Starting phenix.real_space_refine
on Wed Jul 30 21:37:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x93_33065/07_2025/7x93_33065_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x93_33065/07_2025/7x93_33065.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x93_33065/07_2025/7x93_33065.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x93_33065/07_2025/7x93_33065.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x93_33065/07_2025/7x93_33065_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x93_33065/07_2025/7x93_33065_trim.cif"
  }
  resolution = 3.3
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    4191      2.51       5
     N    1093      2.21       5
     O    1265      1.98       5
     H    6162      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12742
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3057
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 3057
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 11, 'TRANS': 186}
    Chain: "D"
      Number of atoms: 3113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 3113
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "E"
      Number of atoms: 1797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 1797
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "F"
      Number of atoms: 1581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 1581
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 7, 'TRANS': 102}
    Chain: "G"
      Number of atoms: 3091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 3091
          Classifications: {'peptide': 200}
          Link IDs: {'PTRANS': 12, 'TRANS': 187}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "G"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 7.77, per 1000 atoms: 0.61
  Number of scatterers: 12742
  At special positions: 0
  Unit cell: (92.848, 103.625, 102.796, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      31     16.00
     O    1265      8.00
     N    1093      7.00
     C    4191      6.00
     H    6162      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 336 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 379 " - pdb=" SG  CYS D 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 391 " - pdb=" SG  CYS D 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 480 " - pdb=" SG  CYS D 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 336 " - pdb=" SG  CYS G 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 379 " - pdb=" SG  CYS G 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 391 " - pdb=" SG  CYS G 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G 480 " - pdb=" SG  CYS G 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA C   3 " - " MAN C   4 "
    ALPHA1-6
      " BMA C   3 " - " MAN C   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
      " NAG C   1 " - " ASN D 343 "
      " NAG G1301 " - " ASN G 343 "
  Time building additional restraints: 3.91
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1512

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 16 sheets defined
      15.3% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 344
      removed outlier: 4.013A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 371
      removed outlier: 4.526A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 4.150A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.665A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'D' and resid 337 through 344
      removed outlier: 3.698A  pdb=" N   VAL D 341 " --> pdb=" O   PRO D 337 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 349 through 353
    Processing helix  chain 'D' and resid 364 through 370
      removed outlier: 4.318A  pdb=" N   LEU D 368 " --> pdb=" O   ASP D 364 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 384 through 390
      removed outlier: 3.829A  pdb=" N   ASN D 388 " --> pdb=" O   THR D 385 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 406 through 410
    Processing helix  chain 'D' and resid 438 through 443
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.597A  pdb=" N   TYR E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'F' and resid 81 through 85
    Processing helix  chain 'G' and resid 337 through 343
      removed outlier: 3.557A  pdb=" N   VAL G 341 " --> pdb=" O   PRO G 337 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 349 through 353
    Processing helix  chain 'G' and resid 364 through 371
      removed outlier: 4.340A  pdb=" N   LEU G 368 " --> pdb=" O   ASP G 364 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 383 through 389
      removed outlier: 4.135A  pdb=" N   ASN G 388 " --> pdb=" O   THR G 385 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 405 through 410
      removed outlier: 4.140A  pdb=" N   ARG G 408 " --> pdb=" O   ASP G 405 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 416 through 422
    Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 453
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'D' and resid 354 through 358
    Processing sheet with id=AA6, first strand: chain 'D' and resid 452 through 454
    Processing sheet with id=AA7, first strand: chain 'D' and resid 473 through 474
    Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 6
    Processing sheet with id=AA9, first strand: chain 'E' and resid 58 through 60
      removed outlier: 6.531A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   LEU E  50 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   ILE E  34 " --> pdb=" O   LEU E  50 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 9 through 12
      removed outlier: 6.626A  pdb=" N   VAL F  10 " --> pdb=" O   THR F 108 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR F 105 " --> pdb=" O   TYR F  88 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ASP F  87 " --> pdb=" O   HIS F  40 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   TRP F  37 " --> pdb=" O   MET F  49 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 9 through 12
      removed outlier: 6.626A  pdb=" N   VAL F  10 " --> pdb=" O   THR F 108 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR F 105 " --> pdb=" O   TYR F  88 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 18 through 23
    Processing sheet with id=AB4, first strand: chain 'G' and resid 354 through 358
    Processing sheet with id=AB5, first strand: chain 'G' and resid 391 through 392
      removed outlier: 3.524A  pdb=" N   PHE G 392 " --> pdb=" O   VAL G 524 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   VAL G 524 " --> pdb=" O   PHE G 392 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'G' and resid 452 through 454
    Processing sheet with id=AB7, first strand: chain 'G' and resid 473 through 474
      removed outlier: 3.612A  pdb=" N   TYR G 489 " --> pdb=" O   TYR G 473 " (cutoff:3.500A)

    184 hydrogen bonds defined for protein.
    411 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: 5.36

  Time building geometry restraints manager: 4.61 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 6161
        1.03 -     1.23: 112
        1.23 -     1.43: 2915
        1.43 -     1.62: 3698
        1.62 -     1.82: 33
  Bond restraints: 12919
  Sorted by residual:
  bond pdb=" C1  BMA C   3 "
       pdb=" C2  BMA C   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.573 -0.054 2.00e-02 2.50e+03 7.18e+00
  bond pdb=" C1  BMA C   3 "
       pdb=" O5  BMA C   3 "
    ideal  model  delta    sigma   weight residual
    1.410  1.455 -0.045 2.00e-02 2.50e+03 5.15e+00
  bond pdb=" N   GLN E   1 "
       pdb=" CA  GLN E   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.91e+00
  bond pdb=" C5  MAN C   4 "
       pdb=" O5  MAN C   4 "
    ideal  model  delta    sigma   weight residual
    1.418  1.451 -0.033 2.00e-02 2.50e+03 2.79e+00
  bond pdb=" C1  NAG G1301 "
       pdb=" O5  NAG G1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.62e+00
  ... (remaining 12914 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.05: 23101
        7.05 -    14.11: 4
       14.11 -    21.16: 0
       21.16 -    28.22: 3
       28.22 -    35.27: 3
  Bond angle restraints: 23111
  Sorted by residual:
  angle pdb=" C   ALA A 344 "
        pdb=" CA  ALA A 344 "
        pdb=" HA  ALA A 344 "
      ideal   model   delta    sigma   weight residual
     109.00   73.73   35.27 3.00e+00 1.11e-01 1.38e+02
  angle pdb=" CB  ALA A 344 "
        pdb=" CA  ALA A 344 "
        pdb=" HA  ALA A 344 "
      ideal   model   delta    sigma   weight residual
     109.00   75.95   33.05 3.00e+00 1.11e-01 1.21e+02
  angle pdb=" N   ALA A 344 "
        pdb=" CA  ALA A 344 "
        pdb=" HA  ALA A 344 "
      ideal   model   delta    sigma   weight residual
     110.00   77.34   32.66 3.00e+00 1.11e-01 1.19e+02
  angle pdb=" CG2 THR A 478 "
        pdb=" CB  THR A 478 "
        pdb=" HB  THR A 478 "
      ideal   model   delta    sigma   weight residual
     108.00   80.59   27.41 3.00e+00 1.11e-01 8.35e+01
  angle pdb=" OG1 THR A 478 "
        pdb=" CB  THR A 478 "
        pdb=" HB  THR A 478 "
      ideal   model   delta    sigma   weight residual
     109.00   83.22   25.78 3.00e+00 1.11e-01 7.38e+01
  ... (remaining 23106 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.16: 5971
       24.16 -    48.33: 327
       48.33 -    72.49: 68
       72.49 -    96.65: 10
       96.65 -   120.82: 5
  Dihedral angle restraints: 6381
    sinusoidal: 3413
      harmonic: 2968
  Sorted by residual:
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.42   44.42     1      1.00e+01 1.00e-02 2.74e+01
  dihedral pdb=" CB  CYS D 480 "
           pdb=" SG  CYS D 480 "
           pdb=" SG  CYS D 488 "
           pdb=" CB  CYS D 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.32   40.32     1      1.00e+01 1.00e-02 2.28e+01
  dihedral pdb=" CB  CYS D 391 "
           pdb=" SG  CYS D 391 "
           pdb=" SG  CYS D 525 "
           pdb=" CB  CYS D 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -124.14   38.14     1      1.00e+01 1.00e-02 2.05e+01
  ... (remaining 6378 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.289: 995
       0.289 -    0.579: 2
       0.579 -    0.868: 0
       0.868 -    1.157: 0
       1.157 -    1.447: 1
  Chirality restraints: 998
  Sorted by residual:
  chirality pdb=" CB  THR A 478 "
            pdb=" CA  THR A 478 "
            pdb=" OG1 THR A 478 "
            pdb=" CG2 THR A 478 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    1.10    1.45 2.00e-01 2.50e+01 5.23e+01
  chirality pdb=" CA  ALA A 344 "
            pdb=" N   ALA A 344 "
            pdb=" C   ALA A 344 "
            pdb=" CB  ALA A 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.07    0.41 2.00e-01 2.50e+01 4.24e+00
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.06   -0.34 2.00e-01 2.50e+01 2.81e+00
  ... (remaining 995 not shown)

  Planarity restraints: 1970
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 346 "   -0.083 9.50e-02 1.11e+02   2.78e-02 9.20e-01
        pdb=" NE  ARG D 346 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 346 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 346 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 346 "    0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG D 346 "    0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG D 346 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG D 346 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG D 346 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG F  56 "    0.015 5.00e-02 4.00e+02   2.27e-02 8.26e-01
        pdb=" N   PRO F  57 "   -0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO F  57 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO F  57 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN G 506 "   -0.012 5.00e-02 4.00e+02   1.85e-02 5.50e-01
        pdb=" N   PRO G 507 "    0.032 5.00e-02 4.00e+02
        pdb=" CA  PRO G 507 "   -0.009 5.00e-02 4.00e+02
        pdb=" CD  PRO G 507 "   -0.010 5.00e-02 4.00e+02
  ... (remaining 1967 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 477
        2.16 -     2.77: 23876
        2.77 -     3.38: 33387
        3.38 -     3.99: 43760
        3.99 -     4.60: 67306
  Nonbonded interactions: 168806
  Sorted by model distance:
  nonbonded pdb=" H   GLN A 498 "
            pdb=" OD1 ASN A 501 "
     model   vdw
     1.554 2.450
  nonbonded pdb=" O   ASP F  28 "
            pdb=" H   GLY F  31 "
     model   vdw
     1.591 2.450
  nonbonded pdb=" HA  ALA A 344 "
            pdb=" HB3 ALA A 344 "
     model   vdw
     1.634 1.952
  nonbonded pdb="HH22 ARG E  67 "
            pdb=" OD2 ASP E  90 "
     model   vdw
     1.652 2.450
  nonbonded pdb=" OD1 ASN G 439 "
            pdb=" HG  SER G 443 "
     model   vdw
     1.657 2.450
  ... (remaining 168801 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 'D' and ((resid 331 and (name N or name CA or name C or name O or name CB \ 
 or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 or name H \ 
D21 or name HD22)) or resid 332 through 528))
  selection = (chain 'G' and ((resid 331 and (name N or name CA or name C or name O or name CB \ 
 or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 or name H \ 
D21 or name HD22)) or resid 332 through 528))
}

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 individual isotropic
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:             104.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.220
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     36.270
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  145.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6779  Z= 0.144
  Angle     :  0.581  14.649   9247  Z= 0.271
  Chirality :  0.065   1.447    998
  Planarity :  0.003   0.036   1189
  Dihedral  : 14.998 120.819   2516
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.62 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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: -0.89 (0.30), residues: 818
  helix: -1.63 (0.60), residues: 81
  sheet:  0.43 (0.38), residues: 198
  loop : -0.83 (0.27), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP G 436 
 HIS   0.004   0.001   HIS A 519 
 PHE   0.008   0.001   PHE F 101 
 TYR   0.009   0.001   TYR D 369 
 ARG   0.005   0.000   ARG F   8 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00944 (    3)
  link_NAG-ASN         : angle       3.69941 (    9)
  link_ALPHA1-6        : bond        0.00502 (    1)
  link_ALPHA1-6        : angle       1.56087 (    3)
  link_BETA1-4         : bond        0.01480 (    3)
  link_BETA1-4         : angle       5.77120 (    9)
  link_ALPHA1-3        : bond        0.00394 (    1)
  link_ALPHA1-3        : angle       1.61888 (    3)
  hydrogen bonds       : bond        0.16336 (  183)
  hydrogen bonds       : angle       7.11291 (  411)
  SS BOND              : bond        0.00215 (   14)
  SS BOND              : angle       0.71069 (   28)
  covalent geometry    : bond        0.00303 ( 6757)
  covalent geometry    : angle       0.53863 ( 9195)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8374 (m-30) cc_final: 0.8127 (m-30)
REVERT: A  493 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7854 (tm-30)
REVERT: D  417 LYS cc_start: 0.9337 (tppt) cc_final: 0.9016 (tppt)
REVERT: D  467 ASP cc_start: 0.7996 (t0) cc_final: 0.7745 (t70)
REVERT: D  486 PHE cc_start: 0.8782 (p90) cc_final: 0.8572 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.6243
  time to fit residues: 80.3704
Evaluate side-chains
  85 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 2.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 47 optimal weight:    7.9990
   chunk 73 optimal weight:    5.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
G 450 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.074768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.061200 restraints weight = 50947.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 3.68
r_work: 0.2907 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.0907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6779  Z= 0.152
  Angle     :  0.585  13.882   9247  Z= 0.282
  Chirality :  0.064   1.424    998
  Planarity :  0.003   0.036   1189
  Dihedral  : 10.274 116.310   1085
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.50 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  4.99 %
    Favored  : 94.59 %
  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: -1.05 (0.30), residues: 818
  helix: -2.03 (0.54), residues: 86
  sheet:  0.51 (0.39), residues: 190
  loop : -0.94 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 353 
 HIS   0.002   0.001   HIS G 519 
 PHE   0.015   0.001   PHE G 486 
 TYR   0.014   0.001   TYR G 380 
 ARG   0.003   0.000   ARG F   8 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01003 (    3)
  link_NAG-ASN         : angle       4.12763 (    9)
  link_ALPHA1-6        : bond        0.00590 (    1)
  link_ALPHA1-6        : angle       2.08846 (    3)
  link_BETA1-4         : bond        0.01607 (    3)
  link_BETA1-4         : angle       5.36125 (    9)
  link_ALPHA1-3        : bond        0.00928 (    1)
  link_ALPHA1-3        : angle       3.25508 (    3)
  hydrogen bonds       : bond        0.03526 (  183)
  hydrogen bonds       : angle       5.68874 (  411)
  SS BOND              : bond        0.00291 (   14)
  SS BOND              : angle       0.67275 (   28)
  covalent geometry    : bond        0.00342 ( 6757)
  covalent geometry    : angle       0.54154 ( 9195)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 1.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8594 (m-30) cc_final: 0.8387 (m-30)
REVERT: D  417 LYS cc_start: 0.9407 (tppt) cc_final: 0.9169 (tppt)
REVERT: D  467 ASP cc_start: 0.8462 (t0) cc_final: 0.8090 (t0)
REVERT: D  486 PHE cc_start: 0.8889 (p90) cc_final: 0.8563 (p90)
REVERT: D  516 GLU cc_start: 0.8407 (tt0) cc_final: 0.8149 (tt0)
  outliers start: 3
  outliers final: 3
  residues processed: 94
  average time/residue: 0.6534
  time to fit residues: 79.9089
Evaluate side-chains
  92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 1.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain D residue  340 GLU
Chi-restraints excluded: chain F residue   77 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 75 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 8 optimal weight:    0.4980
   chunk 35 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 60 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
** F  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.073787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.060287 restraints weight = 51017.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 3.67
r_work: 0.2879 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6779  Z= 0.186
  Angle     :  0.574  12.482   9247  Z= 0.279
  Chirality :  0.064   1.427    998
  Planarity :  0.003   0.033   1189
  Dihedral  :  9.076 117.504   1085
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.72 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  6.84 %
    Favored  : 92.45 %
  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: -1.28 (0.29), residues: 818
  helix: -2.28 (0.51), residues: 92
  sheet:  0.20 (0.38), residues: 198
  loop : -1.01 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G 436 
 HIS   0.001   0.001   HIS G 519 
 PHE   0.008   0.001   PHE G 486 
 TYR   0.009   0.001   TYR E  53 
 ARG   0.003   0.000   ARG F   8 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00920 (    3)
  link_NAG-ASN         : angle       3.77768 (    9)
  link_ALPHA1-6        : bond        0.00636 (    1)
  link_ALPHA1-6        : angle       1.64620 (    3)
  link_BETA1-4         : bond        0.01770 (    3)
  link_BETA1-4         : angle       5.20580 (    9)
  link_ALPHA1-3        : bond        0.01114 (    1)
  link_ALPHA1-3        : angle       3.20664 (    3)
  hydrogen bonds       : bond        0.03291 (  183)
  hydrogen bonds       : angle       5.46654 (  411)
  SS BOND              : bond        0.00278 (   14)
  SS BOND              : angle       0.66263 (   28)
  covalent geometry    : bond        0.00415 ( 6757)
  covalent geometry    : angle       0.53453 ( 9195)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 2.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8607 (m-30) cc_final: 0.8404 (m-30)
REVERT: A  484 GLU cc_start: 0.7595 (tp30) cc_final: 0.7257 (tp30)
REVERT: D  406 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8674 (tt0)
REVERT: D  417 LYS cc_start: 0.9402 (tppt) cc_final: 0.9166 (tppt)
REVERT: D  467 ASP cc_start: 0.8520 (t0) cc_final: 0.8025 (t0)
REVERT: D  486 PHE cc_start: 0.8954 (p90) cc_final: 0.8577 (p90)
REVERT: D  516 GLU cc_start: 0.8373 (tt0) cc_final: 0.8098 (tt0)
  outliers start: 5
  outliers final: 4
  residues processed: 92
  average time/residue: 0.6976
  time to fit residues: 81.1277
Evaluate side-chains
  91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain D residue  340 GLU
Chi-restraints excluded: chain D residue  406 GLU
Chi-restraints excluded: chain F residue   77 ILE
Chi-restraints excluded: chain G residue  444 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** F  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.072976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.059464 restraints weight = 51158.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 3.66
r_work: 0.2860 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   6779  Z= 0.201
  Angle     :  0.581  12.424   9247  Z= 0.283
  Chirality :  0.064   1.433    998
  Planarity :  0.003   0.039   1189
  Dihedral  :  8.615 115.332   1085
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.58 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  7.83 %
    Favored  : 91.60 %
  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: -1.37 (0.29), residues: 818
  helix: -2.29 (0.50), residues: 92
  sheet:  0.26 (0.38), residues: 193
  loop : -1.14 (0.27), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G 436 
 HIS   0.001   0.001   HIS G 519 
 PHE   0.011   0.001   PHE F 101 
 TYR   0.009   0.001   TYR G 380 
 ARG   0.003   0.000   ARG F   8 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00886 (    3)
  link_NAG-ASN         : angle       3.78030 (    9)
  link_ALPHA1-6        : bond        0.00475 (    1)
  link_ALPHA1-6        : angle       1.47006 (    3)
  link_BETA1-4         : bond        0.01706 (    3)
  link_BETA1-4         : angle       5.06065 (    9)
  link_ALPHA1-3        : bond        0.01145 (    1)
  link_ALPHA1-3        : angle       3.15432 (    3)
  hydrogen bonds       : bond        0.03224 (  183)
  hydrogen bonds       : angle       5.39180 (  411)
  SS BOND              : bond        0.00288 (   14)
  SS BOND              : angle       0.64168 (   28)
  covalent geometry    : bond        0.00449 ( 6757)
  covalent geometry    : angle       0.54291 ( 9195)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8593 (m-30) cc_final: 0.8378 (m-30)
REVERT: A  484 GLU cc_start: 0.7585 (tp30) cc_final: 0.7267 (tp30)
REVERT: D  406 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8675 (tt0)
REVERT: D  417 LYS cc_start: 0.9390 (tppt) cc_final: 0.9152 (tppt)
REVERT: D  467 ASP cc_start: 0.8514 (t0) cc_final: 0.7972 (t0)
REVERT: D  486 PHE cc_start: 0.8979 (p90) cc_final: 0.8570 (p90)
REVERT: D  516 GLU cc_start: 0.8361 (tt0) cc_final: 0.8058 (tt0)
REVERT: G  484 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8518 (mm-30)
  outliers start: 4
  outliers final: 3
  residues processed: 87
  average time/residue: 0.5203
  time to fit residues: 57.0415
Evaluate side-chains
  89 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain D residue  340 GLU
Chi-restraints excluded: chain D residue  406 GLU
Chi-restraints excluded: chain F residue   77 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 14 optimal weight:   10.0000
   chunk 69 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 11 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
** F  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.073131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.059706 restraints weight = 51105.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 3.63
r_work: 0.2867 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6779  Z= 0.169
  Angle     :  0.573  12.306   9247  Z= 0.279
  Chirality :  0.064   1.428    998
  Planarity :  0.003   0.033   1189
  Dihedral  :  8.399 113.476   1085
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.60 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  8.55 %
    Favored  : 90.88 %
  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: -1.38 (0.29), residues: 818
  helix: -2.16 (0.52), residues: 92
  sheet:  0.15 (0.38), residues: 198
  loop : -1.13 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G 436 
 HIS   0.002   0.001   HIS G 519 
 PHE   0.009   0.001   PHE F 101 
 TYR   0.007   0.001   TYR G 380 
 ARG   0.003   0.000   ARG F   8 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00899 (    3)
  link_NAG-ASN         : angle       3.72443 (    9)
  link_ALPHA1-6        : bond        0.00363 (    1)
  link_ALPHA1-6        : angle       1.53482 (    3)
  link_BETA1-4         : bond        0.01662 (    3)
  link_BETA1-4         : angle       5.03316 (    9)
  link_ALPHA1-3        : bond        0.01048 (    1)
  link_ALPHA1-3        : angle       2.92585 (    3)
  hydrogen bonds       : bond        0.03114 (  183)
  hydrogen bonds       : angle       5.30822 (  411)
  SS BOND              : bond        0.00264 (   14)
  SS BOND              : angle       0.55500 (   28)
  covalent geometry    : bond        0.00381 ( 6757)
  covalent geometry    : angle       0.53625 ( 9195)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8542 (m-30) cc_final: 0.8335 (m-30)
REVERT: A  484 GLU cc_start: 0.7624 (tp30) cc_final: 0.7323 (tp30)
REVERT: D  406 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8669 (tt0)
REVERT: D  417 LYS cc_start: 0.9391 (tppt) cc_final: 0.9152 (tppt)
REVERT: D  467 ASP cc_start: 0.8492 (t0) cc_final: 0.7947 (t0)
REVERT: D  486 PHE cc_start: 0.8992 (p90) cc_final: 0.8557 (p90)
REVERT: D  516 GLU cc_start: 0.8341 (tt0) cc_final: 0.8032 (tt0)
REVERT: G  420 ASP cc_start: 0.8992 (m-30) cc_final: 0.8773 (m-30)
REVERT: G  484 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8494 (mm-30)
  outliers start: 4
  outliers final: 3
  residues processed: 86
  average time/residue: 0.5014
  time to fit residues: 54.5595
Evaluate side-chains
  87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain D residue  340 GLU
Chi-restraints excluded: chain D residue  406 GLU
Chi-restraints excluded: chain F residue   77 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 32 optimal weight:    0.0670
   chunk 69 optimal weight:    4.9990
   chunk 40 optimal weight:    0.5980
   chunk 71 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 47 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   chunk 76 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 27 optimal weight:    0.0010
   overall best weight:    1.1126

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

Flipped N/Q/H residues before XYZ refinement:
** F  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.074110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.060592 restraints weight = 51209.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 3.69
r_work: 0.2886 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6779  Z= 0.110
  Angle     :  0.560  12.227   9247  Z= 0.271
  Chirality :  0.064   1.430    998
  Planarity :  0.003   0.031   1189
  Dihedral  :  8.110 111.025   1085
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.11 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  9.26 %
    Favored  : 90.17 %
  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: -1.28 (0.29), residues: 818
  helix: -2.14 (0.51), residues: 92
  sheet:  0.23 (0.38), residues: 198
  loop : -1.06 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 436 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.007   0.001   PHE F 101 
 TYR   0.006   0.001   TYR F  88 
 ARG   0.004   0.000   ARG F   8 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00924 (    3)
  link_NAG-ASN         : angle       3.63806 (    9)
  link_ALPHA1-6        : bond        0.00421 (    1)
  link_ALPHA1-6        : angle       1.47827 (    3)
  link_BETA1-4         : bond        0.01658 (    3)
  link_BETA1-4         : angle       4.96063 (    9)
  link_ALPHA1-3        : bond        0.01135 (    1)
  link_ALPHA1-3        : angle       2.78941 (    3)
  hydrogen bonds       : bond        0.02868 (  183)
  hydrogen bonds       : angle       5.25975 (  411)
  SS BOND              : bond        0.00220 (   14)
  SS BOND              : angle       0.45960 (   28)
  covalent geometry    : bond        0.00251 ( 6757)
  covalent geometry    : angle       0.52440 ( 9195)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8495 (m-30) cc_final: 0.8281 (m-30)
REVERT: A  484 GLU cc_start: 0.7633 (tp30) cc_final: 0.7335 (tp30)
REVERT: D  406 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8660 (tt0)
REVERT: D  417 LYS cc_start: 0.9375 (tppt) cc_final: 0.9127 (tppt)
REVERT: D  467 ASP cc_start: 0.8481 (t0) cc_final: 0.8054 (t70)
REVERT: D  486 PHE cc_start: 0.8977 (p90) cc_final: 0.8504 (p90)
  outliers start: 4
  outliers final: 1
  residues processed: 85
  average time/residue: 0.5013
  time to fit residues: 53.9111
Evaluate side-chains
  82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  406 GLU
Chi-restraints excluded: chain F residue   77 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 47 optimal weight:    8.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** F  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.073308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.059894 restraints weight = 50860.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 3.63
r_work: 0.2875 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
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      :  0.004   0.029   6779  Z= 0.156
  Angle     :  0.569  12.371   9247  Z= 0.276
  Chirality :  0.064   1.430    998
  Planarity :  0.003   0.030   1189
  Dihedral  :  8.010 109.181   1085
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.21 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  9.54 %
    Favored  : 89.74 %
  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: -1.29 (0.29), residues: 818
  helix: -2.13 (0.51), residues: 92
  sheet:  0.28 (0.38), residues: 193
  loop : -1.09 (0.27), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 436 
 HIS   0.002   0.001   HIS G 519 
 PHE   0.009   0.001   PHE F 101 
 TYR   0.007   0.001   TYR A 380 
 ARG   0.004   0.000   ARG F   8 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00933 (    3)
  link_NAG-ASN         : angle       3.65707 (    9)
  link_ALPHA1-6        : bond        0.00358 (    1)
  link_ALPHA1-6        : angle       1.49349 (    3)
  link_BETA1-4         : bond        0.01680 (    3)
  link_BETA1-4         : angle       5.02031 (    9)
  link_ALPHA1-3        : bond        0.01062 (    1)
  link_ALPHA1-3        : angle       2.94975 (    3)
  hydrogen bonds       : bond        0.03019 (  183)
  hydrogen bonds       : angle       5.21093 (  411)
  SS BOND              : bond        0.00243 (   14)
  SS BOND              : angle       0.50755 (   28)
  covalent geometry    : bond        0.00352 ( 6757)
  covalent geometry    : angle       0.53278 ( 9195)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8502 (m-30) cc_final: 0.8284 (m-30)
REVERT: A  484 GLU cc_start: 0.7622 (tp30) cc_final: 0.7315 (tp30)
REVERT: D  406 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8673 (tt0)
REVERT: D  417 LYS cc_start: 0.9387 (tppt) cc_final: 0.9147 (tppt)
REVERT: D  467 ASP cc_start: 0.8510 (t0) cc_final: 0.8071 (t70)
REVERT: D  486 PHE cc_start: 0.8986 (p90) cc_final: 0.8527 (p90)
REVERT: D  516 GLU cc_start: 0.8330 (tt0) cc_final: 0.8029 (tt0)
REVERT: G  484 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8471 (mm-30)
  outliers start: 5
  outliers final: 3
  residues processed: 85
  average time/residue: 0.5212
  time to fit residues: 56.7892
Evaluate side-chains
  83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  406 GLU
Chi-restraints excluded: chain F residue   39 GLN
Chi-restraints excluded: chain F residue   77 ILE
Chi-restraints excluded: chain G residue  398 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   chunk 47 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.074336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.060849 restraints weight = 50954.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 3.69
r_work: 0.2892 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6779  Z= 0.106
  Angle     :  0.564  12.311   9247  Z= 0.273
  Chirality :  0.064   1.436    998
  Planarity :  0.003   0.030   1189
  Dihedral  :  7.784 107.313   1085
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.99 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  9.83 %
    Favored  : 89.60 %
  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: -1.14 (0.29), residues: 818
  helix: -2.00 (0.54), residues: 86
  sheet:  0.29 (0.38), residues: 197
  loop : -0.97 (0.27), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 436 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.006   0.001   PHE F 101 
 TYR   0.010   0.001   TYR D 369 
 ARG   0.004   0.000   ARG F   8 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00930 (    3)
  link_NAG-ASN         : angle       3.59401 (    9)
  link_ALPHA1-6        : bond        0.00413 (    1)
  link_ALPHA1-6        : angle       1.45485 (    3)
  link_BETA1-4         : bond        0.01674 (    3)
  link_BETA1-4         : angle       4.96699 (    9)
  link_ALPHA1-3        : bond        0.01097 (    1)
  link_ALPHA1-3        : angle       2.75574 (    3)
  hydrogen bonds       : bond        0.02823 (  183)
  hydrogen bonds       : angle       5.18179 (  411)
  SS BOND              : bond        0.00211 (   14)
  SS BOND              : angle       0.44668 (   28)
  covalent geometry    : bond        0.00243 ( 6757)
  covalent geometry    : angle       0.52862 ( 9195)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8490 (m-30) cc_final: 0.8268 (m-30)
REVERT: A  484 GLU cc_start: 0.7622 (tp30) cc_final: 0.7322 (tp30)
REVERT: D  406 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8651 (tt0)
REVERT: D  417 LYS cc_start: 0.9374 (tppt) cc_final: 0.9123 (tppt)
REVERT: D  467 ASP cc_start: 0.8487 (t0) cc_final: 0.8055 (t70)
REVERT: D  486 PHE cc_start: 0.8979 (p90) cc_final: 0.8488 (p90)
REVERT: D  516 GLU cc_start: 0.8347 (tt0) cc_final: 0.8048 (tt0)
  outliers start: 4
  outliers final: 3
  residues processed: 86
  average time/residue: 0.4959
  time to fit residues: 54.2822
Evaluate side-chains
  83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  340 GLU
Chi-restraints excluded: chain D residue  406 GLU
Chi-restraints excluded: chain F residue   39 GLN
Chi-restraints excluded: chain G residue  398 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0570
   chunk 5 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.1502

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.074394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.060873 restraints weight = 50628.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 3.68
r_work: 0.2895 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6779  Z= 0.111
  Angle     :  0.562  12.296   9247  Z= 0.271
  Chirality :  0.064   1.433    998
  Planarity :  0.003   0.029   1189
  Dihedral  :  7.581 104.769   1085
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.87 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  9.83 %
    Favored  : 89.60 %
  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: -1.11 (0.29), residues: 818
  helix: -2.11 (0.55), residues: 78
  sheet:  0.22 (0.37), residues: 200
  loop : -0.91 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 436 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.007   0.001   PHE F 101 
 TYR   0.007   0.001   TYR G 369 
 ARG   0.004   0.000   ARG F   8 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00942 (    3)
  link_NAG-ASN         : angle       3.60230 (    9)
  link_ALPHA1-6        : bond        0.00375 (    1)
  link_ALPHA1-6        : angle       1.48170 (    3)
  link_BETA1-4         : bond        0.01663 (    3)
  link_BETA1-4         : angle       4.96242 (    9)
  link_ALPHA1-3        : bond        0.01075 (    1)
  link_ALPHA1-3        : angle       2.85227 (    3)
  hydrogen bonds       : bond        0.02767 (  183)
  hydrogen bonds       : angle       5.11984 (  411)
  SS BOND              : bond        0.00198 (   14)
  SS BOND              : angle       0.47400 (   28)
  covalent geometry    : bond        0.00255 ( 6757)
  covalent geometry    : angle       0.52592 ( 9195)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8470 (m-30) cc_final: 0.8246 (m-30)
REVERT: A  484 GLU cc_start: 0.7642 (tp30) cc_final: 0.7332 (tp30)
REVERT: D  406 GLU cc_start: 0.9209 (OUTLIER) cc_final: 0.8664 (tt0)
REVERT: D  417 LYS cc_start: 0.9377 (tppt) cc_final: 0.9125 (tppt)
REVERT: D  467 ASP cc_start: 0.8501 (t0) cc_final: 0.8059 (t70)
REVERT: D  486 PHE cc_start: 0.8987 (p90) cc_final: 0.8496 (p90)
REVERT: D  516 GLU cc_start: 0.8344 (tt0) cc_final: 0.8041 (tt0)
  outliers start: 4
  outliers final: 3
  residues processed: 80
  average time/residue: 0.5315
  time to fit residues: 53.5972
Evaluate side-chains
  81 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  340 GLU
Chi-restraints excluded: chain D residue  406 GLU
Chi-restraints excluded: chain F residue   39 GLN
Chi-restraints excluded: chain G residue  398 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    0.1980
   chunk 6 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 77 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.6782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.074881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.061348 restraints weight = 50605.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 3.69
r_work: 0.2912 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6779  Z= 0.096
  Angle     :  0.565  12.219   9247  Z= 0.272
  Chirality :  0.064   1.435    998
  Planarity :  0.003   0.031   1189
  Dihedral  :  7.391 102.932   1085
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.50 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 10.40 %
    Favored  : 89.03 %
  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: -1.02 (0.29), residues: 818
  helix: -1.96 (0.56), residues: 78
  sheet:  0.29 (0.38), residues: 200
  loop : -0.87 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 436 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.006   0.001   PHE G 486 
 TYR   0.014   0.001   TYR D 369 
 ARG   0.003   0.000   ARG F   8 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00953 (    3)
  link_NAG-ASN         : angle       3.58755 (    9)
  link_ALPHA1-6        : bond        0.00452 (    1)
  link_ALPHA1-6        : angle       1.47112 (    3)
  link_BETA1-4         : bond        0.01644 (    3)
  link_BETA1-4         : angle       4.92265 (    9)
  link_ALPHA1-3        : bond        0.01152 (    1)
  link_ALPHA1-3        : angle       2.82104 (    3)
  hydrogen bonds       : bond        0.02660 (  183)
  hydrogen bonds       : angle       5.07960 (  411)
  SS BOND              : bond        0.00189 (   14)
  SS BOND              : angle       0.43099 (   28)
  covalent geometry    : bond        0.00223 ( 6757)
  covalent geometry    : angle       0.52981 ( 9195)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 1.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8458 (m-30) cc_final: 0.8230 (m-30)
REVERT: A  484 GLU cc_start: 0.7637 (tp30) cc_final: 0.7327 (tp30)
REVERT: D  406 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8659 (tt0)
REVERT: D  417 LYS cc_start: 0.9376 (tppt) cc_final: 0.8904 (tppt)
REVERT: D  467 ASP cc_start: 0.8484 (t0) cc_final: 0.8051 (t70)
REVERT: D  486 PHE cc_start: 0.8978 (p90) cc_final: 0.8472 (p90)
  outliers start: 4
  outliers final: 3
  residues processed: 86
  average time/residue: 0.5650
  time to fit residues: 60.9340
Evaluate side-chains
  83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  340 GLU
Chi-restraints excluded: chain D residue  406 GLU
Chi-restraints excluded: chain F residue   39 GLN
Chi-restraints excluded: chain G residue  398 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 56 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 14 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0370
   chunk 20 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.7258

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.075110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.061519 restraints weight = 50579.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 3.69
r_work: 0.2915 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6779  Z= 0.098
  Angle     :  0.564  12.194   9247  Z= 0.272
  Chirality :  0.064   1.432    998
  Planarity :  0.003   0.030   1189
  Dihedral  :  7.266 101.174   1085
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.38 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.54 %
    Favored  : 88.75 %
  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: -0.97 (0.30), residues: 818
  helix: -1.82 (0.57), residues: 78
  sheet:  0.31 (0.38), residues: 200
  loop : -0.84 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 436 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.006   0.001   PHE G 486 
 TYR   0.010   0.001   TYR D 369 
 ARG   0.004   0.000   ARG F   8 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00961 (    3)
  link_NAG-ASN         : angle       3.60258 (    9)
  link_ALPHA1-6        : bond        0.00426 (    1)
  link_ALPHA1-6        : angle       1.48957 (    3)
  link_BETA1-4         : bond        0.01658 (    3)
  link_BETA1-4         : angle       4.91361 (    9)
  link_ALPHA1-3        : bond        0.01150 (    1)
  link_ALPHA1-3        : angle       2.90052 (    3)
  hydrogen bonds       : bond        0.02654 (  183)
  hydrogen bonds       : angle       5.05051 (  411)
  SS BOND              : bond        0.00179 (   14)
  SS BOND              : angle       0.44119 (   28)
  covalent geometry    : bond        0.00227 ( 6757)
  covalent geometry    : angle       0.52856 ( 9195)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6569.19 seconds
wall clock time: 118 minutes 45.52 seconds (7125.52 seconds total)