Starting phenix.real_space_refine
on Wed Mar  4 10:11:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x93_33065/03_2026/7x93_33065_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x93_33065/03_2026/7x93_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x93_33065/03_2026/7x93_33065_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x93_33065/03_2026/7x93_33065_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x93_33065/03_2026/7x93_33065.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x93_33065/03_2026/7x93_33065.map"
  }
  resolution = 3.3
  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
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.58, per 1000 atoms: 0.20
  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: 1.26
  Conformation dependent library (CDL) restraints added in 420.5 milliseconds
  

  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: 0.33
  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: 2.62

  Time building geometry restraints manager: 1.69 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:             0.710
  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:             0.060
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.140
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.650
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.005   0.000   ARG F   8 
 TYR   0.009   0.001   TYR D 369 
 PHE   0.008   0.001   PHE F 101 
 TRP   0.005   0.001   TRP G 436 
 HIS   0.004   0.001   HIS A 519 

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

*********************** 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  : 0.342 
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: 0.2378
  time to fit residues: 30.1450
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  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0000
   chunk 74 optimal weight:    0.5980
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.3319 r_free = 0.3319 target = 0.075102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.061567 restraints weight = 50743.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 3.68
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: 0.8258
moved from start:          0.0918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6779  Z= 0.139
  Angle     :  0.583  13.401   9247  Z= 0.281
  Chirality :  0.064   1.424    998
  Planarity :  0.003   0.037   1189
  Dihedral  : 10.184 116.361   1085
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.38 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  4.70 %
    Favored  : 94.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.30), residues: 818
  helix: -2.15 (0.51), residues: 92
  sheet:  0.52 (0.39), residues: 190
  loop : -0.92 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 457 
 TYR   0.013   0.001   TYR E  53 
 PHE   0.014   0.001   PHE G 486 
 TRP   0.006   0.001   TRP D 353 
 HIS   0.002   0.001   HIS G 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6757)
  covalent geometry    : angle       0.54032 ( 9195)
  SS BOND              : bond        0.00281 (   14)
  SS BOND              : angle       0.64785 (   28)
  hydrogen bonds       : bond        0.03339 (  183)
  hydrogen bonds       : angle       5.66555 (  411)
  link_ALPHA1-3        : bond        0.00901 (    1)
  link_ALPHA1-3        : angle       3.25149 (    3)
  link_ALPHA1-6        : bond        0.00762 (    1)
  link_ALPHA1-6        : angle       2.15367 (    3)
  link_BETA1-4         : bond        0.01680 (    3)
  link_BETA1-4         : angle       5.21685 (    9)
  link_NAG-ASN         : bond        0.00985 (    3)
  link_NAG-ASN         : angle       4.14430 (    9)

*********************** 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  : 0.360 
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: 0.8590 (m-30) cc_final: 0.8384 (m-30)
REVERT: D  417 LYS cc_start: 0.9405 (tppt) cc_final: 0.9162 (tppt)
REVERT: D  467 ASP cc_start: 0.8463 (t0) cc_final: 0.8098 (t0)
REVERT: D  486 PHE cc_start: 0.8884 (p90) cc_final: 0.8559 (p90)
REVERT: D  516 GLU cc_start: 0.8408 (tt0) cc_final: 0.8151 (tt0)
  outliers start: 3
  outliers final: 3
  residues processed: 94
  average time/residue: 0.2396
  time to fit residues: 28.0925
Evaluate side-chains
  91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
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 76 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.073979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.060466 restraints weight = 51356.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 3.66
r_work: 0.2892 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6779  Z= 0.171
  Angle     :  0.567  12.625   9247  Z= 0.274
  Chirality :  0.064   1.425    998
  Planarity :  0.003   0.033   1189
  Dihedral  :  9.082 116.992   1085
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.11 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  6.70 %
    Favored  : 92.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.29), residues: 818
  helix: -2.24 (0.52), residues: 92
  sheet:  0.24 (0.38), residues: 198
  loop : -0.99 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F   8 
 TYR   0.012   0.001   TYR E  53 
 PHE   0.009   0.001   PHE G 486 
 TRP   0.008   0.001   TRP G 436 
 HIS   0.002   0.001   HIS G 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 6757)
  covalent geometry    : angle       0.52662 ( 9195)
  SS BOND              : bond        0.00269 (   14)
  SS BOND              : angle       0.63021 (   28)
  hydrogen bonds       : bond        0.03220 (  183)
  hydrogen bonds       : angle       5.45072 (  411)
  link_ALPHA1-3        : bond        0.00924 (    1)
  link_ALPHA1-3        : angle       3.05024 (    3)
  link_ALPHA1-6        : bond        0.00667 (    1)
  link_ALPHA1-6        : angle       1.55132 (    3)
  link_BETA1-4         : bond        0.01794 (    3)
  link_BETA1-4         : angle       5.21173 (    9)
  link_NAG-ASN         : bond        0.00907 (    3)
  link_NAG-ASN         : angle       3.79687 (    9)

*********************** 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
  94 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.314 
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: 0.8605 (m-30) cc_final: 0.8400 (m-30)
REVERT: A  484 GLU cc_start: 0.7570 (tp30) cc_final: 0.7243 (tp30)
REVERT: D  406 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8669 (tt0)
REVERT: D  417 LYS cc_start: 0.9396 (tppt) cc_final: 0.8931 (tppt)
REVERT: D  467 ASP cc_start: 0.8491 (t0) cc_final: 0.7966 (t0)
REVERT: D  486 PHE cc_start: 0.8946 (p90) cc_final: 0.8592 (p90)
REVERT: D  516 GLU cc_start: 0.8383 (tt0) cc_final: 0.8095 (tt0)
  outliers start: 4
  outliers final: 3
  residues processed: 92
  average time/residue: 0.2385
  time to fit residues: 27.3749
Evaluate side-chains
  91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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   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 79 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0970
   chunk 51 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 76 optimal weight:    9.9990
   chunk 12 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    2.4186

-------------------------------------------------------------------------------
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 = 0.3285 r_free = 0.3285 target = 0.073794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.060301 restraints weight = 50778.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 3.66
r_work: 0.2882 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1230

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= 0.169
  Angle     :  0.568  12.383   9247  Z= 0.275
  Chirality :  0.064   1.425    998
  Planarity :  0.003   0.031   1189
  Dihedral  :  8.704 115.703   1085
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.60 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  7.41 %
    Favored  : 91.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.29), residues: 818
  helix: -2.22 (0.52), residues: 92
  sheet:  0.22 (0.38), residues: 198
  loop : -1.04 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F   8 
 TYR   0.006   0.001   TYR A 351 
 PHE   0.008   0.001   PHE G 486 
 TRP   0.008   0.001   TRP G 436 
 HIS   0.002   0.001   HIS G 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 6757)
  covalent geometry    : angle       0.52950 ( 9195)
  SS BOND              : bond        0.00265 (   14)
  SS BOND              : angle       0.59085 (   28)
  hydrogen bonds       : bond        0.03098 (  183)
  hydrogen bonds       : angle       5.36180 (  411)
  link_ALPHA1-3        : bond        0.01083 (    1)
  link_ALPHA1-3        : angle       3.08925 (    3)
  link_ALPHA1-6        : bond        0.00469 (    1)
  link_ALPHA1-6        : angle       1.56099 (    3)
  link_BETA1-4         : bond        0.01727 (    3)
  link_BETA1-4         : angle       5.07481 (    9)
  link_NAG-ASN         : bond        0.00908 (    3)
  link_NAG-ASN         : angle       3.74933 (    9)

*********************** 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
  92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.340 
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: 0.8574 (m-30) cc_final: 0.8347 (m-30)
REVERT: A  484 GLU cc_start: 0.7609 (tp30) cc_final: 0.7278 (tp30)
REVERT: D  406 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8681 (tt0)
REVERT: D  417 LYS cc_start: 0.9397 (tppt) cc_final: 0.8934 (tppt)
REVERT: D  467 ASP cc_start: 0.8521 (t0) cc_final: 0.8006 (t0)
REVERT: D  486 PHE cc_start: 0.8964 (p90) cc_final: 0.8629 (p90)
REVERT: D  516 GLU cc_start: 0.8364 (tt0) cc_final: 0.8080 (tt0)
  outliers start: 5
  outliers final: 4
  residues processed: 88
  average time/residue: 0.2523
  time to fit residues: 27.6584
Evaluate side-chains
  90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  486 PHE
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 19 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 = 0.3300 r_free = 0.3300 target = 0.074496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.060931 restraints weight = 50903.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 3.70
r_work: 0.2897 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6779  Z= 0.112
  Angle     :  0.553  12.172   9247  Z= 0.267
  Chirality :  0.064   1.425    998
  Planarity :  0.003   0.035   1189
  Dihedral  :  8.431 114.216   1085
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.75 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  8.26 %
    Favored  : 91.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.30), residues: 818
  helix: -2.24 (0.55), residues: 84
  sheet:  0.24 (0.38), residues: 200
  loop : -0.96 (0.27), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F   8 
 TYR   0.005   0.001   TYR A 351 
 PHE   0.007   0.001   PHE G 486 
 TRP   0.007   0.001   TRP G 436 
 HIS   0.002   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6757)
  covalent geometry    : angle       0.51560 ( 9195)
  SS BOND              : bond        0.00234 (   14)
  SS BOND              : angle       0.49212 (   28)
  hydrogen bonds       : bond        0.02890 (  183)
  hydrogen bonds       : angle       5.29802 (  411)
  link_ALPHA1-3        : bond        0.01188 (    1)
  link_ALPHA1-3        : angle       2.87753 (    3)
  link_ALPHA1-6        : bond        0.00357 (    1)
  link_ALPHA1-6        : angle       1.51143 (    3)
  link_BETA1-4         : bond        0.01691 (    3)
  link_BETA1-4         : angle       4.99234 (    9)
  link_NAG-ASN         : bond        0.00929 (    3)
  link_NAG-ASN         : angle       3.69084 (    9)

*********************** 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
  92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.342 
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: 0.8549 (m-30) cc_final: 0.8326 (m-30)
REVERT: A  484 GLU cc_start: 0.7611 (tp30) cc_final: 0.7284 (tp30)
REVERT: D  406 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8661 (tt0)
REVERT: D  417 LYS cc_start: 0.9384 (tppt) cc_final: 0.8914 (tppt)
REVERT: D  467 ASP cc_start: 0.8498 (t0) cc_final: 0.7973 (t0)
REVERT: D  486 PHE cc_start: 0.8966 (p90) cc_final: 0.8541 (p90)
  outliers start: 4
  outliers final: 2
  residues processed: 89
  average time/residue: 0.2333
  time to fit residues: 25.9938
Evaluate side-chains
  86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  486 PHE
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 38 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   chunk 41 optimal weight:    8.9990
   chunk 16 optimal weight:    0.6980
   chunk 73 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    2.1184

-------------------------------------------------------------------------------
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 = 0.3293 r_free = 0.3293 target = 0.074112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.060581 restraints weight = 50852.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 3.66
r_work: 0.2885 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6779  Z= 0.152
  Angle     :  0.563  12.278   9247  Z= 0.272
  Chirality :  0.064   1.429    998
  Planarity :  0.003   0.034   1189
  Dihedral  :  8.283 112.506   1085
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.21 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  8.55 %
    Favored  : 91.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.29), residues: 818
  helix: -2.16 (0.54), residues: 86
  sheet:  0.36 (0.38), residues: 193
  loop : -1.01 (0.27), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F   8 
 TYR   0.008   0.001   TYR G 380 
 PHE   0.007   0.001   PHE F 101 
 TRP   0.008   0.001   TRP G 436 
 HIS   0.001   0.001   HIS G 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6757)
  covalent geometry    : angle       0.52590 ( 9195)
  SS BOND              : bond        0.00237 (   14)
  SS BOND              : angle       0.52133 (   28)
  hydrogen bonds       : bond        0.02976 (  183)
  hydrogen bonds       : angle       5.24162 (  411)
  link_ALPHA1-3        : bond        0.01082 (    1)
  link_ALPHA1-3        : angle       2.91434 (    3)
  link_ALPHA1-6        : bond        0.00328 (    1)
  link_ALPHA1-6        : angle       1.49071 (    3)
  link_BETA1-4         : bond        0.01693 (    3)
  link_BETA1-4         : angle       5.01029 (    9)
  link_NAG-ASN         : bond        0.00917 (    3)
  link_NAG-ASN         : angle       3.67291 (    9)

*********************** 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: 3
    poor density    : 84
  time to evaluate  : 0.342 
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: 0.8566 (m-30) cc_final: 0.8340 (m-30)
REVERT: A  484 GLU cc_start: 0.7614 (tp30) cc_final: 0.7287 (tp30)
REVERT: D  406 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8676 (tt0)
REVERT: D  417 LYS cc_start: 0.9389 (tppt) cc_final: 0.8920 (tppt)
REVERT: D  467 ASP cc_start: 0.8492 (t0) cc_final: 0.7939 (t0)
REVERT: D  486 PHE cc_start: 0.8985 (p90) cc_final: 0.8554 (p90)
REVERT: D  516 GLU cc_start: 0.8357 (tt0) cc_final: 0.8055 (tt0)
  outliers start: 3
  outliers final: 1
  residues processed: 85
  average time/residue: 0.2475
  time to fit residues: 26.3508
Evaluate side-chains
  83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
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 71 optimal weight:    4.9990
   chunk 47 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3254 r_free = 0.3254 target = 0.072136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.058348 restraints weight = 52020.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 3.68
r_work: 0.2839 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   6779  Z= 0.263
  Angle     :  0.610  12.498   9247  Z= 0.300
  Chirality :  0.064   1.432    998
  Planarity :  0.004   0.032   1189
  Dihedral  :  8.297 110.876   1085
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.68 %
    Favored  : 91.20 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.42 (0.29), residues: 818
  helix: -2.15 (0.51), residues: 92
  sheet:  0.16 (0.37), residues: 193
  loop : -1.18 (0.27), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F   8 
 TYR   0.011   0.001   TYR G 380 
 PHE   0.016   0.001   PHE F 101 
 TRP   0.009   0.001   TRP G 436 
 HIS   0.002   0.001   HIS G 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 ( 6757)
  covalent geometry    : angle       0.57348 ( 9195)
  SS BOND              : bond        0.00326 (   14)
  SS BOND              : angle       0.70990 (   28)
  hydrogen bonds       : bond        0.03448 (  183)
  hydrogen bonds       : angle       5.34422 (  411)
  link_ALPHA1-3        : bond        0.00951 (    1)
  link_ALPHA1-3        : angle       3.16973 (    3)
  link_ALPHA1-6        : bond        0.00397 (    1)
  link_ALPHA1-6        : angle       1.53241 (    3)
  link_BETA1-4         : bond        0.01724 (    3)
  link_BETA1-4         : angle       5.10342 (    9)
  link_NAG-ASN         : bond        0.00903 (    3)
  link_NAG-ASN         : angle       3.83363 (    9)

*********************** 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
  86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8535 (m-30) cc_final: 0.8316 (m-30)
REVERT: A  484 GLU cc_start: 0.7584 (tp30) cc_final: 0.7281 (tp30)
REVERT: D  406 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8677 (tt0)
REVERT: D  417 LYS cc_start: 0.9400 (tppt) cc_final: 0.9170 (tppt)
REVERT: D  467 ASP cc_start: 0.8551 (t0) cc_final: 0.7976 (t0)
REVERT: D  486 PHE cc_start: 0.8975 (p90) cc_final: 0.8519 (p90)
REVERT: D  516 GLU cc_start: 0.8356 (tt0) cc_final: 0.8054 (tt0)
REVERT: G  484 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8565 (mm-30)
  outliers start: 5
  outliers final: 3
  residues processed: 83
  average time/residue: 0.2565
  time to fit residues: 26.5027
Evaluate side-chains
  84 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 44 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   overall best weight:    1.7388

-------------------------------------------------------------------------------
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 = 0.3274 r_free = 0.3274 target = 0.073236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.059744 restraints weight = 50622.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 3.65
r_work: 0.2869 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6779  Z= 0.135
  Angle     :  0.574  12.389   9247  Z= 0.279
  Chirality :  0.064   1.438    998
  Planarity :  0.003   0.031   1189
  Dihedral  :  8.034 109.316   1085
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.23 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 10.11 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.29), residues: 818
  helix: -2.04 (0.51), residues: 92
  sheet:  0.25 (0.38), residues: 193
  loop : -1.10 (0.27), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F   8 
 TYR   0.007   0.001   TYR A 369 
 PHE   0.009   0.001   PHE F 101 
 TRP   0.008   0.001   TRP G 436 
 HIS   0.002   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6757)
  covalent geometry    : angle       0.53815 ( 9195)
  SS BOND              : bond        0.00246 (   14)
  SS BOND              : angle       0.52220 (   28)
  hydrogen bonds       : bond        0.03053 (  183)
  hydrogen bonds       : angle       5.26049 (  411)
  link_ALPHA1-3        : bond        0.01088 (    1)
  link_ALPHA1-3        : angle       2.84771 (    3)
  link_ALPHA1-6        : bond        0.00569 (    1)
  link_ALPHA1-6        : angle       1.52566 (    3)
  link_BETA1-4         : bond        0.01665 (    3)
  link_BETA1-4         : angle       5.00537 (    9)
  link_NAG-ASN         : bond        0.00907 (    3)
  link_NAG-ASN         : angle       3.70177 (    9)

*********************** 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
  86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.341 
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: 0.8477 (m-30) cc_final: 0.8256 (m-30)
REVERT: A  484 GLU cc_start: 0.7583 (tp30) cc_final: 0.7298 (tp30)
REVERT: D  406 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8650 (tt0)
REVERT: D  417 LYS cc_start: 0.9378 (tppt) cc_final: 0.9138 (tppt)
REVERT: D  467 ASP cc_start: 0.8490 (t0) cc_final: 0.8041 (t70)
REVERT: D  486 PHE cc_start: 0.8979 (p90) cc_final: 0.8517 (p90)
REVERT: D  516 GLU cc_start: 0.8315 (tt0) cc_final: 0.8011 (tt0)
REVERT: G  484 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8564 (mm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 84
  average time/residue: 0.2475
  time to fit residues: 25.9529
Evaluate side-chains
  83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
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   77 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 76 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3302 r_free = 0.3302 target = 0.074633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.061159 restraints weight = 50638.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 3.67
r_work: 0.2898 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6779  Z= 0.100
  Angle     :  0.563  12.291   9247  Z= 0.273
  Chirality :  0.064   1.441    998
  Planarity :  0.003   0.031   1189
  Dihedral  :  7.686 106.252   1085
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.23 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  9.97 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.29), residues: 818
  helix: -1.94 (0.53), residues: 86
  sheet:  0.24 (0.38), residues: 198
  loop : -0.96 (0.27), residues: 534

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 6757)
  covalent geometry    : angle       0.52748 ( 9195)
  SS BOND              : bond        0.00203 (   14)
  SS BOND              : angle       0.45833 (   28)
  hydrogen bonds       : bond        0.02774 (  183)
  hydrogen bonds       : angle       5.16560 (  411)
  link_ALPHA1-3        : bond        0.01147 (    1)
  link_ALPHA1-3        : angle       2.75381 (    3)
  link_ALPHA1-6        : bond        0.00413 (    1)
  link_ALPHA1-6        : angle       1.45809 (    3)
  link_BETA1-4         : bond        0.01651 (    3)
  link_BETA1-4         : angle       4.95909 (    9)
  link_NAG-ASN         : bond        0.00973 (    3)
  link_NAG-ASN         : angle       3.60694 (    9)

*********************** 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
  86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.338 
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: 0.8472 (m-30) cc_final: 0.8243 (m-30)
REVERT: A  484 GLU cc_start: 0.7600 (tp30) cc_final: 0.7294 (tp30)
REVERT: D  406 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8652 (tt0)
REVERT: D  417 LYS cc_start: 0.9375 (tppt) cc_final: 0.9130 (tppt)
REVERT: D  467 ASP cc_start: 0.8476 (t0) cc_final: 0.8060 (t70)
REVERT: D  486 PHE cc_start: 0.8982 (p90) cc_final: 0.8525 (p90)
REVERT: G  484 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8499 (mm-30)
  outliers start: 3
  outliers final: 1
  residues processed: 84
  average time/residue: 0.2469
  time to fit residues: 25.8588
Evaluate side-chains
  81 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  406 GLU
Chi-restraints excluded: chain F residue   39 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 34 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0970
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.3293 r_free = 0.3293 target = 0.074149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.060645 restraints weight = 51255.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 3.69
r_work: 0.2889 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6779  Z= 0.111
  Angle     :  0.567  12.307   9247  Z= 0.274
  Chirality :  0.064   1.435    998
  Planarity :  0.003   0.029   1189
  Dihedral  :  7.543 104.234   1085
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.87 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 10.26 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.29), residues: 818
  helix: -1.82 (0.54), residues: 86
  sheet:  0.25 (0.38), residues: 198
  loop : -0.94 (0.27), residues: 534

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6757)
  covalent geometry    : angle       0.53165 ( 9195)
  SS BOND              : bond        0.00203 (   14)
  SS BOND              : angle       0.46858 (   28)
  hydrogen bonds       : bond        0.02769 (  183)
  hydrogen bonds       : angle       5.11982 (  411)
  link_ALPHA1-3        : bond        0.01087 (    1)
  link_ALPHA1-3        : angle       2.86509 (    3)
  link_ALPHA1-6        : bond        0.00377 (    1)
  link_ALPHA1-6        : angle       1.47200 (    3)
  link_BETA1-4         : bond        0.01658 (    3)
  link_BETA1-4         : angle       4.97346 (    9)
  link_NAG-ASN         : bond        0.00941 (    3)
  link_NAG-ASN         : angle       3.62532 (    9)

********************** 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
  81 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.359 
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: 0.8474 (m-30) cc_final: 0.8246 (m-30)
REVERT: A  484 GLU cc_start: 0.7625 (tp30) cc_final: 0.7318 (tp30)
REVERT: D  406 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8673 (tt0)
REVERT: D  417 LYS cc_start: 0.9378 (tppt) cc_final: 0.9131 (tppt)
REVERT: D  467 ASP cc_start: 0.8496 (t0) cc_final: 0.8060 (t70)
REVERT: D  486 PHE cc_start: 0.8989 (p90) cc_final: 0.8524 (p90)
REVERT: D  516 GLU cc_start: 0.8353 (tt0) cc_final: 0.8069 (tt0)
  outliers start: 2
  outliers final: 1
  residues processed: 80
  average time/residue: 0.2576
  time to fit residues: 25.6612
Evaluate side-chains
  80 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 78
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  406 GLU
Chi-restraints excluded: chain F residue   39 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 78 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 36 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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 = 0.3293 r_free = 0.3293 target = 0.074192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.060692 restraints weight = 50563.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 3.66
r_work: 0.2891 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1607

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= 0.131
  Angle     :  0.573  12.386   9247  Z= 0.277
  Chirality :  0.064   1.433    998
  Planarity :  0.003   0.028   1189
  Dihedral  :  7.475 102.688   1085
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.23 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 10.40 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.29), residues: 818
  helix: -1.77 (0.55), residues: 86
  sheet:  0.23 (0.37), residues: 198
  loop : -0.95 (0.27), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F   8 
 TYR   0.006   0.001   TYR G 369 
 PHE   0.008   0.001   PHE F 101 
 TRP   0.007   0.001   TRP G 436 
 HIS   0.002   0.001   HIS G 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6757)
  covalent geometry    : angle       0.53756 ( 9195)
  SS BOND              : bond        0.00211 (   14)
  SS BOND              : angle       0.49047 (   28)
  hydrogen bonds       : bond        0.02851 (  183)
  hydrogen bonds       : angle       5.10607 (  411)
  link_ALPHA1-3        : bond        0.01056 (    1)
  link_ALPHA1-3        : angle       2.95751 (    3)
  link_ALPHA1-6        : bond        0.00397 (    1)
  link_ALPHA1-6        : angle       1.48154 (    3)
  link_BETA1-4         : bond        0.01681 (    3)
  link_BETA1-4         : angle       4.99628 (    9)
  link_NAG-ASN         : bond        0.00936 (    3)
  link_NAG-ASN         : angle       3.63360 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2849.68 seconds
wall clock time: 49 minutes 8.60 seconds (2948.60 seconds total)