Starting phenix.real_space_refine (version: dev)
on Sat May 14 08:26:21 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/05_2022/6vqu_21357.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/05_2022/6vqu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/05_2022/6vqu_21357.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/05_2022/6vqu_21357.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/05_2022/6vqu_21357.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/05_2022/6vqu_21357.pdb"
  }
  resolution = 3.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  195": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  382": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  195": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  382": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib"
  Total number of atoms: 9156
  Number of models: 1
  Model: ""
    Number of chains: 2
    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}
    Chain: "B"
      Number of atoms: 4578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 589, 4578
          Classifications: {'peptide': 589}
          Link IDs: {'PTRANS': 15, 'TRANS': 573}
  Time building chain proxies: 5.74, per 1000 atoms: 0.63
  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  - 3.50
        Amino acid           : False - 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: 4.10
  Conformation dependent library (CDL) restraints added in 1.6 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: 0.49
  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: 2.81

  Time building geometry restraints manager: 4.35 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:
       98.89 -   105.91: 142
      105.91 -   112.93: 5135
      112.93 -   119.94: 3197
      119.94 -   126.96: 4094
      126.96 -   133.98: 100
  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 2.440
  nonbonded pdb=" O   THR B 199 "
            pdb=" OG1 THR B 203 "
     model   vdw
     2.276 2.440
  nonbonded pdb=" OG1 THR B 429 "
            pdb=" OG  SER B 432 "
     model   vdw
     2.293 2.440
  nonbonded pdb=" O   ASP B  15 "
            pdb=" OG1 THR B  19 "
     model   vdw
     2.293 2.440
  nonbonded pdb=" O   ASP A  15 "
            pdb=" OG1 THR A  19 "
     model   vdw
     2.293 2.440
  ... (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
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
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.
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:             3.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.120
  Construct map_model_manager:             0.010
  Extract box with map and model:          13.360
  Check model and map are aligned:         0.150
  Convert atoms to be neutral:             0.080
  Process input model:                     29.190
  Find NCS groups from input model:        0.510
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  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:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
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= 0.439
  Angle     :  0.942   8.779  12668  Z= 0.539
  Chirality :  0.056   0.266   1484
  Planarity :  0.007   0.054   1616
  Dihedral  : 14.623  69.440   3352
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer Outliers :  1.70 %
  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

*********************** 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 fitting.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 2
  residues processed: 74
  average time/residue: 0.2693
  time to fit residues: 27.0258
Evaluate side-chains
  41 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 1.191 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0858
  time to fit residues: 1.8983
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.0170
   chunk 87 optimal weight:    0.7980
   chunk 48 optimal weight:    9.9990
   chunk 30 optimal weight:    0.3980
   chunk 59 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9980
   chunk 105 optimal weight:    6.9990
   overall best weight:    0.6420

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

Flipped N/Q/H residues before XYZ refinement:
A  74 GLN
A 119 ASN
A 125 HIS
A 305 ASN
A 504 GLN
B  14 HIS
B  74 GLN
B 119 ASN
B 125 HIS
B 504 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9326  Z= 0.154
  Angle     :  0.572   7.340  12668  Z= 0.299
  Chirality :  0.039   0.148   1484
  Planarity :  0.005   0.124   1616
  Dihedral  :  4.165  20.485   1306
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer Outliers :  2.02 %
  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:  0.20 (0.23), residues: 1174
  helix:  0.77 (0.17), residues: 790
  sheet: -1.31 (0.61), residues: 72
  loop : -0.96 (0.33), residues: 312

*********************** 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 fitting.
    rotamer outliers: 19
    poor density    : 48
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 19
  outliers final: 9
  residues processed: 65
  average time/residue: 0.2049
  time to fit residues: 19.7551
Evaluate side-chains
  42 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 1.125 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0821
  time to fit residues: 2.8287
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 105 optimal weight:    7.9990
   chunk 114 optimal weight:    9.9990
   chunk 93 optimal weight:    1.9990
   chunk 104 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 119 ASN
B 125 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9326  Z= 0.154
  Angle     :  0.540   8.838  12668  Z= 0.282
  Chirality :  0.038   0.144   1484
  Planarity :  0.003   0.036   1616
  Dihedral  :  3.747  16.894   1306
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer Outliers :  1.60 %
  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:  1.26 (0.24), residues: 1174
  helix:  1.59 (0.18), residues: 796
  sheet: -1.14 (0.60), residues: 72
  loop : -0.56 (0.34), residues: 306

*********************** 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
  50 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 35
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 4
  residues processed: 49
  average time/residue: 0.2008
  time to fit residues: 15.1436
Evaluate side-chains
  37 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 1.161 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0866
  time to fit residues: 2.1736
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 104 optimal weight:    0.0970
   chunk 79 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 105 optimal weight:    7.9990
   chunk 112 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
A 442 GLN
B 119 ASN
B 125 HIS
B 442 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9326  Z= 0.192
  Angle     :  0.567   9.866  12668  Z= 0.294
  Chirality :  0.039   0.161   1484
  Planarity :  0.003   0.045   1616
  Dihedral  :  3.694  16.827   1306
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer Outliers :  0.96 %
  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:  1.72 (0.24), residues: 1174
  helix:  1.85 (0.18), residues: 800
  sheet: -0.96 (0.60), residues: 72
  loop : -0.12 (0.36), residues: 302

*********************** 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
  40 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 2
  residues processed: 40
  average time/residue: 0.1728
  time to fit residues: 11.5514
Evaluate side-chains
  34 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 1.088 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0833
  time to fit residues: 1.7920
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 93 optimal weight:    7.9990
   chunk 63 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 83 optimal weight:    0.5980
   chunk 46 optimal weight:    0.1980
   chunk 95 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 100 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 442 GLN
B 119 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9326  Z= 0.176
  Angle     :  0.556  10.276  12668  Z= 0.285
  Chirality :  0.039   0.158   1484
  Planarity :  0.003   0.025   1616
  Dihedral  :  3.647  17.681   1306
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer Outliers :  1.49 %
  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:  1.99 (0.25), residues: 1174
  helix:  2.03 (0.18), residues: 800
  sheet: -0.84 (0.61), residues: 72
  loop :  0.02 (0.37), residues: 302

*********************** 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
  46 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 32
  time to evaluate  : 1.231 
Fit side-chains
  outliers start: 14
  outliers final: 2
  residues processed: 44
  average time/residue: 0.1960
  time to fit residues: 13.6669
Evaluate side-chains
  32 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 1.175 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0887
  time to fit residues: 1.9125
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 93 optimal weight:    8.9990
   chunk 51 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 58 optimal weight:   10.0000
   chunk 108 optimal weight:    2.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
A 442 GLN
B 125 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.2693

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= 0.247
  Angle     :  0.609  10.748  12668  Z= 0.312
  Chirality :  0.040   0.170   1484
  Planarity :  0.003   0.028   1616
  Dihedral  :  3.782  17.762   1306
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer Outliers :  0.85 %
  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:  1.92 (0.25), residues: 1174
  helix:  1.96 (0.18), residues: 802
  sheet: -0.81 (0.61), residues: 72
  loop :  0.01 (0.37), residues: 300

*********************** 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
  39 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 2
  residues processed: 37
  average time/residue: 0.1835
  time to fit residues: 11.2881
Evaluate side-chains
  35 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 1.044 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1068
  time to fit residues: 1.8076
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9990
   chunk 62 optimal weight:    0.4980
   chunk 111 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9980
   chunk 51 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
B 305 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9326  Z= 0.203
  Angle     :  0.579  10.426  12668  Z= 0.296
  Chirality :  0.039   0.190   1484
  Planarity :  0.003   0.031   1616
  Dihedral  :  3.768  18.795   1306
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer Outliers :  1.06 %
  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:  2.03 (0.25), residues: 1174
  helix:  2.01 (0.18), residues: 806
  sheet: -0.76 (0.61), residues: 72
  loop :  0.17 (0.38), residues: 296

*********************** 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
  42 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 2
  residues processed: 40
  average time/residue: 0.1813
  time to fit residues: 12.1747
Evaluate side-chains
  32 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 1.110 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1068
  time to fit residues: 1.8433
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 55 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 87 optimal weight:    0.4980
   chunk 101 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 104 optimal weight:    5.9990
   overall best weight:    1.2988

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9326  Z= 0.183
  Angle     :  0.605  11.612  12668  Z= 0.304
  Chirality :  0.040   0.182   1484
  Planarity :  0.003   0.022   1616
  Dihedral  :  3.751  19.241   1306
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer Outliers :  0.64 %
  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:  2.05 (0.25), residues: 1174
  helix:  2.00 (0.18), residues: 806
  sheet: -0.72 (0.61), residues: 72
  loop :  0.24 (0.38), residues: 296

*********************** 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
  39 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 1
  residues processed: 36
  average time/residue: 0.1795
  time to fit residues: 10.9357
Evaluate side-chains
  32 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 1.130 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0879
  time to fit residues: 1.6692
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 107 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 94 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   chunk 103 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 110 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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: 0.8560
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9326  Z= 0.176
  Angle     :  0.625  13.447  12668  Z= 0.312
  Chirality :  0.040   0.212   1484
  Planarity :  0.003   0.023   1616
  Dihedral  :  3.731  20.682   1306
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer Outliers :  0.74 %
  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:  1.94 (0.25), residues: 1174
  helix:  1.91 (0.18), residues: 794
  sheet: -0.61 (0.62), residues: 72
  loop :  0.24 (0.37), residues: 308

*********************** 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
  41 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 1.053 
Fit side-chains
  outliers start: 7
  outliers final: 1
  residues processed: 41
  average time/residue: 0.1776
  time to fit residues: 12.2145
Evaluate side-chains
  35 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 1.136 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1304
  time to fit residues: 1.8111
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 52 optimal weight:    0.0980
   chunk 76 optimal weight:    0.8980
   chunk 115 optimal weight:    8.9990
   chunk 106 optimal weight:    9.9990
   chunk 92 optimal weight:    8.9990
   chunk 9 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   chunk 56 optimal weight:   20.0000
   chunk 73 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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: 0.8534
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9326  Z= 0.166
  Angle     :  0.643  12.516  12668  Z= 0.318
  Chirality :  0.041   0.218   1484
  Planarity :  0.003   0.025   1616
  Dihedral  :  3.668  19.083   1306
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.00 (0.25), residues: 1174
  helix:  1.96 (0.18), residues: 794
  sheet: -0.52 (0.61), residues: 72
  loop :  0.24 (0.38), residues: 308

********************** 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
  42 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 1.174 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1835
  time to fit residues: 12.9035
Evaluate side-chains
  37 residues out of total 940 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 1.214 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5064
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 92 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 80 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    2.3186

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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.034278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.025728 restraints weight = 87407.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.026581 restraints weight = 53219.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.027201 restraints weight = 38413.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8829
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9326  Z= 0.258
  Angle     :  0.736  14.172  12668  Z= 0.367
  Chirality :  0.042   0.199   1484
  Planarity :  0.003   0.026   1616
  Dihedral  :  3.871  21.848   1306
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer Outliers :  0.11 %
  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:  1.83 (0.25), residues: 1174
  helix:  1.80 (0.18), residues: 800
  sheet: -0.45 (0.63), residues: 72
  loop :  0.21 (0.38), residues: 302

===============================================================================
Job complete
usr+sys time: 1529.45 seconds
wall clock time: 29 minutes 1.19 seconds (1741.19 seconds total)