Starting phenix.real_space_refine
on Tue Dec 31 18:30:19 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vqu_21357/12_2024/6vqu_21357.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vqu_21357/12_2024/6vqu_21357.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vqu_21357/12_2024/6vqu_21357.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vqu_21357/12_2024/6vqu_21357.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vqu_21357/12_2024/6vqu_21357.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vqu_21357/12_2024/6vqu_21357.cif"
  }
  resolution = 3.88
  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=   0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 8895 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    5846      2.51       5
     N    1624      2.21       5
     O    1662      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 9156
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 589, 4578
          Classifications: {'peptide': 589}
          Link IDs: {'PTRANS': 15, 'TRANS': 573}
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.34, per 1000 atoms: 1.02
  Number of scatterers: 9156
  At special positions: 0
  Unit cell: (110.922, 86.736, 140.946, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O    1662      8.00
     N    1624      7.00
     C    5846      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.47
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2184

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 4 sheets defined
      73.5% alpha, 7.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 28
      Proline residue:  A  25  - end of helix
    Processing helix  chain 'A' and resid 32 through 69
      Proline residue:  A  57  - end of helix
    Processing helix  chain 'A' and resid 75 through 127
      removed outlier: 4.534A  pdb=" N   ARG A 107 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   VAL A 108 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 135
      removed outlier: 3.878A  pdb=" N   HIS A 132 " --> pdb=" O   SER A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 161
    Processing helix  chain 'A' and resid 161 through 178
    Processing helix  chain 'A' and resid 181 through 230
      removed outlier: 3.962A  pdb=" N   VAL A 185 " --> pdb=" O   GLY A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 238
    Processing helix  chain 'A' and resid 239 through 293
    Processing helix  chain 'A' and resid 298 through 312
      removed outlier: 4.021A  pdb=" N   VAL A 302 " --> pdb=" O   VAL A 298 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR A 309 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.929A  pdb=" N   ASP A 316 " --> pdb=" O   ARG A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 317 through 341
    Processing helix  chain 'A' and resid 401 through 408
      removed outlier: 4.535A  pdb=" N   ARG A 405 " --> pdb=" O   SER A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 428
      No H-bonds generated for 'chain 'A' and resid 426 through 428'
    Processing helix  chain 'A' and resid 429 through 436
    Processing helix  chain 'A' and resid 450 through 456
    Processing helix  chain 'A' and resid 457 through 459
      No H-bonds generated for 'chain 'A' and resid 457 through 459'
    Processing helix  chain 'A' and resid 463 through 474
    Processing helix  chain 'A' and resid 476 through 483
    Processing helix  chain 'A' and resid 485 through 489
      removed outlier: 3.546A  pdb=" N   THR A 489 " --> pdb=" O   GLY A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 515
    Processing helix  chain 'A' and resid 529 through 544
      removed outlier: 4.389A  pdb=" N   SER A 538 " --> pdb=" O   GLN A 534 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   THR A 539 " --> pdb=" O   ASP A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 560
    Processing helix  chain 'A' and resid 578 through 586
    Processing helix  chain 'A' and resid 587 through 602
    Processing helix  chain 'B' and resid 15 through 28
      Proline residue:  B  25  - end of helix
    Processing helix  chain 'B' and resid 32 through 69
      Proline residue:  B  57  - end of helix
    Processing helix  chain 'B' and resid 75 through 127
      removed outlier: 4.533A  pdb=" N   ARG B 107 " --> pdb=" O   ILE B 103 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   VAL B 108 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 135
      removed outlier: 3.879A  pdb=" N   HIS B 132 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 161
    Processing helix  chain 'B' and resid 161 through 178
    Processing helix  chain 'B' and resid 181 through 230
      removed outlier: 3.962A  pdb=" N   VAL B 185 " --> pdb=" O   GLY B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 238
    Processing helix  chain 'B' and resid 239 through 293
    Processing helix  chain 'B' and resid 298 through 312
      removed outlier: 4.020A  pdb=" N   VAL B 302 " --> pdb=" O   VAL B 298 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR B 309 " --> pdb=" O   ASN B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 316
      removed outlier: 3.928A  pdb=" N   ASP B 316 " --> pdb=" O   ARG B 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 313 through 316'
    Processing helix  chain 'B' and resid 317 through 341
    Processing helix  chain 'B' and resid 401 through 408
      removed outlier: 4.535A  pdb=" N   ARG B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 428
      No H-bonds generated for 'chain 'B' and resid 426 through 428'
    Processing helix  chain 'B' and resid 429 through 436
    Processing helix  chain 'B' and resid 450 through 456
    Processing helix  chain 'B' and resid 457 through 459
      No H-bonds generated for 'chain 'B' and resid 457 through 459'
    Processing helix  chain 'B' and resid 463 through 474
    Processing helix  chain 'B' and resid 476 through 483
    Processing helix  chain 'B' and resid 485 through 489
      removed outlier: 3.546A  pdb=" N   THR B 489 " --> pdb=" O   GLY B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 515
    Processing helix  chain 'B' and resid 529 through 544
      removed outlier: 4.389A  pdb=" N   SER B 538 " --> pdb=" O   GLN B 534 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   THR B 539 " --> pdb=" O   ASP B 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 560
    Processing helix  chain 'B' and resid 578 through 586
    Processing helix  chain 'B' and resid 587 through 602
    Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 384
      removed outlier: 4.166A  pdb=" N   GLY A 379 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   VAL A 366 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   SER A 381 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   ASP A 364 " --> pdb=" O   SER A 381 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   GLU A 383 " --> pdb=" O   THR A 362 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   THR A 362 " --> pdb=" O   GLU A 383 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   PHE A 363 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LEU A 419 " --> pdb=" O   PHE A 363 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   ASN A 365 " --> pdb=" O   ARG A 417 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   ARG A 417 " --> pdb=" O   ASN A 365 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 440
      removed outlier: 6.724A  pdb=" N   GLY A 438 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
      removed outlier: 7.416A  pdb=" N   ASP A 522 " --> pdb=" O   GLY A 438 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   VAL A 440 " --> pdb=" O   ASP A 522 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   LEU A 519 " --> pdb=" O   ILE A 550 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   ILE A 552 " --> pdb=" O   LEU A 519 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   PHE A 521 " --> pdb=" O   ILE A 552 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ARG A 389 " --> pdb=" O   THR A 564 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   LEU A 566 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   ALA A 391 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   LEU A 568 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   VAL A 393 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ASP A 569 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   LEU A 573 " --> pdb=" O   ASP A 569 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 377 through 384
      removed outlier: 4.166A  pdb=" N   GLY B 379 " --> pdb=" O   VAL B 366 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   VAL B 366 " --> pdb=" O   GLY B 379 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   SER B 381 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ASP B 364 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   GLU B 383 " --> pdb=" O   THR B 362 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   THR B 362 " --> pdb=" O   GLU B 383 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   PHE B 363 " --> pdb=" O   LEU B 419 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU B 419 " --> pdb=" O   PHE B 363 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   ASN B 365 " --> pdb=" O   ARG B 417 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   ARG B 417 " --> pdb=" O   ASN B 365 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 437 through 440
      removed outlier: 6.725A  pdb=" N   GLY B 438 " --> pdb=" O   LEU B 520 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   ASP B 522 " --> pdb=" O   GLY B 438 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   VAL B 440 " --> pdb=" O   ASP B 522 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   LEU B 519 " --> pdb=" O   ILE B 550 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   ILE B 552 " --> pdb=" O   LEU B 519 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   PHE B 521 " --> pdb=" O   ILE B 552 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ARG B 389 " --> pdb=" O   THR B 564 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   LEU B 566 " --> pdb=" O   ARG B 389 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   ALA B 391 " --> pdb=" O   LEU B 566 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   LEU B 568 " --> pdb=" O   ALA B 391 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   VAL B 393 " --> pdb=" O   LEU B 568 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ASP B 569 " --> pdb=" O   LEU B 573 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   LEU B 573 " --> pdb=" O   ASP B 569 " (cutoff:3.500A)

    668 hydrogen bonds defined for protein.
    1962 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: 2.83

  Time building geometry restraints manager: 2.77 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: 2965
        1.34 -     1.45: 1418
        1.45 -     1.57: 4895
        1.57 -     1.69: 0
        1.69 -     1.80: 48
  Bond restraints: 9326
  Sorted by residual:
  bond pdb=" CB  PRO B  57 "
       pdb=" CG  PRO B  57 "
    ideal  model  delta    sigma   weight residual
    1.492  1.384  0.108 5.00e-02 4.00e+02 4.68e+00
  bond pdb=" CB  PRO A  57 "
       pdb=" CG  PRO A  57 "
    ideal  model  delta    sigma   weight residual
    1.492  1.384  0.108 5.00e-02 4.00e+02 4.66e+00
  bond pdb=" C   GLN B  74 "
       pdb=" N   PRO B  75 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.048 2.34e-02 1.83e+03 4.13e+00
  bond pdb=" C   GLN A  74 "
       pdb=" N   PRO A  75 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 2.34e-02 1.83e+03 4.08e+00
  bond pdb=" CA  LEU A  56 "
       pdb=" C   LEU A  56 "
    ideal  model  delta    sigma   weight residual
    1.522  1.545 -0.023 1.26e-02 6.30e+03 3.47e+00
  ... (remaining 9321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 11912
        1.76 -     3.51: 618
        3.51 -     5.27: 107
        5.27 -     7.02: 19
        7.02 -     8.78: 12
  Bond angle restraints: 12668
  Sorted by residual:
  angle pdb=" CA  ARG A 494 "
        pdb=" CB  ARG A 494 "
        pdb=" CG  ARG A 494 "
      ideal   model   delta    sigma   weight residual
     114.10  121.37   -7.27 2.00e+00 2.50e-01 1.32e+01
  angle pdb=" CA  ARG B 494 "
        pdb=" CB  ARG B 494 "
        pdb=" CG  ARG B 494 "
      ideal   model   delta    sigma   weight residual
     114.10  121.36   -7.26 2.00e+00 2.50e-01 1.32e+01
  angle pdb=" C   ASP B 569 "
        pdb=" N   GLN B 570 "
        pdb=" CA  GLN B 570 "
      ideal   model   delta    sigma   weight residual
     122.46  127.56   -5.10 1.41e+00 5.03e-01 1.31e+01
  angle pdb=" C   ASP A 569 "
        pdb=" N   GLN A 570 "
        pdb=" CA  GLN A 570 "
      ideal   model   delta    sigma   weight residual
     122.46  127.49   -5.03 1.41e+00 5.03e-01 1.27e+01
  angle pdb=" C   GLU B 493 "
        pdb=" N   ARG B 494 "
        pdb=" CA  ARG B 494 "
      ideal   model   delta    sigma   weight residual
     122.08  127.09   -5.01 1.47e+00 4.63e-01 1.16e+01
  ... (remaining 12663 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.89: 4673
       13.89 -    27.78: 621
       27.78 -    41.66: 174
       41.66 -    55.55: 50
       55.55 -    69.44: 18
  Dihedral angle restraints: 5536
    sinusoidal: 2140
      harmonic: 3396
  Sorted by residual:
  dihedral pdb=" CA  PHE A 368 "
           pdb=" C   PHE A 368 "
           pdb=" N   GLY A 369 "
           pdb=" CA  GLY A 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.61   26.39     0      5.00e+00 4.00e-02 2.79e+01
  dihedral pdb=" CA  PHE B 368 "
           pdb=" C   PHE B 368 "
           pdb=" N   GLY B 369 "
           pdb=" CA  GLY B 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.70   26.30     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  ALA A  76 "
           pdb=" C   ALA A  76 "
           pdb=" N   LEU A  77 "
           pdb=" CA  LEU A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.89   20.11     0      5.00e+00 4.00e-02 1.62e+01
  ... (remaining 5533 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1079
       0.053 -    0.106: 279
       0.106 -    0.160: 111
       0.160 -    0.213: 9
       0.213 -    0.266: 6
  Chirality restraints: 1484
  Sorted by residual:
  chirality pdb=" CB  VAL B 543 "
            pdb=" CA  VAL B 543 "
            pdb=" CG1 VAL B 543 "
            pdb=" CG2 VAL B 543 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CB  VAL A 543 "
            pdb=" CA  VAL A 543 "
            pdb=" CG1 VAL A 543 "
            pdb=" CG2 VAL A 543 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CB  ILE A 559 "
            pdb=" CA  ILE A 559 "
            pdb=" CG1 ILE A 559 "
            pdb=" CG2 ILE A 559 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 1481 not shown)

  Planarity restraints: 1616
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 543 "    0.018 2.00e-02 2.50e+03   3.62e-02 1.31e+01
        pdb=" C   VAL A 543 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   VAL A 543 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ALA A 544 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 543 "   -0.018 2.00e-02 2.50e+03   3.60e-02 1.30e+01
        pdb=" C   VAL B 543 "    0.062 2.00e-02 2.50e+03
        pdb=" O   VAL B 543 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ALA B 544 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 303 "    0.024 2.00e-02 2.50e+03   1.70e-02 5.03e+00
        pdb=" CG  PHE A 303 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 303 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 303 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 303 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 303 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 303 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1613 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2554
        2.80 -     3.33: 9066
        3.33 -     3.85: 15907
        3.85 -     4.38: 17055
        4.38 -     4.90: 28934
  Nonbonded interactions: 73516
  Sorted by model distance:
  nonbonded pdb=" O   THR A 199 "
            pdb=" OG1 THR A 203 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   THR B 199 "
            pdb=" OG1 THR B 203 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG1 THR B 429 "
            pdb=" OG  SER B 432 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   ASP B  15 "
            pdb=" OG1 THR B  19 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   ASP A  15 "
            pdb=" OG1 THR A  19 "
     model   vdw
     2.293 3.040
  ... (remaining 73511 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'
  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:             2.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     27.340
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
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      :  0.007   0.108   9326  Z= 0.438
  Angle     :  0.942   8.779  12668  Z= 0.539
  Chirality :  0.056   0.266   1484
  Planarity :  0.007   0.054   1616
  Dihedral  : 14.622  69.440   3352
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  8.09 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.26 (0.21), residues: 1174
  helix: -1.29 (0.15), residues: 788
  sheet: -1.53 (0.62), residues: 72
  loop : -1.51 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  28 
 HIS   0.005   0.001   HIS B 125 
 PHE   0.035   0.003   PHE B 303 
 TYR   0.018   0.003   TYR A  60 
 ARG   0.016   0.001   ARG A 434 

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9435 (tmm) cc_final: 0.9034 (tmm)
REVERT: A  592 MET cc_start: 0.9194 (mtp) cc_final: 0.8905 (mtp)
REVERT: B  154 MET cc_start: 0.9437 (tmm) cc_final: 0.9124 (tmm)
REVERT: B  592 MET cc_start: 0.9240 (mtp) cc_final: 0.8992 (mtp)
  outliers start: 16
  outliers final: 2
  residues processed: 74
  average time/residue: 0.2858
  time to fit residues: 28.4698
Evaluate side-chains
  41 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  543 VAL
Chi-restraints excluded: chain B residue  543 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.0670
   chunk 87 optimal weight:    0.6980
   chunk 48 optimal weight:    8.9990
   chunk 30 optimal weight:    0.0020
   chunk 59 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 90 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:   10.0000
   chunk 67 optimal weight:    0.7980
   chunk 105 optimal weight:    8.9990
   overall best weight:    0.4326

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

Flipped N/Q/H residues before XYZ refinement:
A  14 HIS
A 119 ASN
B  14 HIS
B 119 ASN
B 125 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9326  Z= 0.158
  Angle     :  0.575   7.377  12668  Z= 0.304
  Chirality :  0.040   0.144   1484
  Planarity :  0.005   0.108   1616
  Dihedral  :  4.186  20.836   1308
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.02 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.14 (0.23), residues: 1174
  helix:  0.69 (0.17), residues: 798
  sheet: -1.37 (0.61), residues: 72
  loop : -0.90 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 291 
 HIS   0.003   0.001   HIS B 125 
 PHE   0.021   0.001   PHE A 105 
 TYR   0.011   0.001   TYR A 195 
 ARG   0.006   0.000   ARG A 146 

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 49
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9457 (tmm) cc_final: 0.9053 (tmm)
REVERT: A  320 MET cc_start: 0.9121 (ptp) cc_final: 0.8814 (pmm)
REVERT: A  592 MET cc_start: 0.9122 (mtp) cc_final: 0.8864 (mtp)
REVERT: B  154 MET cc_start: 0.9470 (tmm) cc_final: 0.9144 (tmm)
REVERT: B  335 MET cc_start: 0.9296 (mpp) cc_final: 0.9083 (mpp)
REVERT: B  592 MET cc_start: 0.9175 (mtp) cc_final: 0.8953 (mtp)
  outliers start: 18
  outliers final: 8
  residues processed: 65
  average time/residue: 0.2185
  time to fit residues: 20.9938
Evaluate side-chains
  43 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  552 ILE
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  543 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 58 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 87 optimal weight:    0.5980
   chunk 71 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 105 optimal weight:    9.9990
   chunk 114 optimal weight:    9.9990
   chunk 93 optimal weight:    8.9990
   chunk 104 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    3.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
A 305 ASN
A 504 GLN
B 119 ASN
B 125 HIS
B 305 ASN
B 504 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8771
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.083   9326  Z= 0.368
  Angle     :  0.695   9.260  12668  Z= 0.371
  Chirality :  0.042   0.153   1484
  Planarity :  0.004   0.038   1616
  Dihedral  :  4.164  23.846   1307
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.47 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.24), residues: 1174
  helix:  1.46 (0.18), residues: 782
  sheet: -1.35 (0.62), residues: 72
  loop : -0.20 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  28 
 HIS   0.004   0.001   HIS A 125 
 PHE   0.017   0.002   PHE B 105 
 TYR   0.014   0.002   TYR B  60 
 ARG   0.006   0.001   ARG A 541 

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 33
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9525 (tmm) cc_final: 0.9106 (tmm)
REVERT: A  159 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9402 (tt)
REVERT: A  433 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9397 (pp)
REVERT: A  592 MET cc_start: 0.9152 (mtp) cc_final: 0.8869 (mtp)
REVERT: B  154 MET cc_start: 0.9533 (tmm) cc_final: 0.9177 (tmm)
REVERT: B  159 LEU cc_start: 0.9672 (OUTLIER) cc_final: 0.9323 (tt)
REVERT: B  335 MET cc_start: 0.9352 (mpp) cc_final: 0.9129 (mpp)
REVERT: B  592 MET cc_start: 0.9205 (mtp) cc_final: 0.8927 (mtp)
  outliers start: 26
  outliers final: 8
  residues processed: 56
  average time/residue: 0.1755
  time to fit residues: 15.7099
Evaluate side-chains
  44 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 33
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  168 GLU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  168 GLU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  356 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 54 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 105 optimal weight:    8.9990
   chunk 112 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0970
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9326  Z= 0.167
  Angle     :  0.570  13.041  12668  Z= 0.294
  Chirality :  0.040   0.142   1484
  Planarity :  0.003   0.036   1616
  Dihedral  :  3.895  22.788   1306
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 16.28 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.24), residues: 1174
  helix:  1.78 (0.18), residues: 800
  sheet: -1.29 (0.61), residues: 72
  loop : -0.03 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  17 
 HIS   0.003   0.000   HIS A 125 
 PHE   0.016   0.001   PHE B 105 
 TYR   0.011   0.001   TYR A 589 
 ARG   0.014   0.000   ARG A 531 

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 36
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9482 (tmm) cc_final: 0.9051 (tmm)
REVERT: A  159 LEU cc_start: 0.9727 (OUTLIER) cc_final: 0.9448 (tt)
REVERT: A  320 MET cc_start: 0.9083 (ptp) cc_final: 0.8660 (pmm)
REVERT: A  592 MET cc_start: 0.9103 (mtp) cc_final: 0.8824 (mtp)
REVERT: B  154 MET cc_start: 0.9495 (tmm) cc_final: 0.9120 (tmm)
REVERT: B  159 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9399 (tt)
REVERT: B  332 MET cc_start: 0.9092 (ttt) cc_final: 0.8728 (tpp)
REVERT: B  335 MET cc_start: 0.9239 (mpp) cc_final: 0.8854 (mpp)
REVERT: B  592 MET cc_start: 0.9171 (mtp) cc_final: 0.8896 (mtp)
  outliers start: 17
  outliers final: 9
  residues processed: 53
  average time/residue: 0.1801
  time to fit residues: 15.1516
Evaluate side-chains
  44 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 33
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  552 ILE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  356 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 93 optimal weight:    8.9990
   chunk 63 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.9786

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8725
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9326  Z= 0.223
  Angle     :  0.574  10.282  12668  Z= 0.303
  Chirality :  0.040   0.148   1484
  Planarity :  0.003   0.030   1616
  Dihedral  :  3.909  25.415   1306
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.55 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.79 (0.24), residues: 1174
  helix:  1.90 (0.18), residues: 806
  sheet: -1.29 (0.61), residues: 72
  loop : -0.02 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  17 
 HIS   0.004   0.001   HIS A 125 
 PHE   0.024   0.002   PHE B 105 
 TYR   0.009   0.001   TYR A 195 
 ARG   0.004   0.000   ARG B 101 

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 38
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9509 (tmm) cc_final: 0.9110 (tmm)
REVERT: A  159 LEU cc_start: 0.9731 (OUTLIER) cc_final: 0.9379 (tt)
REVERT: A  280 MET cc_start: 0.9287 (ttp) cc_final: 0.8998 (tpp)
REVERT: A  307 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7507 (t80)
REVERT: A  332 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8621 (tpp)
REVERT: A  433 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9353 (pp)
REVERT: A  592 MET cc_start: 0.9114 (mtp) cc_final: 0.8829 (mtp)
REVERT: B  154 MET cc_start: 0.9520 (tmm) cc_final: 0.9125 (tmm)
REVERT: B  159 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9304 (tt)
REVERT: B  307 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7464 (t80)
REVERT: B  332 MET cc_start: 0.9203 (ttt) cc_final: 0.8830 (tpp)
REVERT: B  335 MET cc_start: 0.9197 (mpp) cc_final: 0.8864 (mpp)
REVERT: B  592 MET cc_start: 0.9170 (mtp) cc_final: 0.8876 (mtp)
  outliers start: 21
  outliers final: 7
  residues processed: 56
  average time/residue: 0.1994
  time to fit residues: 17.1628
Evaluate side-chains
  48 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 35
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  345 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 100 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 93 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 108 optimal weight:    3.9990
   overall best weight:    2.1588

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9326  Z= 0.228
  Angle     :  0.597  11.177  12668  Z= 0.310
  Chirality :  0.041   0.171   1484
  Planarity :  0.003   0.032   1616
  Dihedral  :  3.931  23.264   1306
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.87 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.82 (0.24), residues: 1174
  helix:  1.87 (0.18), residues: 800
  sheet: -1.26 (0.61), residues: 72
  loop :  0.18 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  17 
 HIS   0.003   0.001   HIS A 125 
 PHE   0.024   0.002   PHE B 157 
 TYR   0.010   0.001   TYR A 195 
 ARG   0.009   0.000   ARG A 531 

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 35
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9528 (tmm) cc_final: 0.9121 (tmm)
REVERT: A  159 LEU cc_start: 0.9740 (OUTLIER) cc_final: 0.9431 (tt)
REVERT: A  280 MET cc_start: 0.9282 (ttp) cc_final: 0.9052 (tpp)
REVERT: A  592 MET cc_start: 0.9141 (mtp) cc_final: 0.8846 (mtp)
REVERT: B   45 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8781 (tmm)
REVERT: B   98 ASP cc_start: 0.9334 (m-30) cc_final: 0.9111 (m-30)
REVERT: B  154 MET cc_start: 0.9530 (tmm) cc_final: 0.9127 (tmm)
REVERT: B  159 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9329 (tt)
REVERT: B  307 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7459 (t80)
REVERT: B  332 MET cc_start: 0.9218 (ttt) cc_final: 0.8875 (tpt)
REVERT: B  592 MET cc_start: 0.9181 (mtp) cc_final: 0.8884 (mtp)
  outliers start: 21
  outliers final: 10
  residues processed: 51
  average time/residue: 0.1595
  time to fit residues: 13.6198
Evaluate side-chains
  49 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 35
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  345 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 63 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   chunk 111 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 68 optimal weight:    0.6980
   chunk 51 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    1.5186

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9326  Z= 0.192
  Angle     :  0.608  13.859  12668  Z= 0.305
  Chirality :  0.041   0.179   1484
  Planarity :  0.003   0.032   1616
  Dihedral  :  3.895  23.503   1306
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 18.83 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.86 (0.24), residues: 1174
  helix:  1.89 (0.18), residues: 800
  sheet: -1.17 (0.61), residues: 72
  loop :  0.21 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  17 
 HIS   0.003   0.001   HIS A 125 
 PHE   0.018   0.001   PHE B 157 
 TYR   0.010   0.001   TYR A 195 
 ARG   0.008   0.000   ARG A 531 

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 35
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.9522 (tmm) cc_final: 0.9188 (tmm)
REVERT: A  159 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9431 (tt)
REVERT: A  280 MET cc_start: 0.9241 (ttp) cc_final: 0.8956 (tpp)
REVERT: A  320 MET cc_start: 0.9167 (pmm) cc_final: 0.8898 (pmm)
REVERT: A  592 MET cc_start: 0.9135 (mtp) cc_final: 0.8834 (mtp)
REVERT: B   45 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8747 (tmm)
REVERT: B   98 ASP cc_start: 0.9306 (m-30) cc_final: 0.9088 (m-30)
REVERT: B  154 MET cc_start: 0.9521 (tmm) cc_final: 0.9112 (tmm)
REVERT: B  159 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9333 (tt)
REVERT: B  592 MET cc_start: 0.9172 (mtp) cc_final: 0.8873 (mtp)
  outliers start: 21
  outliers final: 10
  residues processed: 52
  average time/residue: 0.1804
  time to fit residues: 14.8648
Evaluate side-chains
  48 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 35
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  345 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 101 optimal weight:    6.9990
   chunk 107 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    1.5386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8714
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9326  Z= 0.193
  Angle     :  0.626  12.537  12668  Z= 0.312
  Chirality :  0.041   0.187   1484
  Planarity :  0.003   0.032   1616
  Dihedral  :  3.866  24.913   1306
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 19.68 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.91 (0.24), residues: 1174
  helix:  1.92 (0.18), residues: 800
  sheet: -1.10 (0.61), residues: 72
  loop :  0.24 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  17 
 HIS   0.003   0.001   HIS A 125 
 PHE   0.020   0.001   PHE B 105 
 TYR   0.010   0.001   TYR A 195 
 ARG   0.007   0.000   ARG A 531 

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 36
  time to evaluate  : 1.043 
Fit side-chains
REVERT: A  154 MET cc_start: 0.9504 (tmm) cc_final: 0.9163 (tmm)
REVERT: A  159 LEU cc_start: 0.9751 (OUTLIER) cc_final: 0.9496 (tt)
REVERT: A  280 MET cc_start: 0.9232 (ttp) cc_final: 0.8960 (tpp)
REVERT: A  320 MET cc_start: 0.9091 (pmm) cc_final: 0.8880 (pmm)
REVERT: A  592 MET cc_start: 0.9137 (mtp) cc_final: 0.8837 (mtp)
REVERT: B   45 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8758 (tmm)
REVERT: B   98 ASP cc_start: 0.9301 (m-30) cc_final: 0.9081 (m-30)
REVERT: B  154 MET cc_start: 0.9515 (tmm) cc_final: 0.9108 (tmm)
REVERT: B  159 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9310 (tt)
REVERT: B  592 MET cc_start: 0.9168 (mtp) cc_final: 0.8865 (mtp)
  outliers start: 18
  outliers final: 10
  residues processed: 50
  average time/residue: 0.1843
  time to fit residues: 14.6801
Evaluate side-chains
  47 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 34
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  345 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 94 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 110 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.0584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9326  Z= 0.170
  Angle     :  0.630  12.471  12668  Z= 0.315
  Chirality :  0.041   0.196   1484
  Planarity :  0.004   0.069   1616
  Dihedral  :  3.794  21.448   1306
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 20.11 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.98 (0.24), residues: 1174
  helix:  1.98 (0.18), residues: 800
  sheet: -0.99 (0.60), residues: 72
  loop :  0.21 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 291 
 HIS   0.003   0.000   HIS A 125 
 PHE   0.017   0.001   PHE B 105 
 TYR   0.010   0.001   TYR A 195 
 ARG   0.007   0.000   ARG A 531 

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 39
  time to evaluate  : 1.127 
Fit side-chains
REVERT: A  154 MET cc_start: 0.9476 (tmm) cc_final: 0.9145 (tmm)
REVERT: A  159 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9493 (tt)
REVERT: A  280 MET cc_start: 0.9208 (ttp) cc_final: 0.8966 (tpp)
REVERT: A  592 MET cc_start: 0.9120 (mtp) cc_final: 0.8825 (mtp)
REVERT: B   45 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8739 (tmm)
REVERT: B   98 ASP cc_start: 0.9282 (m-30) cc_final: 0.9075 (m-30)
REVERT: B  154 MET cc_start: 0.9504 (tmm) cc_final: 0.9089 (tmm)
REVERT: B  159 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9333 (tt)
REVERT: B  592 MET cc_start: 0.9156 (mtp) cc_final: 0.8851 (mtp)
  outliers start: 18
  outliers final: 10
  residues processed: 54
  average time/residue: 0.1672
  time to fit residues: 14.8636
Evaluate side-chains
  49 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  345 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 115 optimal weight:    2.9990
   chunk 106 optimal weight:    8.9990
   chunk 92 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 56 optimal weight:    0.1980
   chunk 73 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.8386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9326  Z= 0.167
  Angle     :  0.646  12.775  12668  Z= 0.322
  Chirality :  0.041   0.203   1484
  Planarity :  0.004   0.066   1616
  Dihedral  :  3.786  21.309   1306
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 20.85 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.95 (0.24), residues: 1174
  helix:  1.98 (0.18), residues: 794
  sheet: -0.70 (0.61), residues: 72
  loop :  0.10 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 291 
 HIS   0.003   0.000   HIS A 125 
 PHE   0.016   0.001   PHE B 105 
 TYR   0.010   0.001   TYR A 195 
 ARG   0.007   0.000   ARG A 531 

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 1.026 
Fit side-chains
REVERT: A  154 MET cc_start: 0.9486 (tmm) cc_final: 0.9153 (tmm)
REVERT: A  159 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9474 (tt)
REVERT: A  280 MET cc_start: 0.9209 (ttp) cc_final: 0.8975 (tpp)
REVERT: A  592 MET cc_start: 0.9118 (mtp) cc_final: 0.8818 (mtp)
REVERT: B   45 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8901 (tmm)
REVERT: B   98 ASP cc_start: 0.9284 (m-30) cc_final: 0.9071 (m-30)
REVERT: B  154 MET cc_start: 0.9485 (tmm) cc_final: 0.9128 (tmm)
REVERT: B  159 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9337 (tt)
REVERT: B  592 MET cc_start: 0.9153 (mtp) cc_final: 0.8845 (mtp)
  outliers start: 16
  outliers final: 10
  residues processed: 56
  average time/residue: 0.1583
  time to fit residues: 14.7997
Evaluate side-chains
  53 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  312 PHE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  345 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 92 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 94 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.033479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.025049 restraints weight = 88150.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.025903 restraints weight = 53745.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.026500 restraints weight = 38816.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8907
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9326  Z= 0.271
  Angle     :  0.706  14.602  12668  Z= 0.355
  Chirality :  0.042   0.241   1484
  Planarity :  0.004   0.048   1616
  Dihedral  :  3.932  20.162   1306
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 21.28 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.80 (0.24), residues: 1174
  helix:  1.86 (0.18), residues: 794
  sheet: -0.82 (0.62), residues: 72
  loop :  0.07 (0.37), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  28 
 HIS   0.003   0.001   HIS A 125 
 PHE   0.014   0.002   PHE B 157 
 TYR   0.009   0.001   TYR B 289 
 ARG   0.006   0.001   ARG A 531 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1615.27 seconds
wall clock time: 30 minutes 30.46 seconds (1830.46 seconds total)