Starting phenix.real_space_refine
on Sat Nov 16 01:39:27 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yet_39203/11_2024/8yet_39203.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yet_39203/11_2024/8yet_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yet_39203/11_2024/8yet_39203.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yet_39203/11_2024/8yet_39203.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yet_39203/11_2024/8yet_39203.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yet_39203/11_2024/8yet_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-5513/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: 6.00, per 1000 atoms: 0.59
  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: 2.59
  Conformation dependent library (CDL) restraints added in 992.9 milliseconds
  

  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: 2.64

  Time building geometry restraints manager: 2.92 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:             2.050
  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:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.410
  Find NCS groups from input model:        0.390
  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:             0.010
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.370
-------------------------------------------------------------------------------
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  : 1.130 
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: 0.2160
  time to fit residues: 53.7810
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  : 1.212 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
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  : 1.213 
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   25 PHE cc_start: 0.7889 (m-10) cc_final: 0.7608 (m-80)
REVERT: A   27 ASP cc_start: 0.8914 (m-30) cc_final: 0.8674 (p0)
REVERT: A  489 MET cc_start: 0.8326 (mmm) cc_final: 0.7975 (ttm)
REVERT: A  575 ILE cc_start: 0.8636 (tp) cc_final: 0.8261 (tt)
REVERT: B   25 PHE cc_start: 0.7344 (m-80) cc_final: 0.6844 (m-80)
REVERT: B  195 ILE cc_start: 0.7095 (pt) cc_final: 0.6811 (pt)
REVERT: B  383 THR cc_start: 0.7313 (p) cc_final: 0.6974 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 179
  average time/residue: 0.2043
  time to fit residues: 53.1513
Evaluate side-chains
  133 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 109 optimal weight:    0.0770
   chunk 117 optimal weight:    4.9990
   chunk 97 optimal weight:    0.7980
   chunk 108 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 87 optimal weight:    0.4980
   overall best weight:    0.6338

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.1090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10392  Z= 0.168
  Angle     :  0.573   9.247  14112  Z= 0.289
  Chirality :  0.040   0.196   1532
  Planarity :  0.003   0.052   1744
  Dihedral  : 15.638 122.146   1408
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.42 %
    Favored  : 95.41 %
  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:  1.60 (0.25), residues: 1198
  helix:  1.81 (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   0.023   0.001   PHE A  51 
 TYR   0.018   0.001   TYR A  73 
 ARG   0.008   0.000   ARG B 465 

*********************** 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  : 1.060 
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   25 PHE cc_start: 0.7910 (m-10) cc_final: 0.7580 (m-80)
REVERT: A   26 LYS cc_start: 0.9278 (mttp) cc_final: 0.8716 (mttp)
REVERT: A   27 ASP cc_start: 0.8790 (m-30) cc_final: 0.8554 (p0)
REVERT: A  152 ASN cc_start: 0.8337 (m-40) cc_final: 0.8126 (m-40)
REVERT: A  489 MET cc_start: 0.8437 (mmm) cc_final: 0.8115 (ttm)
REVERT: A  575 ILE cc_start: 0.8606 (tp) cc_final: 0.8170 (tt)
REVERT: B   25 PHE cc_start: 0.7397 (m-80) cc_final: 0.6889 (m-80)
REVERT: B   66 LEU cc_start: 0.9432 (tt) cc_final: 0.9223 (tt)
REVERT: B  145 LEU cc_start: 0.9417 (mt) cc_final: 0.9175 (mt)
REVERT: B  195 ILE cc_start: 0.7050 (pt) cc_final: 0.6805 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1997
  time to fit residues: 51.6815
Evaluate side-chains
  127 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0040
   chunk 73 optimal weight:    5.9990
   chunk 109 optimal weight:    0.8980
   chunk 115 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.6794

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.1302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10392  Z= 0.175
  Angle     :  0.570   9.523  14112  Z= 0.288
  Chirality :  0.040   0.188   1532
  Planarity :  0.003   0.043   1744
  Dihedral  : 15.225 119.259   1408
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.01 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.23 %
    Favored  : 97.67 %
  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:  1.81 (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   0.004   0.001   HIS B 476 
 PHE   0.024   0.001   PHE A 511 
 TYR   0.017   0.001   TYR B 518 
 ARG   0.003   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
  176 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 1.111 
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   25 PHE cc_start: 0.7847 (m-10) cc_final: 0.7580 (m-80)
REVERT: A   27 ASP cc_start: 0.8702 (m-30) cc_final: 0.8307 (p0)
REVERT: A  152 ASN cc_start: 0.8376 (m-40) cc_final: 0.8011 (m-40)
REVERT: A  489 MET cc_start: 0.8458 (mmm) cc_final: 0.7954 (ttm)
REVERT: A  575 ILE cc_start: 0.8649 (tp) cc_final: 0.8211 (tt)
REVERT: B   25 PHE cc_start: 0.7426 (m-80) cc_final: 0.6933 (m-80)
REVERT: B   27 ASP cc_start: 0.8593 (m-30) cc_final: 0.8125 (m-30)
REVERT: B  145 LEU cc_start: 0.9433 (mt) cc_final: 0.9175 (mt)
REVERT: B  195 ILE cc_start: 0.7056 (pt) cc_final: 0.6842 (pt)
REVERT: B  383 THR cc_start: 0.7237 (p) cc_final: 0.6902 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 175
  average time/residue: 0.2088
  time to fit residues: 53.4802
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  : 1.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   chunk 80 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 212 GLN
A 288 ASN
** 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**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10392  Z= 0.265
  Angle     :  0.632  10.239  14112  Z= 0.327
  Chirality :  0.042   0.254   1532
  Planarity :  0.004   0.041   1744
  Dihedral  : 14.644 116.344   1408
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.26 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.10 %
    Favored  : 95.72 %
  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:  1.63 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop : -1.44 (0.40), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 607 
 HIS   0.007   0.001   HIS B 476 
 PHE   0.020   0.002   PHE B  54 
 TYR   0.021   0.002   TYR B 483 
 ARG   0.006   0.000   ARG B 465 

*********************** 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
  170 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 168
  time to evaluate  : 1.155 
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: 0.8497 (m-40) cc_final: 0.8157 (m-40)
REVERT: A  408 MET cc_start: 0.8366 (tpt) cc_final: 0.8069 (tpt)
REVERT: A  489 MET cc_start: 0.8497 (mmm) cc_final: 0.8005 (ttm)
REVERT: B   25 PHE cc_start: 0.7516 (m-80) cc_final: 0.7011 (m-80)
REVERT: B   26 LYS cc_start: 0.8410 (tptm) cc_final: 0.7306 (tptt)
REVERT: B   27 ASP cc_start: 0.8571 (m-30) cc_final: 0.8284 (m-30)
REVERT: B  195 ILE cc_start: 0.7104 (pt) cc_final: 0.6881 (pt)
REVERT: B  383 THR cc_start: 0.7277 (p) cc_final: 0.6931 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 170
  average time/residue: 0.2009
  time to fit residues: 50.4670
Evaluate side-chains
  122 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 28 optimal weight:    0.4980
   chunk 116 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 60 optimal weight:    8.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 387 HIS
B 452 GLN
B 476 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10392  Z= 0.226
  Angle     :  0.616  10.850  14112  Z= 0.319
  Chirality :  0.042   0.227   1532
  Planarity :  0.003   0.037   1744
  Dihedral  : 14.374 114.071   1408
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.26 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  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:  1.23 (0.25), residues: 1198
  helix:  1.55 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.57 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 607 
 HIS   0.007   0.001   HIS B 476 
 PHE   0.018   0.002   PHE A  25 
 TYR   0.029   0.002   TYR A 483 
 ARG   0.003   0.000   ARG A 459 

*********************** 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
  179 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.035 
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  152 ASN cc_start: 0.8447 (m-40) cc_final: 0.8046 (m-40)
REVERT: A  489 MET cc_start: 0.8510 (mmm) cc_final: 0.7994 (ttm)
REVERT: B   25 PHE cc_start: 0.7300 (m-80) cc_final: 0.6824 (m-80)
REVERT: B   26 LYS cc_start: 0.8553 (tptm) cc_final: 0.8322 (tptt)
REVERT: B   27 ASP cc_start: 0.8603 (m-30) cc_final: 0.8344 (m-30)
REVERT: B   30 TYR cc_start: 0.8079 (m-80) cc_final: 0.7574 (m-80)
REVERT: B  195 ILE cc_start: 0.7039 (pt) cc_final: 0.6765 (pt)
REVERT: B  383 THR cc_start: 0.7162 (p) cc_final: 0.6811 (p)
REVERT: B  496 TYR cc_start: 0.7481 (t80) cc_final: 0.6892 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1984
  time to fit residues: 52.0472
Evaluate side-chains
  126 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 111 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   chunk 64 optimal weight:    5.9990
   chunk 115 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 70 optimal weight:    9.9990
   chunk 53 optimal weight:    0.0970
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 387 HIS
B 452 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10392  Z= 0.173
  Angle     :  0.585  11.149  14112  Z= 0.298
  Chirality :  0.041   0.238   1532
  Planarity :  0.004   0.056   1744
  Dihedral  : 14.051 111.938   1408
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.09 %
    Favored  : 94.74 %
  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:  1.35 (0.25), residues: 1198
  helix:  1.65 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.58 (0.39), 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 163 
 PHE   0.022   0.001   PHE B  54 
 TYR   0.039   0.002   TYR A 483 
 ARG   0.007   0.000   ARG B 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  : 1.110 
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: 0.8437 (m-40) cc_final: 0.8108 (m-40)
REVERT: A  288 ASN cc_start: 0.8459 (m110) cc_final: 0.7949 (m110)
REVERT: A  489 MET cc_start: 0.8489 (mmm) cc_final: 0.7927 (ttm)
REVERT: B   25 PHE cc_start: 0.7237 (m-80) cc_final: 0.6715 (m-80)
REVERT: B   27 ASP cc_start: 0.8638 (m-30) cc_final: 0.8188 (p0)
REVERT: B  195 ILE cc_start: 0.7070 (pt) cc_final: 0.6781 (pt)
REVERT: B  383 THR cc_start: 0.7121 (p) cc_final: 0.6699 (p)
REVERT: B  496 TYR cc_start: 0.7543 (t80) cc_final: 0.7018 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1946
  time to fit residues: 53.0197
Evaluate side-chains
  137 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0470
   chunk 22 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0980
   chunk 57 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 90 optimal weight:    1.9990
   chunk 105 optimal weight:    0.4980
   overall best weight:    0.6480

-------------------------------------------------------------------------------
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 387 HIS
A 452 GLN
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 HIS
B 452 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10392  Z= 0.180
  Angle     :  0.624  11.382  14112  Z= 0.317
  Chirality :  0.042   0.233   1532
  Planarity :  0.003   0.044   1744
  Dihedral  : 13.837 110.801   1408
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.18 %
    Favored  : 94.66 %
  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:  1.40 (0.25), residues: 1198
  helix:  1.69 (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   0.002   0.001   HIS B 163 
 PHE   0.019   0.001   PHE B 335 
 TYR   0.032   0.002   TYR A 483 
 ARG   0.006   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
  176 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 1.325 
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  137 GLU cc_start: 0.8249 (pp20) cc_final: 0.7792 (tm-30)
REVERT: A  152 ASN cc_start: 0.8448 (m-40) cc_final: 0.8108 (m-40)
REVERT: B   25 PHE cc_start: 0.7221 (m-80) cc_final: 0.6777 (m-80)
REVERT: B   26 LYS cc_start: 0.8002 (tttt) cc_final: 0.6783 (tttt)
REVERT: B   27 ASP cc_start: 0.8555 (m-30) cc_final: 0.8316 (m-30)
REVERT: B   30 TYR cc_start: 0.8122 (m-80) cc_final: 0.7609 (m-80)
REVERT: B  195 ILE cc_start: 0.7074 (pt) cc_final: 0.6782 (pt)
REVERT: B  496 TYR cc_start: 0.7471 (t80) cc_final: 0.6812 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1915
  time to fit residues: 50.2908
Evaluate side-chains
  127 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 70 optimal weight:    4.9990
   chunk 113 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 HIS
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10392  Z= 0.260
  Angle     :  0.656  11.952  14112  Z= 0.339
  Chirality :  0.043   0.215   1532
  Planarity :  0.004   0.051   1744
  Dihedral  : 13.655 109.204   1408
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.76 %
    Favored  : 94.07 %
  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:  1.13 (0.25), residues: 1198
  helix:  1.47 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop : -1.55 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 607 
 HIS   0.004   0.001   HIS A 499 
 PHE   0.016   0.002   PHE B  54 
 TYR   0.028   0.002   TYR A 483 
 ARG   0.006   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
  172 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  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: A   25 PHE cc_start: 0.7844 (m-80) cc_final: 0.7598 (m-80)
REVERT: A   30 TYR cc_start: 0.8258 (m-80) cc_final: 0.7998 (m-80)
REVERT: A  137 GLU cc_start: 0.8318 (pp20) cc_final: 0.7840 (tm-30)
REVERT: A  152 ASN cc_start: 0.8558 (m-40) cc_final: 0.8180 (m-40)
REVERT: B   25 PHE cc_start: 0.7324 (m-80) cc_final: 0.6869 (m-80)
REVERT: B   27 ASP cc_start: 0.8521 (m-30) cc_final: 0.8099 (m-30)
REVERT: B  195 ILE cc_start: 0.7121 (pt) cc_final: 0.6860 (pt)
REVERT: B  383 THR cc_start: 0.7156 (p) cc_final: 0.6898 (p)
REVERT: B  496 TYR cc_start: 0.7543 (t80) cc_final: 0.6808 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1819
  time to fit residues: 47.5744
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  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 119 optimal weight:    0.5980
   chunk 110 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   chunk 101 optimal weight:   10.0000
   chunk 29 optimal weight:    0.1980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 387 HIS
B 452 GLN
B 479 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
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      :  0.003   0.037  10392  Z= 0.189
  Angle     :  0.633  11.926  14112  Z= 0.322
  Chirality :  0.042   0.238   1532
  Planarity :  0.003   0.034   1744
  Dihedral  : 13.342 108.535   1408
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.18 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  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:  1.25 (0.25), residues: 1198
  helix:  1.57 (0.17), residues: 906
  sheet:  None (None), residues: 0
  loop : -1.55 (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 B 163 
 PHE   0.028   0.001   PHE B  54 
 TYR   0.029   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
  177 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 TYR cc_start: 0.8312 (m-80) cc_final: 0.8014 (m-80)
REVERT: A  131 LEU cc_start: 0.9218 (tt) cc_final: 0.9017 (tp)
REVERT: A  137 GLU cc_start: 0.8297 (pp20) cc_final: 0.7818 (tm-30)
REVERT: A  152 ASN cc_start: 0.8484 (m-40) cc_final: 0.8084 (m-40)
REVERT: A  249 ILE cc_start: 0.9170 (tp) cc_final: 0.8883 (mt)
REVERT: B   25 PHE cc_start: 0.7400 (m-80) cc_final: 0.6912 (m-80)
REVERT: B  195 ILE cc_start: 0.7105 (pt) cc_final: 0.6853 (pt)
REVERT: B  383 THR cc_start: 0.7164 (p) cc_final: 0.6867 (p)
REVERT: B  496 TYR cc_start: 0.7545 (t80) cc_final: 0.6870 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1874
  time to fit residues: 49.6727
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  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 95 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 387 HIS
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 = 0.156122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.129290 restraints weight = 17453.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.128260 restraints weight = 15039.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.130159 restraints weight = 14241.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2329

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= 0.188
  Angle     :  0.630  11.901  14112  Z= 0.319
  Chirality :  0.042   0.229   1532
  Planarity :  0.003   0.034   1744
  Dihedral  : 13.133 108.032   1408
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.59 %
    Favored  : 94.24 %
  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:  1.22 (0.25), residues: 1198
  helix:  1.56 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.63 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 607 
 HIS   0.003   0.001   HIS A  10 
 PHE   0.029   0.001   PHE B  54 
 TYR   0.027   0.002   TYR A 483 
 ARG   0.006   0.000   ARG B 459 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1963.19 seconds
wall clock time: 36 minutes 53.17 seconds (2213.17 seconds total)