4.087  15.520   1370
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.24 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  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:  1.20 (0.24), residues: 1250
  helix:  1.58 (0.18), residues: 792
  sheet:  0.97 (0.84), residues: 40
  loop : -0.72 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 618 
 TYR   0.022   0.002   TYR B 377 
 PHE   0.027   0.002   PHE A 521 
 TRP   0.014   0.002   TRP A 186 
 HIS   0.005   0.001   HIS B 459 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00514 /  0.22 (10312)
  covalent geometry    : angle       0.64478 /  0.32 (14008)
  hydrogen bonds       : bond        0.04195 /  2.72 (  614)
  hydrogen bonds       : angle       3.96442 /  2.77 ( 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
  208 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8470 (mt) cc_final: 0.7972 (tt)
REVERT: A  121 MET cc_start: 0.7622 (tpp) cc_final: 0.7372 (tpp)
REVERT: A  217 TYR cc_start: 0.8713 (t80) cc_final: 0.8497 (t80)
REVERT: A  259 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7799 (mm-30)
REVERT: A  270 TYR cc_start: 0.8848 (t80) cc_final: 0.8535 (t80)
REVERT: A  373 MET cc_start: 0.8392 (ttm) cc_final: 0.7760 (tpp)
REVERT: A  405 LEU cc_start: 0.9516 (tp) cc_final: 0.9232 (tp)
REVERT: A  427 LYS cc_start: 0.8256 (pttt) cc_final: 0.7984 (tptp)
REVERT: A  507 TYR cc_start: 0.9062 (m-80) cc_final: 0.8847 (m-80)
REVERT: A  528 THR cc_start: 0.9149 (p) cc_final: 0.8580 (t)
REVERT: B   81 LEU cc_start: 0.8534 (mt) cc_final: 0.7997 (tt)
REVERT: B  217 TYR cc_start: 0.8685 (t80) cc_final: 0.8412 (t80)
REVERT: B  270 TYR cc_start: 0.8966 (t80) cc_final: 0.8571 (t80)
REVERT: B  373 MET cc_start: 0.8347 (ttp) cc_final: 0.7791 (tpp)
REVERT: B  427 LYS cc_start: 0.8145 (pttt) cc_final: 0.7892 (tptp)
REVERT: B  528 THR cc_start: 0.9267 (p) cc_final: 0.8741 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.0704
  time to fit residues: 23.4168
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  : 0.387 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 94 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 121 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 72 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    2.3788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.127325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.103560 restraints weight = 15728.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.105364 restraints weight = 11648.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.106496 restraints weight = 9501.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.107460 restraints weight = 8303.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.107880 restraints weight = 7554.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.4208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10312  Z= 0.166
  Angle     :  0.593  11.216  14008  Z= 0.298
  Chirality :  0.039   0.168   1588
  Planarity :  0.004   0.036   1742
  Dihedral  :  4.022  16.874   1370
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.56 %
    Favored  : 97.28 %
  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:  1.31 (0.24), residues: 1250
  helix:  1.66 (0.18), residues: 792
  sheet:  1.09 (0.87), residues: 40
  loop : -0.67 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 618 
 TYR   0.021   0.001   TYR B 308 
 PHE   0.034   0.002   PHE A 611 
 TRP   0.016   0.001   TRP B 261 
 HIS   0.005   0.001   HIS B 459 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00385 /  0.17 (10312)
  covalent geometry    : angle       0.59335 /  0.30 (14008)
  hydrogen bonds       : bond        0.03877 /  2.50 (  614)
  hydrogen bonds       : angle       3.90281 /  2.72 ( 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
  203 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.394 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8528 (mt) cc_final: 0.8073 (tp)
REVERT: A  121 MET cc_start: 0.7584 (tpp) cc_final: 0.7315 (tpp)
REVERT: A  217 TYR cc_start: 0.8635 (t80) cc_final: 0.8332 (t80)
REVERT: A  259 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7755 (mm-30)
REVERT: A  270 TYR cc_start: 0.8839 (t80) cc_final: 0.8433 (t80)
REVERT: A  373 MET cc_start: 0.8309 (ttm) cc_final: 0.7627 (tpp)
REVERT: A  528 THR cc_start: 0.9176 (p) cc_final: 0.8549 (t)
REVERT: B   81 LEU cc_start: 0.8590 (mt) cc_final: 0.8068 (tp)
REVERT: B  217 TYR cc_start: 0.8568 (t80) cc_final: 0.8200 (t80)
REVERT: B  270 TYR cc_start: 0.8906 (t80) cc_final: 0.8519 (t80)
REVERT: B  373 MET cc_start: 0.8328 (ttp) cc_final: 0.7768 (tpp)
REVERT: B  427 LYS cc_start: 0.8124 (pttt) cc_final: 0.7799 (tptp)
REVERT: B  528 THR cc_start: 0.9269 (p) cc_final: 0.8800 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.0692
  time to fit residues: 22.6446
Evaluate side-chains
  159 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 62 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9980
   chunk 58 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 110 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   overall best weight:    0.9384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.130503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.106666 restraints weight = 15462.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.108614 restraints weight = 11200.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.109942 restraints weight = 9032.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.110696 restraints weight = 7837.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.111334 restraints weight = 7153.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.4408

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= 0.116
  Angle     :  0.555  11.097  14008  Z= 0.276
  Chirality :  0.038   0.196   1588
  Planarity :  0.003   0.035   1742
  Dihedral  :  3.873  15.075   1370
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.40 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.45 (0.24), residues: 1250
  helix:  1.78 (0.19), residues: 794
  sheet:  0.51 (0.88), residues: 40
  loop : -0.55 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 539 
 TYR   0.019   0.001   TYR A 187 
 PHE   0.031   0.002   PHE A 611 
 TRP   0.020   0.001   TRP B 261 
 HIS   0.005   0.001   HIS B 459 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 (10312)
  covalent geometry    : angle       0.55538 /  0.28 (14008)
  hydrogen bonds       : bond        0.03569 /  2.30 (  614)
  hydrogen bonds       : angle       3.81927 /  2.69 ( 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
  203 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A   81 LEU cc_start: 0.8603 (mt) cc_final: 0.8127 (tt)
REVERT: A  121 MET cc_start: 0.7510 (tpp) cc_final: 0.7216 (tpp)
REVERT: A  217 TYR cc_start: 0.8424 (t80) cc_final: 0.8099 (t80)
REVERT: A  259 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7621 (mm-30)
REVERT: A  371 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7813 (tp30)
REVERT: A  373 MET cc_start: 0.8312 (ttm) cc_final: 0.7531 (tpp)
REVERT: A  528 THR cc_start: 0.9221 (p) cc_final: 0.8624 (t)
REVERT: B   81 LEU cc_start: 0.8699 (mt) cc_final: 0.8215 (tt)
REVERT: B  169 GLN cc_start: 0.7759 (pm20) cc_final: 0.7534 (pm20)
REVERT: B  217 TYR cc_start: 0.8406 (t80) cc_final: 0.8076 (t80)
REVERT: B  373 MET cc_start: 0.8350 (ttp) cc_final: 0.7680 (tpp)
REVERT: B  528 THR cc_start: 0.9302 (p) cc_final: 0.8816 (t)
REVERT: B  608 ILE cc_start: 0.9301 (mt) cc_final: 0.9060 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.0708
  time to fit residues: 23.2461
Evaluate side-chains
  166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 108 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 94 optimal weight:   10.0000
   chunk 6 optimal weight:    8.9990
   chunk 56 optimal weight:    1.9990
   chunk 104 optimal weight:    5.9990
   overall best weight:    2.3990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.128670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.104194 restraints weight = 15745.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.106239 restraints weight = 11325.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.107574 restraints weight = 9074.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.108599 restraints weight = 7833.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.109134 restraints weight = 7105.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.4429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10312  Z= 0.169
  Angle     :  0.616  11.213  14008  Z= 0.311
  Chirality :  0.040   0.187   1588
  Planarity :  0.004   0.035   1742
  Dihedral  :  4.008  18.509   1370
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.72 %
    Favored  : 97.12 %
  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:  1.43 (0.24), residues: 1250
  helix:  1.80 (0.19), residues: 790
  sheet: -0.92 (1.15), residues: 20
  loop : -0.51 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 201 
 TYR   0.020   0.001   TYR A 187 
 PHE   0.030   0.002   PHE B 407 
 TRP   0.058   0.003   TRP B 186 
 HIS   0.005   0.001   HIS B 459 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.17 (10312)
  covalent geometry    : angle       0.61624 /  0.31 (14008)
  hydrogen bonds       : bond        0.03916 /  2.52 (  614)
  hydrogen bonds       : angle       3.84934 /  2.69 ( 1806)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1461.81 seconds
wall clock time: 26 minutes 5.54 seconds (1565.54 seconds total)