Starting phenix.real_space_refine
on Tue Feb  3 18:03:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mfl_48234/02_2026/9mfl_48234.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mfl_48234/02_2026/9mfl_48234.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mfl_48234/02_2026/9mfl_48234.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mfl_48234/02_2026/9mfl_48234.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mfl_48234/02_2026/9mfl_48234.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mfl_48234/02_2026/9mfl_48234.cif"
  }
  resolution = 3.73
  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=   0.034
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: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    3948      2.51       5
     N     872      2.21       5
     O     976      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5850
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 2799
          Classifications: {'peptide': 354}
          Link IDs: {'PTRANS': 10, 'TRANS': 343}
          Chain breaks: 7
    Chain: "A"
      Number of atoms: 126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 126
          Unusual residues: {'QNJ': 2, 'Y01': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.99, per 1000 atoms: 0.34
  Number of scatterers: 5850
  At special positions: 0
  Unit cell: (86.25, 81.65, 67.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O     976      8.00
     N     872      7.00
     C    3948      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 315.8 milliseconds
  

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1328

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      92.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 76
      removed outlier: 3.514A  pdb=" N   GLU A  53 " --> pdb=" O   GLN A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 108
      removed outlier: 3.767A  pdb=" N   LEU A  86 " --> pdb=" O   LYS A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 149
      removed outlier: 3.575A  pdb=" N   ASP A 142 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   PHE A 149 " --> pdb=" O   ARG A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 181
    Processing helix  chain 'A' and resid 184 through 188
      removed outlier: 3.963A  pdb=" N   LYS A 188 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 214
      removed outlier: 3.603A  pdb=" N   ILE A 198 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU A 206 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   CYS A 209 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 277
      Proline residue:  A 263  - end of helix
    Processing helix  chain 'A' and resid 307 through 326
      removed outlier: 3.621A  pdb=" N   ALA A 315 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   VAL A 318 " --> pdb=" O   LEU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 364
    Processing helix  chain 'A' and resid 381 through 410
      removed outlier: 4.592A  pdb=" N   GLY A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   SER A 393 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   GLN A 410 " --> pdb=" O   ALA A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 441
      removed outlier: 3.971A  pdb=" N   LEU A 435 " --> pdb=" O   CYS A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 529
      removed outlier: 4.427A  pdb=" N   ILE A 516 " --> pdb=" O   ARG A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 537
      Proline residue:  A 535  - end of helix
    Processing helix  chain 'A' and resid 541 through 544
    Processing helix  chain 'A' and resid 545 through 553
      removed outlier: 3.775A  pdb=" N   ASN A 549 " --> pdb=" O   ASN A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 583
      Proline residue:  A 566  - end of helix
      removed outlier: 3.626A  pdb=" N   PHE A 570 " --> pdb=" O   PRO A 566 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   MET A 573 " --> pdb=" O   LEU A 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.512A  pdb=" N   GLU B  53 " --> pdb=" O   GLN B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 108
      removed outlier: 3.769A  pdb=" N   LEU B  86 " --> pdb=" O   LYS B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 149
      removed outlier: 3.575A  pdb=" N   ASP B 142 " --> pdb=" O   SER B 138 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   PHE B 149 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 181
    Processing helix  chain 'B' and resid 184 through 188
      removed outlier: 3.963A  pdb=" N   LYS B 188 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 214
      removed outlier: 3.601A  pdb=" N   ILE B 198 " --> pdb=" O   ARG B 194 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU B 206 " --> pdb=" O   PHE B 202 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   CYS B 209 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 277
      Proline residue:  B 263  - end of helix
    Processing helix  chain 'B' and resid 307 through 326
      removed outlier: 3.621A  pdb=" N   ALA B 315 " --> pdb=" O   LEU B 311 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   VAL B 318 " --> pdb=" O   LEU B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 364
    Processing helix  chain 'B' and resid 381 through 410
      removed outlier: 4.594A  pdb=" N   GLY B 392 " --> pdb=" O   ALA B 388 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   SER B 393 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   GLN B 410 " --> pdb=" O   ALA B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 441
      removed outlier: 3.974A  pdb=" N   LEU B 435 " --> pdb=" O   CYS B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 529
      removed outlier: 4.407A  pdb=" N   ILE B 516 " --> pdb=" O   ARG B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 529 through 537
      Proline residue:  B 535  - end of helix
    Processing helix  chain 'B' and resid 541 through 544
    Processing helix  chain 'B' and resid 545 through 553
      removed outlier: 3.777A  pdb=" N   ASN B 549 " --> pdb=" O   ASN B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 553 through 583
      Proline residue:  B 566  - end of helix
      removed outlier: 3.624A  pdb=" N   PHE B 570 " --> pdb=" O   PRO B 566 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   MET B 573 " --> pdb=" O   LEU B 569 " (cutoff:3.500A)

    476 hydrogen bonds defined for protein.
    1416 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: 0.92

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1641
        1.34 -     1.46: 1426
        1.46 -     1.58: 2773
        1.58 -     1.70: 82
        1.70 -     1.81: 88
  Bond restraints: 6010
  Sorted by residual:
  bond pdb=" C5  QNJ B 603 "
       pdb=" C6  QNJ B 603 "
    ideal  model  delta    sigma   weight residual
    1.524  1.363  0.161 2.00e-02 2.50e+03 6.45e+01
  bond pdb=" C5  QNJ A 603 "
       pdb=" C6  QNJ A 603 "
    ideal  model  delta    sigma   weight residual
    1.524  1.364  0.160 2.00e-02 2.50e+03 6.40e+01
  bond pdb=" C5  QNJ A 604 "
       pdb=" C6  QNJ A 604 "
    ideal  model  delta    sigma   weight residual
    1.524  1.365  0.159 2.00e-02 2.50e+03 6.32e+01
  bond pdb=" C5  QNJ B 604 "
       pdb=" C6  QNJ B 604 "
    ideal  model  delta    sigma   weight residual
    1.524  1.365  0.159 2.00e-02 2.50e+03 6.29e+01
  bond pdb=" C14 QNJ B 603 "
       pdb=" C8  QNJ B 603 "
    ideal  model  delta    sigma   weight residual
    1.521  1.669 -0.148 2.00e-02 2.50e+03 5.45e+01
  ... (remaining 6005 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.20: 7938
        3.20 -     6.40: 212
        6.40 -     9.60: 28
        9.60 -    12.80: 16
       12.80 -    16.00: 6
  Bond angle restraints: 8200
  Sorted by residual:
  angle pdb=" C4  QNJ B 603 "
        pdb=" C5  QNJ B 603 "
        pdb=" C6  QNJ B 603 "
      ideal   model   delta    sigma   weight residual
     113.68  129.68  -16.00 3.00e+00 1.11e-01 2.84e+01
  angle pdb=" C4  QNJ A 603 "
        pdb=" C5  QNJ A 603 "
        pdb=" C6  QNJ A 603 "
      ideal   model   delta    sigma   weight residual
     113.68  129.66  -15.98 3.00e+00 1.11e-01 2.84e+01
  angle pdb=" C4  QNJ B 604 "
        pdb=" C5  QNJ B 604 "
        pdb=" C6  QNJ B 604 "
      ideal   model   delta    sigma   weight residual
     113.68  128.30  -14.62 3.00e+00 1.11e-01 2.38e+01
  angle pdb=" C4  QNJ A 604 "
        pdb=" C5  QNJ A 604 "
        pdb=" C6  QNJ A 604 "
      ideal   model   delta    sigma   weight residual
     113.68  128.25  -14.57 3.00e+00 1.11e-01 2.36e+01
  angle pdb=" C5  QNJ B 604 "
        pdb=" C6  QNJ B 604 "
        pdb=" C7  QNJ B 604 "
      ideal   model   delta    sigma   weight residual
     109.58  122.96  -13.38 3.00e+00 1.11e-01 1.99e+01
  ... (remaining 8195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.51: 3613
       23.51 -    47.03: 177
       47.03 -    70.54: 48
       70.54 -    94.05: 0
       94.05 -   117.56: 14
  Dihedral angle restraints: 3852
    sinusoidal: 1796
      harmonic: 2056
  Sorted by residual:
  dihedral pdb=" CD  ARG A 145 "
           pdb=" NE  ARG A 145 "
           pdb=" CZ  ARG A 145 "
           pdb=" NH1 ARG A 145 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   57.51  -57.51     1      1.00e+01 1.00e-02 4.44e+01
  dihedral pdb=" CD  ARG B 145 "
           pdb=" NE  ARG B 145 "
           pdb=" CZ  ARG B 145 "
           pdb=" NH1 ARG B 145 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   57.50  -57.50     1      1.00e+01 1.00e-02 4.44e+01
  dihedral pdb=" C3  QNJ A 604 "
           pdb=" C4  QNJ A 604 "
           pdb=" C5  QNJ A 604 "
           pdb=" C6  QNJ A 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
     284.09  166.53  117.56     1      3.00e+01 1.11e-03 1.56e+01
  ... (remaining 3849 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.325: 970
       0.325 -    0.650: 8
       0.650 -    0.975: 0
       0.975 -    1.300: 2
       1.300 -    1.625: 4
  Chirality restraints: 984
  Sorted by residual:
  chirality pdb=" CBF Y01 A 602 "
            pdb=" CAS Y01 A 602 "
            pdb=" CBD Y01 A 602 "
            pdb=" CBH Y01 A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -0.82   -1.63 2.00e-01 2.50e+01 6.61e+01
  chirality pdb=" CBF Y01 B 602 "
            pdb=" CAS Y01 B 602 "
            pdb=" CBD Y01 B 602 "
            pdb=" CBH Y01 B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -0.82   -1.62 2.00e-01 2.50e+01 6.60e+01
  chirality pdb=" C5  QNJ A 603 "
            pdb=" C10 QNJ A 603 "
            pdb=" C4  QNJ A 603 "
            pdb=" C6  QNJ A 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -0.84   -1.61 2.00e-01 2.50e+01 6.48e+01
  ... (remaining 981 not shown)

  Planarity restraints: 930
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 145 "    0.773 9.50e-02 1.11e+02   3.47e-01 8.25e+01
        pdb=" NE  ARG B 145 "   -0.065 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 145 "    0.044 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 145 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 145 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 145 "   -0.772 9.50e-02 1.11e+02   3.47e-01 8.24e+01
        pdb=" NE  ARG A 145 "    0.065 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 145 "   -0.044 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 145 "    0.017 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 145 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 521 "   -0.028 2.00e-02 2.50e+03   5.65e-02 3.20e+01
        pdb=" C   CYS B 521 "    0.098 2.00e-02 2.50e+03
        pdb=" O   CYS B 521 "   -0.036 2.00e-02 2.50e+03
        pdb=" N   MET B 522 "   -0.033 2.00e-02 2.50e+03
  ... (remaining 927 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 1940
        2.88 -     3.38: 6468
        3.38 -     3.89: 9530
        3.89 -     4.39: 11121
        4.39 -     4.90: 18700
  Nonbonded interactions: 47759
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 439 "
            pdb=" ND2 ASN B  51 "
     model   vdw
     2.370 3.120
  nonbonded pdb=" ND2 ASN A  51 "
            pdb=" OE2 GLU B 439 "
     model   vdw
     2.375 3.120
  nonbonded pdb=" O   PRO B 535 "
            pdb=" NH1 ARG B 540 "
     model   vdw
     2.489 3.120
  nonbonded pdb=" O   PRO A 535 "
            pdb=" NH1 ARG A 540 "
     model   vdw
     2.490 3.120
  nonbonded pdb=" O   GLU A 190 "
            pdb=" NH1 ARG A 194 "
     model   vdw
     2.525 3.120
  ... (remaining 47754 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  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:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.970
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6400
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      :  0.012   0.161   6010  Z= 0.600
  Angle     :  1.350  15.998   8200  Z= 0.657
  Chirality :  0.134   1.625    984
  Planarity :  0.019   0.347    930
  Dihedral  : 16.104 117.563   2524
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 1.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  0.97 %
    Favored  : 98.39 %
  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:  0.24 (0.31), residues: 676
  helix:  0.47 (0.19), residues: 612
  sheet:  None (None), residues: 0
  loop : -1.90 (0.90), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.053   0.004   ARG A 145 
 TYR   0.015   0.003   TYR A 262 
 PHE   0.043   0.003   PHE A 525 
 TRP   0.027   0.003   TRP A 126 
 HIS   0.005   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.01202 ( 6010)
  covalent geometry    : angle       1.35034 ( 8200)
  hydrogen bonds       : bond        0.11806 (  476)
  hydrogen bonds       : angle       5.89702 ( 1416)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 205
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 TRP cc_start: 0.7674 (OUTLIER) cc_final: 0.2656 (m100)
REVERT: A  193 GLU cc_start: 0.7553 (mp0) cc_final: 0.6956 (mp0)
REVERT: A  275 MET cc_start: 0.5723 (mtp) cc_final: 0.5391 (ttt)
REVERT: A  349 MET cc_start: 0.7095 (tpp) cc_final: 0.6839 (tpp)
REVERT: A  353 MET cc_start: 0.7596 (mmm) cc_final: 0.7185 (tpp)
REVERT: A  417 TRP cc_start: 0.7504 (OUTLIER) cc_final: 0.7163 (m100)
REVERT: B  126 TRP cc_start: 0.7616 (OUTLIER) cc_final: 0.2649 (m100)
REVERT: B  193 GLU cc_start: 0.7570 (mp0) cc_final: 0.7006 (mp0)
REVERT: B  275 MET cc_start: 0.5709 (mtp) cc_final: 0.5371 (ttt)
REVERT: B  349 MET cc_start: 0.6931 (tpp) cc_final: 0.6716 (tpp)
REVERT: B  353 MET cc_start: 0.7583 (mmm) cc_final: 0.7217 (tpp)
REVERT: B  417 TRP cc_start: 0.7511 (OUTLIER) cc_final: 0.7181 (m100)
  outliers start: 4
  outliers final: 0
  residues processed: 209
  average time/residue: 0.0939
  time to fit residues: 24.9279
Evaluate side-chains
  108 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 TRP
Chi-restraints excluded: chain A residue  417 TRP
Chi-restraints excluded: chain B residue  126 TRP
Chi-restraints excluded: chain B residue  417 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0060
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 HIS
A 528 ASN
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 269 HIS
B 528 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.192931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.180641 restraints weight = 6565.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.180877 restraints weight = 6089.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.180885 restraints weight = 5791.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.181397 restraints weight = 5808.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.181397 restraints weight = 5487.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6010  Z= 0.155
  Angle     :  0.670   8.428   8200  Z= 0.335
  Chirality :  0.038   0.155    984
  Planarity :  0.004   0.031    930
  Dihedral  :  8.037  58.255   1306
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  6.45 %
    Favored  : 91.61 %
  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:  3.03 (0.33), residues: 676
  helix:  2.19 (0.20), residues: 622
  sheet:  None (None), residues: 0
  loop : -0.11 (1.15), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 108 
 TYR   0.018   0.002   TYR A 262 
 PHE   0.037   0.002   PHE A 525 
 TRP   0.022   0.002   TRP B 179 
 HIS   0.005   0.001   HIS A 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6010)
  covalent geometry    : angle       0.66961 ( 8200)
  hydrogen bonds       : bond        0.04705 (  476)
  hydrogen bonds       : angle       3.76605 ( 1416)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: A  179 TRP cc_start: 0.7946 (t-100) cc_final: 0.7485 (m100)
REVERT: A  353 MET cc_start: 0.7662 (mmm) cc_final: 0.7227 (tpp)
REVERT: B  179 TRP cc_start: 0.7914 (t-100) cc_final: 0.7470 (m100)
REVERT: B  353 MET cc_start: 0.7659 (mmm) cc_final: 0.7240 (tpp)
REVERT: B  440 SER cc_start: 0.7409 (p) cc_final: 0.7143 (p)
  outliers start: 12
  outliers final: 10
  residues processed: 127
  average time/residue: 0.0845
  time to fit residues: 13.8959
Evaluate side-chains
  111 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 TRP
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  417 TRP
Chi-restraints excluded: chain B residue  126 TRP
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  417 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 19 optimal weight:    0.2980
   chunk 27 optimal weight:    0.2980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.207625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.195893 restraints weight = 6639.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.195819 restraints weight = 6819.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.195819 restraints weight = 6941.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.195819 restraints weight = 6941.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.195819 restraints weight = 6941.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6848
moved from start:          0.3656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6010  Z= 0.151
  Angle     :  0.624   8.189   8200  Z= 0.311
  Chirality :  0.037   0.177    984
  Planarity :  0.004   0.029    930
  Dihedral  :  8.002  58.355   1306
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  :  7.90 %
    Favored  : 88.55 %
  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:  3.48 (0.33), residues: 676
  helix:  2.52 (0.20), residues: 616
  sheet:  None (None), residues: 0
  loop : -0.21 (1.04), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 514 
 TYR   0.017   0.002   TYR A 262 
 PHE   0.034   0.002   PHE A 525 
 TRP   0.010   0.001   TRP A 532 
 HIS   0.006   0.002   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6010)
  covalent geometry    : angle       0.62363 ( 8200)
  hydrogen bonds       : bond        0.04319 (  476)
  hydrogen bonds       : angle       3.51662 ( 1416)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  126 TRP cc_start: 0.8015 (OUTLIER) cc_final: 0.2544 (m100)
REVERT: A  179 TRP cc_start: 0.8193 (t-100) cc_final: 0.7806 (m100)
REVERT: A  349 MET cc_start: 0.7635 (tpp) cc_final: 0.6862 (mtt)
REVERT: B  126 TRP cc_start: 0.8073 (OUTLIER) cc_final: 0.2518 (m100)
REVERT: B  179 TRP cc_start: 0.8196 (t-100) cc_final: 0.7827 (m100)
REVERT: B  349 MET cc_start: 0.7635 (tpp) cc_final: 0.6862 (mtt)
  outliers start: 22
  outliers final: 6
  residues processed: 118
  average time/residue: 0.0709
  time to fit residues: 11.1776
Evaluate side-chains
  99 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 TRP
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  417 TRP
Chi-restraints excluded: chain B residue  126 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  417 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   chunk 63 optimal weight:    0.2980
   chunk 11 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.202122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.193180 restraints weight = 6726.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.192379 restraints weight = 9233.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.192585 restraints weight = 9215.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.192527 restraints weight = 9373.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.192664 restraints weight = 8207.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.4242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6010  Z= 0.181
  Angle     :  0.667   5.746   8200  Z= 0.334
  Chirality :  0.040   0.173    984
  Planarity :  0.004   0.033    930
  Dihedral  :  8.173  59.988   1306
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 10.65 %
    Favored  : 87.42 %
  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:  2.95 (0.32), residues: 676
  helix:  2.27 (0.20), residues: 616
  sheet:  None (None), residues: 0
  loop : -1.54 (0.88), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 194 
 TYR   0.017   0.002   TYR A 262 
 PHE   0.031   0.002   PHE B 525 
 TRP   0.010   0.002   TRP B 532 
 HIS   0.008   0.002   HIS A 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 6010)
  covalent geometry    : angle       0.66710 ( 8200)
  hydrogen bonds       : bond        0.04707 (  476)
  hydrogen bonds       : angle       3.74919 ( 1416)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  179 TRP cc_start: 0.8126 (t-100) cc_final: 0.7517 (m100)
REVERT: A  349 MET cc_start: 0.7633 (tpp) cc_final: 0.7232 (ttm)
REVERT: A  417 TRP cc_start: 0.7625 (OUTLIER) cc_final: 0.5741 (t60)
REVERT: B  179 TRP cc_start: 0.8151 (t-100) cc_final: 0.7513 (m100)
REVERT: B  349 MET cc_start: 0.7612 (tpp) cc_final: 0.7223 (ttm)
REVERT: B  417 TRP cc_start: 0.7622 (OUTLIER) cc_final: 0.5732 (t60)
  outliers start: 12
  outliers final: 7
  residues processed: 109
  average time/residue: 0.0724
  time to fit residues: 10.6843
Evaluate side-chains
  101 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  417 TRP
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  350 MET
Chi-restraints excluded: chain B residue  417 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0030
   chunk 66 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.204727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.196199 restraints weight = 6763.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.195199 restraints weight = 9074.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.195688 restraints weight = 10072.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.195641 restraints weight = 7867.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.195632 restraints weight = 7444.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.4213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.4377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6010  Z= 0.141
  Angle     :  0.607   7.101   8200  Z= 0.296
  Chirality :  0.036   0.154    984
  Planarity :  0.004   0.033    930
  Dihedral  :  7.862  59.922   1302
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 13.55 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.27 (0.33), residues: 676
  helix:  2.48 (0.21), residues: 616
  sheet:  None (None), residues: 0
  loop : -1.51 (0.89), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 194 
 TYR   0.015   0.002   TYR B 262 
 PHE   0.030   0.002   PHE B 525 
 TRP   0.011   0.001   TRP A 532 
 HIS   0.005   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6010)
  covalent geometry    : angle       0.60677 ( 8200)
  hydrogen bonds       : bond        0.04112 (  476)
  hydrogen bonds       : angle       3.50776 ( 1416)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  179 TRP cc_start: 0.8016 (t-100) cc_final: 0.7535 (m100)
REVERT: A  349 MET cc_start: 0.7609 (tpp) cc_final: 0.6743 (mtt)
REVERT: A  417 TRP cc_start: 0.7518 (OUTLIER) cc_final: 0.6095 (t60)
REVERT: B  179 TRP cc_start: 0.8002 (t-100) cc_final: 0.7519 (m100)
REVERT: B  349 MET cc_start: 0.7588 (tpp) cc_final: 0.6744 (mtt)
REVERT: B  417 TRP cc_start: 0.7516 (OUTLIER) cc_final: 0.6089 (t60)
  outliers start: 9
  outliers final: 5
  residues processed: 109
  average time/residue: 0.0860
  time to fit residues: 12.2988
Evaluate side-chains
  99 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  417 TRP
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  350 MET
Chi-restraints excluded: chain B residue  417 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 26 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   chunk 8 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   chunk 12 optimal weight:    0.4980
   chunk 21 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.204844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.193692 restraints weight = 6592.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.193692 restraints weight = 6577.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.193692 restraints weight = 6577.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.193692 restraints weight = 6577.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.193692 restraints weight = 6577.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.4175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6887
moved from start:          0.4555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6010  Z= 0.141
  Angle     :  0.597   7.042   8200  Z= 0.295
  Chirality :  0.036   0.144    984
  Planarity :  0.004   0.031    930
  Dihedral  :  7.584  57.989   1302
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.03 %
    Favored  : 83.87 %
  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:  3.49 (0.33), residues: 676
  helix:  2.72 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -1.65 (0.81), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 108 
 TYR   0.015   0.002   TYR B 262 
 PHE   0.025   0.002   PHE B 525 
 TRP   0.007   0.001   TRP B 126 
 HIS   0.005   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6010)
  covalent geometry    : angle       0.59731 ( 8200)
  hydrogen bonds       : bond        0.04024 (  476)
  hydrogen bonds       : angle       3.45474 ( 1416)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A   94 MET cc_start: 0.5346 (OUTLIER) cc_final: 0.4950 (mtm)
REVERT: A  179 TRP cc_start: 0.8024 (t-100) cc_final: 0.7600 (m100)
REVERT: A  349 MET cc_start: 0.7680 (tpp) cc_final: 0.6796 (mtt)
REVERT: A  417 TRP cc_start: 0.7576 (OUTLIER) cc_final: 0.6367 (t60)
REVERT: B  179 TRP cc_start: 0.8087 (t-100) cc_final: 0.7647 (m100)
REVERT: B  349 MET cc_start: 0.7625 (tpp) cc_final: 0.6743 (mtt)
REVERT: B  417 TRP cc_start: 0.7584 (OUTLIER) cc_final: 0.6213 (t60)
  outliers start: 13
  outliers final: 6
  residues processed: 106
  average time/residue: 0.0673
  time to fit residues: 10.0492
Evaluate side-chains
  96 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 MET
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  417 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  350 MET
Chi-restraints excluded: chain B residue  417 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 66 optimal weight:    0.4980
   chunk 45 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.205381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.194294 restraints weight = 6633.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.194293 restraints weight = 6612.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.194290 restraints weight = 6614.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.194289 restraints weight = 6615.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.194289 restraints weight = 6615.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.4178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6887
moved from start:          0.4622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6010  Z= 0.141
  Angle     :  0.597   7.380   8200  Z= 0.295
  Chirality :  0.036   0.143    984
  Planarity :  0.004   0.032    930
  Dihedral  :  7.435  55.612   1302
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.03 %
    Favored  : 83.71 %
  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:  3.45 (0.33), residues: 676
  helix:  2.59 (0.21), residues: 616
  sheet:  None (None), residues: 0
  loop : -1.30 (0.94), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 514 
 TYR   0.014   0.002   TYR B 262 
 PHE   0.024   0.002   PHE B 525 
 TRP   0.007   0.001   TRP B 126 
 HIS   0.005   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6010)
  covalent geometry    : angle       0.59744 ( 8200)
  hydrogen bonds       : bond        0.03997 (  476)
  hydrogen bonds       : angle       3.46255 ( 1416)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   94 MET cc_start: 0.5471 (OUTLIER) cc_final: 0.5048 (mtm)
REVERT: A  179 TRP cc_start: 0.7969 (t-100) cc_final: 0.7586 (m100)
REVERT: A  349 MET cc_start: 0.7676 (tpp) cc_final: 0.6789 (mtt)
REVERT: A  417 TRP cc_start: 0.7715 (OUTLIER) cc_final: 0.6441 (t60)
REVERT: B  179 TRP cc_start: 0.7985 (t-100) cc_final: 0.7611 (m100)
REVERT: B  349 MET cc_start: 0.7643 (tpp) cc_final: 0.6788 (mtt)
REVERT: B  417 TRP cc_start: 0.7567 (OUTLIER) cc_final: 0.6258 (t60)
  outliers start: 14
  outliers final: 8
  residues processed: 108
  average time/residue: 0.0736
  time to fit residues: 10.8457
Evaluate side-chains
  100 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 MET
Chi-restraints excluded: chain A residue  101 MET
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  417 TRP
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  350 MET
Chi-restraints excluded: chain B residue  417 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0870
   chunk 21 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 63 optimal weight:    7.9990
   chunk 23 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0980
   chunk 28 optimal weight:    0.2980
   chunk 50 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.207598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.196379 restraints weight = 6635.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.196379 restraints weight = 6626.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.196379 restraints weight = 6626.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.196379 restraints weight = 6626.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.196379 restraints weight = 6626.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6850
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6010  Z= 0.124
  Angle     :  0.576   7.649   8200  Z= 0.287
  Chirality :  0.036   0.142    984
  Planarity :  0.003   0.031    930
  Dihedral  :  7.252  53.386   1302
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.13 %
    Favored  : 82.26 %
  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:  3.58 (0.33), residues: 676
  helix:  2.66 (0.21), residues: 618
  sheet:  None (None), residues: 0
  loop : -1.19 (1.00), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 108 
 TYR   0.015   0.001   TYR A 571 
 PHE   0.022   0.001   PHE B 525 
 TRP   0.008   0.001   TRP B 532 
 HIS   0.005   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6010)
  covalent geometry    : angle       0.57646 ( 8200)
  hydrogen bonds       : bond        0.03730 (  476)
  hydrogen bonds       : angle       3.38236 ( 1416)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A  179 TRP cc_start: 0.7957 (t-100) cc_final: 0.7614 (m100)
REVERT: A  349 MET cc_start: 0.7613 (tpp) cc_final: 0.6815 (mtt)
REVERT: A  417 TRP cc_start: 0.7677 (OUTLIER) cc_final: 0.6632 (t60)
REVERT: B  179 TRP cc_start: 0.7966 (t-100) cc_final: 0.7613 (m100)
REVERT: B  349 MET cc_start: 0.7632 (tpp) cc_final: 0.6789 (mtt)
REVERT: B  417 TRP cc_start: 0.7684 (OUTLIER) cc_final: 0.6554 (t60)
  outliers start: 10
  outliers final: 5
  residues processed: 103
  average time/residue: 0.0778
  time to fit residues: 10.7494
Evaluate side-chains
  98 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  417 TRP
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  350 MET
Chi-restraints excluded: chain B residue  417 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    0.3980
   chunk 41 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
A 181 HIS
** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.206303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.195047 restraints weight = 6660.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.195047 restraints weight = 6645.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.195047 restraints weight = 6645.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.195047 restraints weight = 6645.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.195047 restraints weight = 6645.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.4748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6010  Z= 0.155
  Angle     :  0.625   7.665   8200  Z= 0.312
  Chirality :  0.037   0.176    984
  Planarity :  0.003   0.031    930
  Dihedral  :  7.296  53.738   1302
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 16.13 %
    Favored  : 82.58 %
  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:  3.27 (0.33), residues: 676
  helix:  2.48 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop : -1.55 (0.97), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 108 
 TYR   0.015   0.002   TYR B 262 
 PHE   0.026   0.002   PHE B 525 
 TRP   0.018   0.002   TRP A 532 
 HIS   0.005   0.001   HIS A 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6010)
  covalent geometry    : angle       0.62533 ( 8200)
  hydrogen bonds       : bond        0.04145 (  476)
  hydrogen bonds       : angle       3.54267 ( 1416)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  179 TRP cc_start: 0.7943 (t-100) cc_final: 0.7628 (m100)
REVERT: A  349 MET cc_start: 0.7629 (tpp) cc_final: 0.6737 (mtt)
REVERT: A  417 TRP cc_start: 0.7704 (OUTLIER) cc_final: 0.7309 (t60)
REVERT: B  179 TRP cc_start: 0.7961 (t-100) cc_final: 0.7624 (m100)
REVERT: B  349 MET cc_start: 0.7610 (tpp) cc_final: 0.6750 (mtt)
REVERT: B  417 TRP cc_start: 0.7706 (OUTLIER) cc_final: 0.6396 (t60)
  outliers start: 8
  outliers final: 6
  residues processed: 103
  average time/residue: 0.0748
  time to fit residues: 10.5104
Evaluate side-chains
  100 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  417 TRP
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  350 MET
Chi-restraints excluded: chain B residue  417 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 50 optimal weight:    0.3980
   chunk 69 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.208364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.197877 restraints weight = 6651.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.197870 restraints weight = 6620.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.197870 restraints weight = 6622.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.197870 restraints weight = 6622.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.197870 restraints weight = 6622.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.4204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6875
moved from start:          0.4832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6010  Z= 0.143
  Angle     :  0.624   7.851   8200  Z= 0.310
  Chirality :  0.036   0.168    984
  Planarity :  0.003   0.031    930
  Dihedral  :  7.220  53.053   1302
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.81 %
    Favored  : 82.58 %
  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:  3.36 (0.33), residues: 676
  helix:  2.53 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop : -1.49 (0.99), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 108 
 TYR   0.014   0.001   TYR B 262 
 PHE   0.026   0.002   PHE B 525 
 TRP   0.021   0.001   TRP B 532 
 HIS   0.004   0.001   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6010)
  covalent geometry    : angle       0.62395 ( 8200)
  hydrogen bonds       : bond        0.03943 (  476)
  hydrogen bonds       : angle       3.49794 ( 1416)

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  179 TRP cc_start: 0.7860 (t-100) cc_final: 0.7597 (m100)
REVERT: A  349 MET cc_start: 0.7598 (tpp) cc_final: 0.6694 (mtt)
REVERT: A  417 TRP cc_start: 0.7740 (OUTLIER) cc_final: 0.7303 (t60)
REVERT: A  534 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6772 (mp)
REVERT: B  179 TRP cc_start: 0.7975 (t-100) cc_final: 0.7602 (m100)
REVERT: B  192 PHE cc_start: 0.7764 (t80) cc_final: 0.7536 (t80)
REVERT: B  349 MET cc_start: 0.7583 (tpp) cc_final: 0.6697 (mtt)
REVERT: B  417 TRP cc_start: 0.7706 (OUTLIER) cc_final: 0.7285 (t60)
REVERT: B  534 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6798 (mp)
  outliers start: 10
  outliers final: 6
  residues processed: 100
  average time/residue: 0.0675
  time to fit residues: 9.4560
Evaluate side-chains
  101 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  417 TRP
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  534 LEU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  350 MET
Chi-restraints excluded: chain B residue  417 TRP
Chi-restraints excluded: chain B residue  534 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.207696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.196712 restraints weight = 6566.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.196708 restraints weight = 6646.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.196708 restraints weight = 6642.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.196708 restraints weight = 6642.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.196708 restraints weight = 6642.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.4862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6010  Z= 0.150
  Angle     :  0.633   7.814   8200  Z= 0.313
  Chirality :  0.037   0.171    984
  Planarity :  0.003   0.031    930
  Dihedral  :  7.202  53.319   1302
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.29 %
    Favored  : 82.10 %
  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:  3.29 (0.33), residues: 676
  helix:  2.49 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop : -1.62 (0.99), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 108 
 TYR   0.014   0.001   TYR B 571 
 PHE   0.026   0.002   PHE B 525 
 TRP   0.030   0.002   TRP B 532 
 HIS   0.004   0.001   HIS A 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6010)
  covalent geometry    : angle       0.63304 ( 8200)
  hydrogen bonds       : bond        0.04040 (  476)
  hydrogen bonds       : angle       3.52366 ( 1416)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 956.55 seconds
wall clock time: 17 minutes 28.52 seconds (1048.52 seconds total)