Starting phenix.real_space_refine
on Mon Jul 28 06:14:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yet_39203/07_2025/8yet_39203.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yet_39203/07_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_39203/07_2025/8yet_39203.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yet_39203/07_2025/8yet_39203.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yet_39203/07_2025/8yet_39203.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yet_39203/07_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-5711/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: 6.93, per 1000 atoms: 0.69
  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: 2.55
  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: 0.75
  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: 2.68

  Time building geometry restraints manager: 3.02 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:             2.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.350
  Find NCS groups from input model:        0.350
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.230
-------------------------------------------------------------------------------
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  10394  Z= 0.161
  Angle     :  0.742  11.741  14116  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10982 (  693)
  hydrogen bonds       : angle       4.66064 ( 2064)
  SS BOND              : bond        0.00053 (    2)
  SS BOND              : angle       1.40445 (    4)
  covalent geometry    : bond        0.00334 (10392)
  covalent geometry    : angle       0.74129 (14112)

*********************** 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  : 1.157 
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: 0.2060
  time to fit residues: 50.9104
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  : 1.154 
-------------------------------------------------------------------------------
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 = 0.131179 restraints weight = 17401.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.131348 restraints weight = 15590.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.132501 restraints weight = 12132.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
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  10394  Z= 0.123
  Angle     :  0.564   8.873  14116  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04359 (  693)
  hydrogen bonds       : angle       3.66393 ( 2064)
  SS BOND              : bond        0.00106 (    2)
  SS BOND              : angle       0.92315 (    4)
  covalent geometry    : bond        0.00258 (10392)
  covalent geometry    : angle       0.56387 (14112)

*********************** 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  : 1.274 
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: 0.8267 (mmm) cc_final: 0.7844 (ttm)
REVERT: A  575 ILE cc_start: 0.8695 (tp) cc_final: 0.8297 (tt)
REVERT: B   25 PHE cc_start: 0.7172 (m-80) cc_final: 0.6720 (m-80)
REVERT: B  195 ILE cc_start: 0.7044 (pt) cc_final: 0.6746 (pt)
REVERT: B  383 THR cc_start: 0.7212 (p) cc_final: 0.6899 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 179
  average time/residue: 0.1991
  time to fit residues: 52.3169
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  : 1.028 
-------------------------------------------------------------------------------
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:    0.8980
   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:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 71 optimal weight:    9.9990
   chunk 83 optimal weight:    2.9990
   chunk 110 optimal weight:    0.7980
   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 = 0.158909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.128865 restraints weight = 17462.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.131547 restraints weight = 20392.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.133192 restraints weight = 12355.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.1107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10394  Z= 0.128
  Angle     :  0.577   9.300  14116  Z= 0.292
  Chirality :  0.040   0.196   1532
  Planarity :  0.003   0.052   1744
  Dihedral  : 15.620 122.099   1408
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.51 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.82 %
    Favored  : 96.09 %
  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 : -1.24 (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   0.023   0.001   PHE A  51 
 TYR   0.017   0.001   TYR A  73 
 ARG   0.006   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04391 (  693)
  hydrogen bonds       : angle       3.58580 ( 2064)
  SS BOND              : bond        0.00208 (    2)
  SS BOND              : angle       1.68814 (    4)
  covalent geometry    : bond        0.00275 (10392)
  covalent geometry    : angle       0.57636 (14112)

*********************** 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  : 1.047 
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  195 ILE cc_start: 0.7171 (pt) cc_final: 0.6957 (pt)
REVERT: A  489 MET cc_start: 0.8341 (mmm) cc_final: 0.7951 (ttm)
REVERT: A  575 ILE cc_start: 0.8674 (tp) cc_final: 0.8216 (tt)
REVERT: B   25 PHE cc_start: 0.7081 (m-80) cc_final: 0.6668 (m-80)
REVERT: B  145 LEU cc_start: 0.9272 (mt) cc_final: 0.9014 (mt)
REVERT: B  195 ILE cc_start: 0.6937 (pt) cc_final: 0.6659 (pt)
REVERT: B  215 MET cc_start: 0.4673 (mtm) cc_final: 0.4471 (mtm)
  outliers start: 1
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1972
  time to fit residues: 50.8774
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  : 1.179 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 87 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 98 optimal weight:    1.9990
   chunk 92 optimal weight:    0.2980
   chunk 11 optimal weight:    8.9990
   chunk 119 optimal weight:    0.6980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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**
B 387 HIS
B 401 ASN
B 452 GLN
** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 618 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.157036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.126900 restraints weight = 17628.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.129782 restraints weight = 20588.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.130902 restraints weight = 12142.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10394  Z= 0.142
  Angle     :  0.586   9.822  14116  Z= 0.298
  Chirality :  0.040   0.192   1532
  Planarity :  0.003   0.044   1744
  Dihedral  : 15.275 119.502   1408
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.76 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.79 %
    Favored  : 97.11 %
  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:  1.49 (0.25), residues: 1198
  helix:  1.75 (0.17), residues: 904
  sheet:  None (None), residues: 0
  loop : -1.45 (0.39), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 607 
 HIS   0.004   0.001   HIS B 476 
 PHE   0.024   0.001   PHE A 511 
 TYR   0.016   0.002   TYR B 518 
 ARG   0.004   0.000   ARG B 548 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04511 (  693)
  hydrogen bonds       : angle       3.62876 ( 2064)
  SS BOND              : bond        0.00090 (    2)
  SS BOND              : angle       1.13321 (    4)
  covalent geometry    : bond        0.00318 (10392)
  covalent geometry    : angle       0.58603 (14112)

*********************** 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
  177 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 176
  time to evaluate  : 1.080 
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: 0.9069 (mttp) cc_final: 0.8577 (mttt)
REVERT: A  152 ASN cc_start: 0.7966 (m-40) cc_final: 0.7607 (m-40)
REVERT: A  195 ILE cc_start: 0.7241 (pt) cc_final: 0.6990 (pt)
REVERT: A  489 MET cc_start: 0.8400 (mmm) cc_final: 0.7817 (ttm)
REVERT: B   25 PHE cc_start: 0.7146 (m-80) cc_final: 0.6744 (m-80)
REVERT: B  145 LEU cc_start: 0.9310 (mt) cc_final: 0.9020 (mt)
REVERT: B  195 ILE cc_start: 0.6983 (pt) cc_final: 0.6698 (pt)
REVERT: B  383 THR cc_start: 0.7207 (p) cc_final: 0.6879 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1887
  time to fit residues: 49.1670
Evaluate side-chains
  125 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0020
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 97 optimal weight:    0.6980
   chunk 4 optimal weight:    4.9990
   chunk 56 optimal weight:    0.1980
   chunk 28 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.4988

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.159937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.129701 restraints weight = 17311.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.131566 restraints weight = 20225.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.133546 restraints weight = 12609.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10394  Z= 0.115
  Angle     :  0.564  10.299  14116  Z= 0.284
  Chirality :  0.040   0.264   1532
  Planarity :  0.003   0.038   1744
  Dihedral  : 14.837 117.240   1408
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.42 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  2.23 %
    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:  1.60 (0.25), residues: 1198
  helix:  1.84 (0.17), residues: 904
  sheet:  None (None), residues: 0
  loop : -1.46 (0.39), residues: 294

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   0.023   0.001   PHE B  54 
 TYR   0.018   0.001   TYR B  50 
 ARG   0.001   0.000   ARG B 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04168 (  693)
  hydrogen bonds       : angle       3.51211 ( 2064)
  SS BOND              : bond        0.00165 (    2)
  SS BOND              : angle       1.03624 (    4)
  covalent geometry    : bond        0.00242 (10392)
  covalent geometry    : angle       0.56428 (14112)

*********************** 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
  176 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 173
  time to evaluate  : 1.173 
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: 0.7904 (m-40) cc_final: 0.7636 (m-40)
REVERT: A  195 ILE cc_start: 0.7162 (pt) cc_final: 0.6945 (pt)
REVERT: A  489 MET cc_start: 0.8376 (mmm) cc_final: 0.7787 (ttm)
REVERT: A  575 ILE cc_start: 0.8760 (tp) cc_final: 0.8383 (tt)
REVERT: B   25 PHE cc_start: 0.7157 (m-80) cc_final: 0.6765 (m-80)
REVERT: B   27 ASP cc_start: 0.8161 (m-30) cc_final: 0.7775 (m-30)
REVERT: B  145 LEU cc_start: 0.9303 (mt) cc_final: 0.9074 (mt)
REVERT: B  195 ILE cc_start: 0.6959 (pt) cc_final: 0.6710 (pt)
REVERT: B  383 THR cc_start: 0.7104 (p) cc_final: 0.6730 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 175
  average time/residue: 0.1949
  time to fit residues: 50.3797
Evaluate side-chains
  129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 111 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 212 GLN
A 499 HIS
B 387 HIS
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.147398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.119812 restraints weight = 18387.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.117518 restraints weight = 15862.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.119249 restraints weight = 17134.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  10394  Z= 0.259
  Angle     :  0.735  11.402  14116  Z= 0.389
  Chirality :  0.046   0.200   1532
  Planarity :  0.005   0.054   1744
  Dihedral  : 14.556 114.394   1408
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.59 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  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:  0.73 (0.24), residues: 1198
  helix:  1.22 (0.17), residues: 904
  sheet:  None (None), residues: 0
  loop : -1.79 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 607 
 HIS   0.003   0.001   HIS A 163 
 PHE   0.024   0.003   PHE A  25 
 TYR   0.025   0.002   TYR B 483 
 ARG   0.003   0.001   ARG B 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06294 (  693)
  hydrogen bonds       : angle       4.14950 ( 2064)
  SS BOND              : bond        0.00209 (    2)
  SS BOND              : angle       2.61105 (    4)
  covalent geometry    : bond        0.00596 (10392)
  covalent geometry    : angle       0.73393 (14112)

*********************** 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
  169 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 1.042 
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  152 ASN cc_start: 0.8204 (m-40) cc_final: 0.7703 (m-40)
REVERT: A  398 ASP cc_start: 0.8426 (m-30) cc_final: 0.7973 (t0)
REVERT: A  408 MET cc_start: 0.8405 (tpt) cc_final: 0.8050 (tpt)
REVERT: B   27 ASP cc_start: 0.8358 (m-30) cc_final: 0.7950 (m-30)
REVERT: B  195 ILE cc_start: 0.7157 (pt) cc_final: 0.6924 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1870
  time to fit residues: 46.4187
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  : 1.028 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4040 r_free = 0.4040 target = 0.154916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.127194 restraints weight = 17786.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.126992 restraints weight = 14112.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.128175 restraints weight = 13305.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10394  Z= 0.142
  Angle     :  0.617  11.457  14116  Z= 0.316
  Chirality :  0.042   0.228   1532
  Planarity :  0.004   0.039   1744
  Dihedral  : 14.173 112.377   1408
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.01 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  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:  1.13 (0.25), residues: 1198
  helix:  1.50 (0.17), residues: 906
  sheet:  None (None), residues: 0
  loop : -1.63 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B 476 
 PHE   0.024   0.002   PHE A  25 
 TYR   0.020   0.002   TYR B 483 
 ARG   0.002   0.000   ARG B 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04988 (  693)
  hydrogen bonds       : angle       3.76005 ( 2064)
  SS BOND              : bond        0.00114 (    2)
  SS BOND              : angle       1.64165 (    4)
  covalent geometry    : bond        0.00310 (10392)
  covalent geometry    : angle       0.61615 (14112)

*********************** 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
  171 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ASN cc_start: 0.8200 (m-40) cc_final: 0.7870 (m-40)
REVERT: A  489 MET cc_start: 0.8223 (mmm) cc_final: 0.7883 (ttm)
REVERT: B   27 ASP cc_start: 0.8338 (m-30) cc_final: 0.8055 (m-30)
REVERT: B  195 ILE cc_start: 0.7015 (pt) cc_final: 0.6749 (pt)
REVERT: B  383 THR cc_start: 0.6970 (p) cc_final: 0.6634 (p)
REVERT: B  496 TYR cc_start: 0.6954 (t80) cc_final: 0.6725 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.1780
  time to fit residues: 45.3906
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  : 1.067 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 112 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0040
   chunk 67 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.7194

-------------------------------------------------------------------------------
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**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.157066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.129606 restraints weight = 17634.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.126292 restraints weight = 13779.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.127936 restraints weight = 14254.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10394  Z= 0.138
  Angle     :  0.608  11.601  14116  Z= 0.314
  Chirality :  0.042   0.233   1532
  Planarity :  0.004   0.040   1744
  Dihedral  : 13.903 111.047   1408
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.43 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  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:  1.12 (0.25), residues: 1198
  helix:  1.50 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.72 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 607 
 HIS   0.002   0.001   HIS B 476 
 PHE   0.036   0.002   PHE A 156 
 TYR   0.022   0.002   TYR B 483 
 ARG   0.009   0.000   ARG B 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04745 (  693)
  hydrogen bonds       : angle       3.72854 ( 2064)
  SS BOND              : bond        0.00077 (    2)
  SS BOND              : angle       1.32162 (    4)
  covalent geometry    : bond        0.00300 (10392)
  covalent geometry    : angle       0.60722 (14112)

*********************** 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
  174 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 1.021 
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: A   95 LEU cc_start: 0.9509 (mt) cc_final: 0.9105 (pp)
REVERT: A  152 ASN cc_start: 0.8367 (m-40) cc_final: 0.8135 (m-40)
REVERT: A  489 MET cc_start: 0.8229 (mmm) cc_final: 0.7941 (ttm)
REVERT: B   25 PHE cc_start: 0.7392 (m-80) cc_final: 0.6967 (m-80)
REVERT: B   27 ASP cc_start: 0.8405 (m-30) cc_final: 0.8003 (m-30)
REVERT: B   95 LEU cc_start: 0.9122 (mm) cc_final: 0.8907 (pp)
REVERT: B  195 ILE cc_start: 0.7141 (pt) cc_final: 0.6891 (pt)
REVERT: B  383 THR cc_start: 0.6922 (p) cc_final: 0.6607 (p)
REVERT: B  496 TYR cc_start: 0.7027 (t80) cc_final: 0.6790 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.1733
  time to fit residues: 45.7510
Evaluate side-chains
  131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.458 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 117 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 115 optimal weight:    0.5980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
A 387 HIS
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.151550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.122938 restraints weight = 18295.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.121635 restraints weight = 16271.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.123067 restraints weight = 16172.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10394  Z= 0.178
  Angle     :  0.662  11.906  14116  Z= 0.345
  Chirality :  0.044   0.222   1532
  Planarity :  0.004   0.037   1744
  Dihedral  : 13.645 109.254   1408
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.76 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  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:  0.98 (0.25), residues: 1198
  helix:  1.39 (0.17), residues: 906
  sheet:  None (None), residues: 0
  loop : -1.68 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 607 
 HIS   0.007   0.001   HIS A 387 
 PHE   0.025   0.002   PHE B  54 
 TYR   0.025   0.002   TYR B 483 
 ARG   0.010   0.000   ARG B 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05261 (  693)
  hydrogen bonds       : angle       3.87894 ( 2064)
  SS BOND              : bond        0.00163 (    2)
  SS BOND              : angle       1.27208 (    4)
  covalent geometry    : bond        0.00405 (10392)
  covalent geometry    : angle       0.66203 (14112)

*********************** 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
  173 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.9342 (mt) cc_final: 0.9043 (pp)
REVERT: A  152 ASN cc_start: 0.8309 (m-40) cc_final: 0.7900 (m-40)
REVERT: A  398 ASP cc_start: 0.8417 (m-30) cc_final: 0.7913 (t0)
REVERT: A  489 MET cc_start: 0.8228 (mmm) cc_final: 0.7816 (ttm)
REVERT: B   25 PHE cc_start: 0.7243 (m-80) cc_final: 0.6846 (m-80)
REVERT: B  195 ILE cc_start: 0.7100 (pt) cc_final: 0.6872 (pt)
REVERT: B  383 THR cc_start: 0.6772 (p) cc_final: 0.6478 (p)
REVERT: B  496 TYR cc_start: 0.7091 (t80) cc_final: 0.6783 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.1734
  time to fit residues: 45.1030
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  : 1.083 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 70 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0870
   overall best weight:    0.6560

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 212 GLN
** 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 = 0.4056 r_free = 0.4056 target = 0.156310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.127157 restraints weight = 17561.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.129800 restraints weight = 16987.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.130840 restraints weight = 10439.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10394  Z= 0.137
  Angle     :  0.635  11.943  14116  Z= 0.326
  Chirality :  0.043   0.241   1532
  Planarity :  0.003   0.035   1744
  Dihedral  : 13.365 107.932   1408
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.18 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  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:  1.07 (0.25), residues: 1198
  helix:  1.46 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.71 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B 163 
 PHE   0.020   0.001   PHE B  54 
 TYR   0.020   0.001   TYR B 483 
 ARG   0.008   0.000   ARG B 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04726 (  693)
  hydrogen bonds       : angle       3.79106 ( 2064)
  SS BOND              : bond        0.00083 (    2)
  SS BOND              : angle       1.24226 (    4)
  covalent geometry    : bond        0.00294 (10392)
  covalent geometry    : angle       0.63485 (14112)

********************** 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
  178 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.9229 (mt) cc_final: 0.8987 (pp)
REVERT: A  137 GLU cc_start: 0.8032 (pp20) cc_final: 0.7530 (tm-30)
REVERT: A  152 ASN cc_start: 0.8200 (m-40) cc_final: 0.7881 (m-40)
REVERT: A  489 MET cc_start: 0.8170 (mmm) cc_final: 0.7885 (ttm)
REVERT: B   25 PHE cc_start: 0.7174 (m-80) cc_final: 0.6780 (m-80)
REVERT: B  195 ILE cc_start: 0.7050 (pt) cc_final: 0.6797 (pt)
REVERT: B  496 TYR cc_start: 0.6947 (t80) cc_final: 0.6608 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1835
  time to fit residues: 48.9820
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  : 1.137 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 116 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 109 optimal weight:    4.9990
   chunk 115 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0070
   overall best weight:    0.9002

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 GLN
** B 462 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 = 0.4056 r_free = 0.4056 target = 0.156357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.129332 restraints weight = 17337.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.127790 restraints weight = 14621.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.129192 restraints weight = 15136.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10394  Z= 0.148
  Angle     :  0.645  11.976  14116  Z= 0.332
  Chirality :  0.043   0.234   1532
  Planarity :  0.004   0.037   1744
  Dihedral  : 13.131 107.019   1408
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.18 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    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:  1.03 (0.25), residues: 1198
  helix:  1.43 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.74 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 292 
 HIS   0.003   0.001   HIS B 499 
 PHE   0.020   0.002   PHE B  54 
 TYR   0.022   0.002   TYR B 483 
 ARG   0.007   0.000   ARG B 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04836 (  693)
  hydrogen bonds       : angle       3.79505 ( 2064)
  SS BOND              : bond        0.00121 (    2)
  SS BOND              : angle       1.18808 (    4)
  covalent geometry    : bond        0.00331 (10392)
  covalent geometry    : angle       0.64465 (14112)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2848.21 seconds
wall clock time: 50 minutes 55.64 seconds (3055.64 seconds total)