Starting phenix.real_space_refine
on Thu Jan 16 23:19:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yet_39203/01_2025/8yet_39203.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yet_39203/01_2025/8yet_39203.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yet_39203/01_2025/8yet_39203.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yet_39203/01_2025/8yet_39203.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yet_39203/01_2025/8yet_39203.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yet_39203/01_2025/8yet_39203.cif"
  }
  resolution = 4.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.047
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
     P      12      5.49       5
     S      42      5.16       5
     C    6618      2.51       5
     N    1652      2.21       5
     O    1778      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 10102
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 603, 5015
          Classifications: {'peptide': 603}
          Link IDs: {'PTRANS': 20, 'TRANS': 582}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 603, 5015
          Classifications: {'peptide': 603}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 582}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 72
          Unusual residues: {'IHP': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.27, per 1000 atoms: 0.62
  Number of scatterers: 10102
  At special positions: 0
  Unit cell: (113.3, 116.6, 108.9, 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)
     S      42     16.00
     P      12     15.00
     O    1778      8.00
     N    1652      7.00
     C    6618      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.97
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2320

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 0 sheets defined
      78.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 11
    Processing helix  chain 'A' and resid 12 through 19
      removed outlier: 6.031A  pdb=" N   LYS A  17 " --> pdb=" O   GLU A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 36
      removed outlier: 3.803A  pdb=" N   ALA A  36 " --> pdb=" O   ALA A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 100
    Processing helix  chain 'A' and resid 119 through 167
    Processing helix  chain 'A' and resid 170 through 180
      removed outlier: 3.613A  pdb=" N   ASP A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 188
    Processing helix  chain 'A' and resid 189 through 206
      removed outlier: 3.649A  pdb=" N   GLN A 193 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 218
    Processing helix  chain 'A' and resid 230 through 258
      removed outlier: 3.654A  pdb=" N   THR A 234 " --> pdb=" O   PRO A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 296
      removed outlier: 4.521A  pdb=" N   ILE A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   PHE A 276 " --> pdb=" O   TYR A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 3.542A  pdb=" N   ILE A 302 " --> pdb=" O   ASN A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 337
      removed outlier: 3.860A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 360
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 391 through 401
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 4.214A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 471
      removed outlier: 3.807A  pdb=" N   ILE A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 476 through 483
      removed outlier: 3.848A  pdb=" N   TYR A 483 " --> pdb=" O   ASN A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 503
      removed outlier: 3.610A  pdb=" N   PHE A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 529
      removed outlier: 3.750A  pdb=" N   PHE A 510 " --> pdb=" O   ASP A 506 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   PHE A 511 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TYR A 512 " --> pdb=" O   MET A 508 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   LEU A 513 " --> pdb=" O   VAL A 509 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   TRP A 514 " --> pdb=" O   PHE A 510 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   TYR A 524 " --> pdb=" O   ILE A 520 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ILE A 527 " --> pdb=" O   CYS A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 583
      removed outlier: 4.319A  pdb=" N   VAL A 567 " --> pdb=" O   ILE A 563 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ILE A 568 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR A 583 " --> pdb=" O   ILE A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 618
      Proline residue:  A 598  - end of helix
      removed outlier: 4.124A  pdb=" N   VAL A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   PHE A 602 " --> pdb=" O   PRO A 598 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU A 617 " --> pdb=" O   GLU A 613 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 10
      removed outlier: 3.589A  pdb=" N   HIS B   6 " --> pdb=" O   LYS B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 36
      removed outlier: 3.643A  pdb=" N   GLN B  35 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ALA B  36 " --> pdb=" O   ALA B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 100
      removed outlier: 3.825A  pdb=" N   VAL B  47 " --> pdb=" O   ASP B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 167
    Processing helix  chain 'B' and resid 170 through 180
    Processing helix  chain 'B' and resid 183 through 188
    Processing helix  chain 'B' and resid 189 through 205
      removed outlier: 3.544A  pdb=" N   GLN B 193 " --> pdb=" O   LYS B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 218
    Processing helix  chain 'B' and resid 230 through 258
      removed outlier: 3.649A  pdb=" N   THR B 234 " --> pdb=" O   PRO B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 296
      removed outlier: 5.287A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
    Processing helix  chain 'B' and resid 312 through 337
      removed outlier: 3.859A  pdb=" N   LEU B 316 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 360
    Processing helix  chain 'B' and resid 367 through 383
    Processing helix  chain 'B' and resid 384 through 387
    Processing helix  chain 'B' and resid 390 through 402
      removed outlier: 3.596A  pdb=" N   TRP B 395 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LEU B 396 " --> pdb=" O   ALA B 392 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   SER B 402 " --> pdb=" O   ASP B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 419
      removed outlier: 4.244A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 471
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 475 through 503
      removed outlier: 4.551A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE B 488 " --> pdb=" O   SER B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 3.820A  pdb=" N   PHE B 510 " --> pdb=" O   ASP B 506 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   PHE B 511 " --> pdb=" O   THR B 507 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TYR B 512 " --> pdb=" O   MET B 508 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LEU B 513 " --> pdb=" O   VAL B 509 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   TYR B 524 " --> pdb=" O   ILE B 520 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ILE B 527 " --> pdb=" O   CYS B 523 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   MET B 532 " --> pdb=" O   TRP B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 583
      removed outlier: 4.359A  pdb=" N   VAL B 567 " --> pdb=" O   ILE B 563 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   ILE B 568 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE B 571 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 618
      removed outlier: 4.529A  pdb=" N   ILE B 591 " --> pdb=" O   HIS B 587 " (cutoff:3.500A)
      Proline residue:  B 598  - end of helix
      removed outlier: 4.141A  pdb=" N   VAL B 601 " --> pdb=" O   ALA B 597 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   PHE B 602 " --> pdb=" O   PRO B 598 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ASN B 608 " --> pdb=" O   ARG B 604 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LEU B 617 " --> pdb=" O   GLU B 613 " (cutoff:3.500A)

    693 hydrogen bonds defined for protein.
    2064 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.73

  Time building geometry restraints manager: 3.30 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: 3086
        1.34 -     1.46: 2286
        1.46 -     1.58: 4946
        1.58 -     1.69: 14
        1.69 -     1.81: 60
  Bond restraints: 10392
  Sorted by residual:
  bond pdb=" O16 IHP A 701 "
       pdb=" P6  IHP A 701 "
    ideal  model  delta    sigma   weight residual
    1.672  1.617  0.055 2.00e-02 2.50e+03 7.57e+00
  bond pdb=" C3  IHP A 701 "
       pdb=" O13 IHP A 701 "
    ideal  model  delta    sigma   weight residual
    1.393  1.343  0.050 2.00e-02 2.50e+03 6.32e+00
  bond pdb=" C3  IHP A 701 "
       pdb=" C4  IHP A 701 "
    ideal  model  delta    sigma   weight residual
    1.535  1.585 -0.050 2.00e-02 2.50e+03 6.24e+00
  bond pdb=" C3  IHP A 702 "
       pdb=" C4  IHP A 702 "
    ideal  model  delta    sigma   weight residual
    1.535  1.584 -0.049 2.00e-02 2.50e+03 6.01e+00
  bond pdb=" O16 IHP A 702 "
       pdb=" P6  IHP A 702 "
    ideal  model  delta    sigma   weight residual
    1.672  1.624  0.048 2.00e-02 2.50e+03 5.64e+00
  ... (remaining 10387 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 13865
        2.35 -     4.70: 174
        4.70 -     7.04: 57
        7.04 -     9.39: 11
        9.39 -    11.74: 5
  Bond angle restraints: 14112
  Sorted by residual:
  angle pdb=" O12 IHP A 702 "
        pdb=" P2  IHP A 702 "
        pdb=" O32 IHP A 702 "
      ideal   model   delta    sigma   weight residual
     100.47  111.70  -11.23 3.00e+00 1.11e-01 1.40e+01
  angle pdb=" O12 IHP A 701 "
        pdb=" P2  IHP A 701 "
        pdb=" O32 IHP A 701 "
      ideal   model   delta    sigma   weight residual
     100.47  111.61  -11.14 3.00e+00 1.11e-01 1.38e+01
  angle pdb=" C   ALA B  78 "
        pdb=" N   GLU B  79 "
        pdb=" CA  GLU B  79 "
      ideal   model   delta    sigma   weight residual
     120.72  114.65    6.07 1.67e+00 3.59e-01 1.32e+01
  angle pdb=" N   GLU B  79 "
        pdb=" CA  GLU B  79 "
        pdb=" CB  GLU B  79 "
      ideal   model   delta    sigma   weight residual
     110.39  116.39   -6.00 1.66e+00 3.63e-01 1.31e+01
  angle pdb=" O13 IHP A 702 "
        pdb=" P3  IHP A 702 "
        pdb=" O43 IHP A 702 "
      ideal   model   delta    sigma   weight residual
     101.78  112.04  -10.26 3.00e+00 1.11e-01 1.17e+01
  ... (remaining 14107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.32: 5704
       26.32 -    52.64: 342
       52.64 -    78.96: 32
       78.96 -   105.29: 12
      105.29 -   131.61: 16
  Dihedral angle restraints: 6106
    sinusoidal: 2526
      harmonic: 3580
  Sorted by residual:
  dihedral pdb=" CB  CYS A 415 "
           pdb=" SG  CYS A 415 "
           pdb=" SG  CYS A 440 "
           pdb=" CB  CYS A 440 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.09  -74.09     1      1.00e+01 1.00e-02 6.97e+01
  dihedral pdb=" CA  CYS B 440 "
           pdb=" C   CYS B 440 "
           pdb=" N   HIS B 441 "
           pdb=" CA  HIS B 441 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.18   26.82     0      5.00e+00 4.00e-02 2.88e+01
  dihedral pdb=" CA  ILE B 342 "
           pdb=" C   ILE B 342 "
           pdb=" N   PRO B 343 "
           pdb=" CA  PRO B 343 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.51  -22.49     0      5.00e+00 4.00e-02 2.02e+01
  ... (remaining 6103 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1411
       0.073 -    0.146: 110
       0.146 -    0.219: 8
       0.219 -    0.293: 1
       0.293 -    0.366: 2
  Chirality restraints: 1532
  Sorted by residual:
  chirality pdb=" C2  IHP A 701 "
            pdb=" C1  IHP A 701 "
            pdb=" C3  IHP A 701 "
            pdb=" O12 IHP A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.15   -0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" C2  IHP A 702 "
            pdb=" C1  IHP A 702 "
            pdb=" C3  IHP A 702 "
            pdb=" O12 IHP A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.22   -0.29 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" C3  IHP A 701 "
            pdb=" C2  IHP A 701 "
            pdb=" C4  IHP A 701 "
            pdb=" O13 IHP A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.34   -2.11   -0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 1529 not shown)

  Planarity restraints: 1744
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 292 "   -0.024 2.00e-02 2.50e+03   1.64e-02 6.74e+00
        pdb=" CG  TRP A 292 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 292 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 292 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 292 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 292 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 292 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 292 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 292 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 292 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 292 "   -0.015 2.00e-02 2.50e+03   1.01e-02 2.54e+00
        pdb=" CG  TRP B 292 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 292 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 292 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 292 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 292 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 292 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 292 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 292 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 292 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 335 "   -0.013 2.00e-02 2.50e+03   1.17e-02 2.41e+00
        pdb=" CG  PHE B 335 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 335 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 335 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 335 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 335 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 335 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1741 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1257
        2.75 -     3.29: 10680
        3.29 -     3.83: 17326
        3.83 -     4.36: 18001
        4.36 -     4.90: 30967
  Nonbonded interactions: 78231
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG B 176 "
            pdb=" OE2 GLU B 181 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" O   HIS A   6 "
            pdb=" ND1 HIS A  10 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" OH  TYR A 345 "
            pdb=" O   TRP A 423 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" NH2 ARG A 273 "
            pdb=" OG1 THR A 594 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" O   TRP B 175 "
            pdb=" ND1 HIS B 179 "
     model   vdw
     2.266 3.120
  ... (remaining 78226 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 1 through 620)
  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:             2.070
  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:          0.300
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.560
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10392  Z= 0.218
  Angle     :  0.741  11.741  14112  Z= 0.343
  Chirality :  0.042   0.366   1532
  Planarity :  0.003   0.029   1744
  Dihedral  : 17.601 131.608   3780
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.84 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.28 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.25), residues: 1198
  helix:  1.65 (0.17), residues: 900
  sheet:  None (None), residues: 0
  loop : -1.51 (0.39), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.001   TRP A 292 
 HIS   0.003   0.001   HIS B 163 
 PHE   0.027   0.001   PHE B 335 
 TYR   0.022   0.001   TYR A  30 
 ARG   0.005   0.000   ARG B 308 

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 172
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 ASP cc_start: 0.8976 (m-30) cc_final: 0.8691 (p0)
REVERT: A  288 ASN cc_start: 0.8231 (m110) cc_final: 0.7674 (m110)
REVERT: B   25 PHE cc_start: 0.7196 (m-80) cc_final: 0.6947 (m-80)
REVERT: B  145 LEU cc_start: 0.9365 (mt) cc_final: 0.9097 (mt)
REVERT: B  215 MET cc_start: 0.4361 (mtm) cc_final: 0.4063 (mtm)
REVERT: B  383 THR cc_start: 0.7313 (p) cc_final: 0.7056 (p)
REVERT: B  575 ILE cc_start: 0.8744 (tp) cc_final: 0.8441 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 172
  average time/residue: 0.2058
  time to fit residues: 50.7340
Evaluate side-chains
  130 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.3980
   chunk 90 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0270
   chunk 48 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 108 optimal weight:    4.9990
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
A 212 GLN
A 387 HIS
A 452 GLN
B 149 GLN
B 387 HIS
B 452 GLN
** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.159421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.131180 restraints weight = 17401.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.131345 restraints weight = 15587.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.132501 restraints weight = 12124.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.0762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10392  Z= 0.166
  Angle     :  0.564   8.873  14112  Z= 0.285
  Chirality :  0.039   0.207   1532
  Planarity :  0.003   0.030   1744
  Dihedral  : 16.172 125.789   1408
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.84 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  5.49 %
    Favored  : 94.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.25), residues: 1198
  helix:  1.85 (0.17), residues: 902
  sheet:  None (None), residues: 0
  loop : -1.34 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 292 
 HIS   0.004   0.001   HIS B 163 
 PHE   0.012   0.001   PHE A  51 
 TYR   0.024   0.001   TYR B 148 
 ARG   0.005   0.000   ARG B 371 

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 178
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  489 MET cc_start: 0.8268 (mmm) cc_final: 0.7843 (ttm)
REVERT: A  575 ILE cc_start: 0.8695 (tp) cc_final: 0.8297 (tt)
REVERT: B   25 PHE cc_start: 0.7171 (m-80) cc_final: 0.6720 (m-80)
REVERT: B  195 ILE cc_start: 0.7047 (pt) cc_final: 0.6749 (pt)
REVERT: B  383 THR cc_start: 0.7212 (p) cc_final: 0.6897 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 179
  average time/residue: 0.1965
  time to fit residues: 51.0846
Evaluate side-chains
  131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 75 optimal weight:    0.5980
   chunk 73 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0370
   chunk 9 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 71 optimal weight:    9.9990
   chunk 83 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9980
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
A 149 GLN
A 387 HIS
A 452 GLN
A 614 ASN
A 618 ASN
B 149 GLN
B 387 HIS
B 452 GLN
** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.158946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.128896 restraints weight = 17451.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.131894 restraints weight = 20062.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.133283 restraints weight = 11766.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.1095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10392  Z= 0.175
  Angle     :  0.573   9.250  14112  Z= 0.290
  Chirality :  0.040   0.196   1532
  Planarity :  0.003   0.052   1744
  Dihedral  : 15.651 122.209   1408
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.59 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.72 %
    Favored  : 96.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.25), residues: 1198
  helix:  1.80 (0.17), residues: 894
  sheet:  None (None), residues: 0
  loop : -1.25 (0.39), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B 476 
 PHE   0.022   0.001   PHE A  51 
 TYR   0.018   0.001   TYR A  73 
 ARG   0.003   0.000   ARG B 570 

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 1.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 ILE cc_start: 0.7188 (pt) cc_final: 0.6976 (pt)
REVERT: A  489 MET cc_start: 0.8357 (mmm) cc_final: 0.7970 (ttm)
REVERT: A  575 ILE cc_start: 0.8666 (tp) cc_final: 0.8211 (tt)
REVERT: B   25 PHE cc_start: 0.7111 (m-80) cc_final: 0.6691 (m-80)
REVERT: B  145 LEU cc_start: 0.9288 (mt) cc_final: 0.9035 (mt)
REVERT: B  195 ILE cc_start: 0.6946 (pt) cc_final: 0.6672 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1942
  time to fit residues: 50.1641
Evaluate side-chains
  124 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 118 optimal weight:    0.0070
   chunk 87 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 119 optimal weight:    0.3980
   overall best weight:    1.2202

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

Flipped N/Q/H residues before XYZ refinement:
A 212 GLN
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 HIS
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 618 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.154990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.124602 restraints weight = 17778.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.126769 restraints weight = 19589.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.128576 restraints weight = 11661.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10392  Z= 0.244
  Angle     :  0.615   9.703  14112  Z= 0.317
  Chirality :  0.041   0.195   1532
  Planarity :  0.004   0.045   1744
  Dihedral  : 15.203 119.088   1408
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.01 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.25), residues: 1198
  helix:  1.61 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop : -1.44 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 607 
 HIS   0.006   0.001   HIS B 476 
 PHE   0.023   0.002   PHE A  51 
 TYR   0.019   0.002   TYR B 518 
 ARG   0.005   0.000   ARG B 548 

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LYS cc_start: 0.9114 (mttp) cc_final: 0.8686 (mttt)
REVERT: A  152 ASN cc_start: 0.8081 (m-40) cc_final: 0.7654 (m-40)
REVERT: A  195 ILE cc_start: 0.7288 (pt) cc_final: 0.7079 (pt)
REVERT: A  489 MET cc_start: 0.8408 (mmm) cc_final: 0.7848 (ttm)
REVERT: B   25 PHE cc_start: 0.7274 (m-80) cc_final: 0.6785 (m-80)
REVERT: B   27 ASP cc_start: 0.8276 (m-30) cc_final: 0.7991 (p0)
REVERT: B  195 ILE cc_start: 0.7009 (pt) cc_final: 0.6772 (pt)
REVERT: B  383 THR cc_start: 0.7202 (p) cc_final: 0.6868 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.1943
  time to fit residues: 48.6154
Evaluate side-chains
  128 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 104 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 61 optimal weight:    0.3980
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    0.5980
   chunk 97 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
A 452 GLN
B 387 HIS
B 452 GLN
B 476 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.157883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.127758 restraints weight = 17545.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.130366 restraints weight = 19383.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.132185 restraints weight = 11215.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10392  Z= 0.170
  Angle     :  0.576  10.247  14112  Z= 0.291
  Chirality :  0.040   0.261   1532
  Planarity :  0.003   0.038   1744
  Dihedral  : 14.660 116.308   1408
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.59 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.33 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.25), residues: 1198
  helix:  1.76 (0.17), residues: 906
  sheet:  None (None), residues: 0
  loop : -1.50 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 607 
 HIS   0.005   0.001   HIS B 476 
 PHE   0.017   0.001   PHE B  54 
 TYR   0.016   0.001   TYR B  50 
 ARG   0.002   0.000   ARG B 548 

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 180
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 ASP cc_start: 0.8341 (m-30) cc_final: 0.8117 (m-30)
REVERT: A  152 ASN cc_start: 0.7891 (m-40) cc_final: 0.7600 (m-40)
REVERT: A  195 ILE cc_start: 0.7208 (pt) cc_final: 0.6969 (pt)
REVERT: A  489 MET cc_start: 0.8386 (mmm) cc_final: 0.7794 (ttm)
REVERT: B   25 PHE cc_start: 0.7163 (m-80) cc_final: 0.6798 (m-80)
REVERT: B   26 LYS cc_start: 0.7989 (tptm) cc_final: 0.6561 (tptt)
REVERT: B   27 ASP cc_start: 0.8182 (m-30) cc_final: 0.7948 (m-30)
REVERT: B  195 ILE cc_start: 0.6968 (pt) cc_final: 0.6731 (pt)
REVERT: B  383 THR cc_start: 0.7135 (p) cc_final: 0.6694 (p)
  outliers start: 2
  outliers final: 2
  residues processed: 182
  average time/residue: 0.2007
  time to fit residues: 53.1823
Evaluate side-chains
  135 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 133
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 111 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 11 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
B 401 ASN
** B 452 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 = 0.4008 r_free = 0.4008 target = 0.151399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.123097 restraints weight = 18069.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.122099 restraints weight = 15726.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.123339 restraints weight = 15933.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10392  Z= 0.286
  Angle     :  0.646  10.881  14112  Z= 0.338
  Chirality :  0.043   0.220   1532
  Planarity :  0.004   0.039   1744
  Dihedral  : 14.434 113.971   1408
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.43 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.25), residues: 1198
  helix:  1.45 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop : -1.74 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B 313 
 PHE   0.016   0.002   PHE A 537 
 TYR   0.029   0.002   TYR A 483 
 ARG   0.004   0.000   ARG B 548 

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ASN cc_start: 0.8149 (m-40) cc_final: 0.7783 (m-40)
REVERT: A  489 MET cc_start: 0.8404 (mmm) cc_final: 0.7806 (ttm)
REVERT: B   25 PHE cc_start: 0.7155 (m-80) cc_final: 0.6711 (m-80)
REVERT: B   26 LYS cc_start: 0.8439 (tptm) cc_final: 0.8182 (tptt)
REVERT: B   27 ASP cc_start: 0.8361 (m-30) cc_final: 0.8140 (m-30)
REVERT: B   30 TYR cc_start: 0.7644 (m-80) cc_final: 0.7277 (m-80)
REVERT: B  195 ILE cc_start: 0.7075 (pt) cc_final: 0.6794 (pt)
REVERT: B  383 THR cc_start: 0.7110 (p) cc_final: 0.6781 (p)
REVERT: B  496 TYR cc_start: 0.6868 (t80) cc_final: 0.6660 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.2101
  time to fit residues: 52.7993
Evaluate side-chains
  133 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 1.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 87 optimal weight:    0.5980
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.156317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.128867 restraints weight = 17739.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.129627 restraints weight = 14951.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.130516 restraints weight = 12991.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10392  Z= 0.194
  Angle     :  0.597  11.212  14112  Z= 0.306
  Chirality :  0.041   0.233   1532
  Planarity :  0.003   0.036   1744
  Dihedral  : 14.042 111.685   1408
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.59 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.25), residues: 1198
  helix:  1.55 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.65 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B 476 
 PHE   0.035   0.001   PHE A 156 
 TYR   0.041   0.002   TYR A 483 
 ARG   0.005   0.000   ARG A 459 

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ASN cc_start: 0.8111 (m-40) cc_final: 0.7910 (m-40)
REVERT: A  489 MET cc_start: 0.8399 (mmm) cc_final: 0.7770 (ttm)
REVERT: B   25 PHE cc_start: 0.7051 (m-80) cc_final: 0.6631 (m-80)
REVERT: B   27 ASP cc_start: 0.8331 (m-30) cc_final: 0.8104 (p0)
REVERT: B  195 ILE cc_start: 0.7067 (pt) cc_final: 0.6791 (pt)
REVERT: B  383 THR cc_start: 0.7024 (p) cc_final: 0.6671 (p)
REVERT: B  496 TYR cc_start: 0.6935 (t80) cc_final: 0.6708 (t80)
REVERT: B  548 ARG cc_start: 0.8275 (ttt180) cc_final: 0.8046 (ttt180)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.2033
  time to fit residues: 55.1936
Evaluate side-chains
  139 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 29 optimal weight:    0.2980
   chunk 112 optimal weight:    0.0050
   chunk 45 optimal weight:    0.0270
   chunk 67 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 34 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.3252

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.159487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.130547 restraints weight = 17345.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.134317 restraints weight = 15947.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.135081 restraints weight = 8705.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10392  Z= 0.158
  Angle     :  0.593  11.446  14112  Z= 0.298
  Chirality :  0.041   0.237   1532
  Planarity :  0.003   0.057   1744
  Dihedral  : 13.801 110.538   1408
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.09 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.25), residues: 1198
  helix:  1.65 (0.17), residues: 906
  sheet:  None (None), residues: 0
  loop : -1.50 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 607 
 HIS   0.002   0.001   HIS A 313 
 PHE   0.032   0.001   PHE A  25 
 TYR   0.030   0.002   TYR A 483 
 ARG   0.007   0.000   ARG B 459 

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ASN cc_start: 0.8071 (m-40) cc_final: 0.7856 (m-40)
REVERT: A  195 ILE cc_start: 0.7238 (pt) cc_final: 0.7035 (pt)
REVERT: B   25 PHE cc_start: 0.6898 (m-80) cc_final: 0.6598 (m-80)
REVERT: B   26 LYS cc_start: 0.7962 (tttt) cc_final: 0.6524 (tttt)
REVERT: B   30 TYR cc_start: 0.7520 (m-80) cc_final: 0.7245 (m-80)
REVERT: B  195 ILE cc_start: 0.7060 (pt) cc_final: 0.6759 (pt)
REVERT: B  383 THR cc_start: 0.7050 (p) cc_final: 0.6583 (p)
REVERT: B  548 ARG cc_start: 0.8202 (ttt180) cc_final: 0.7989 (ttt180)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.1911
  time to fit residues: 50.9693
Evaluate side-chains
  134 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 117 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.151424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.122648 restraints weight = 18305.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.122816 restraints weight = 15830.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.123996 restraints weight = 13771.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10392  Z= 0.272
  Angle     :  0.657  11.902  14112  Z= 0.342
  Chirality :  0.043   0.210   1532
  Planarity :  0.004   0.062   1744
  Dihedral  : 13.665 109.067   1408
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.84 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.25), residues: 1198
  helix:  1.42 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop : -1.57 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 607 
 HIS   0.003   0.001   HIS A 499 
 PHE   0.022   0.002   PHE B  54 
 TYR   0.028   0.002   TYR A 483 
 ARG   0.008   0.000   ARG B 459 

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 PHE cc_start: 0.7627 (m-80) cc_final: 0.7369 (m-80)
REVERT: A   26 LYS cc_start: 0.9124 (mtmm) cc_final: 0.8846 (mtmt)
REVERT: A  152 ASN cc_start: 0.8318 (m-40) cc_final: 0.7912 (m-40)
REVERT: A  489 MET cc_start: 0.8269 (mmm) cc_final: 0.8031 (ttm)
REVERT: B   25 PHE cc_start: 0.7231 (m-80) cc_final: 0.6733 (m-80)
REVERT: B   26 LYS cc_start: 0.8028 (tttt) cc_final: 0.6690 (tttt)
REVERT: B   30 TYR cc_start: 0.7787 (m-80) cc_final: 0.7490 (m-80)
REVERT: B  195 ILE cc_start: 0.7188 (pt) cc_final: 0.6946 (pt)
REVERT: B  383 THR cc_start: 0.7234 (p) cc_final: 0.6897 (p)
REVERT: B  496 TYR cc_start: 0.6750 (t80) cc_final: 0.6380 (t80)
REVERT: B  548 ARG cc_start: 0.8359 (ttt180) cc_final: 0.8102 (ttt180)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1989
  time to fit residues: 51.9693
Evaluate side-chains
  129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 70 optimal weight:    8.9990
   chunk 12 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0070
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0030
   chunk 76 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.5408

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
A 452 GLN
B 387 HIS
B 452 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.158155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.130357 restraints weight = 17562.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.129989 restraints weight = 15504.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.131179 restraints weight = 13885.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10392  Z= 0.172
  Angle     :  0.617  11.909  14112  Z= 0.315
  Chirality :  0.042   0.240   1532
  Planarity :  0.003   0.034   1744
  Dihedral  : 13.367 108.204   1408
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.09 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.25), residues: 1198
  helix:  1.50 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop : -1.49 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B 163 
 PHE   0.017   0.001   PHE B 511 
 TYR   0.028   0.002   TYR A 483 
 ARG   0.007   0.000   ARG B 459 

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LYS cc_start: 0.9060 (mtmm) cc_final: 0.8806 (mtmt)
REVERT: A  137 GLU cc_start: 0.8086 (pp20) cc_final: 0.7572 (tm-30)
REVERT: A  152 ASN cc_start: 0.8262 (m-40) cc_final: 0.7955 (m-40)
REVERT: A  249 ILE cc_start: 0.9165 (tp) cc_final: 0.8862 (mt)
REVERT: A  489 MET cc_start: 0.8182 (mmm) cc_final: 0.7930 (ttm)
REVERT: B   25 PHE cc_start: 0.7197 (m-80) cc_final: 0.6611 (m-80)
REVERT: B   79 GLU cc_start: 0.8335 (pm20) cc_final: 0.7689 (pm20)
REVERT: B  195 ILE cc_start: 0.7098 (pt) cc_final: 0.6835 (pt)
REVERT: B  408 MET cc_start: 0.7983 (tpt) cc_final: 0.7482 (tpt)
REVERT: B  496 TYR cc_start: 0.6602 (t80) cc_final: 0.6280 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1913
  time to fit residues: 52.1540
Evaluate side-chains
  135 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0020
   chunk 116 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 109 optimal weight:    1.9990
   chunk 115 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0870
   chunk 53 optimal weight:    5.9990
   overall best weight:    0.5366

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

Flipped N/Q/H residues before XYZ refinement:
A 212 GLN
A 452 GLN
B 387 HIS
B 452 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.156070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.127948 restraints weight = 17930.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.129317 restraints weight = 15462.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.130119 restraints weight = 11295.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10392  Z= 0.174
  Angle     :  0.619  11.841  14112  Z= 0.315
  Chirality :  0.042   0.237   1532
  Planarity :  0.003   0.033   1744
  Dihedral  : 13.184 107.829   1408
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.34 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.25), residues: 1198
  helix:  1.58 (0.17), residues: 896
  sheet:  None (None), residues: 0
  loop : -1.27 (0.40), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B 163 
 PHE   0.018   0.001   PHE A 511 
 TYR   0.026   0.001   TYR A  30 
 ARG   0.007   0.000   ARG B 459 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2614.24 seconds
wall clock time: 48 minutes 10.26 seconds (2890.26 seconds total)