Starting phenix.real_space_refine
on Sat May 10 10:45:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jfw_36218/05_2025/8jfw_36218.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jfw_36218/05_2025/8jfw_36218.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jfw_36218/05_2025/8jfw_36218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jfw_36218/05_2025/8jfw_36218.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jfw_36218/05_2025/8jfw_36218.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jfw_36218/05_2025/8jfw_36218.cif"
  }
  resolution = 3.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.034
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: 6
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     Zn      1      6.06       5
     S      33      5.16       5
     C    3820      2.51       5
     N    1058      2.21       5
     O    1163      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6076
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1109
          Classifications: {'peptide': 145}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 2, 'TRANS': 142}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 20
    Chain: "D"
      Number of atoms: 4965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 613, 4965
          Classifications: {'peptide': 613}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 24, 'TRANS': 588}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' FE': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.04, per 1000 atoms: 0.66
  Number of scatterers: 6076
  At special positions: 0
  Unit cell: (74.385, 85.5, 103.455, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Fe      1     26.01
     S      33     16.00
     O    1163      8.00
     N    1058      7.00
     C    3820      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: 1.33
  Conformation dependent library (CDL) restraints added in 842.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN D 702 "
        pdb="ZN    ZN D 702 " - pdb=" NE2 HIS D 271 "


  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 5 sheets defined
      57.0% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 18
      removed outlier: 4.060A  pdb=" N   LYS A  14 " --> pdb=" O   ILE A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 40
      removed outlier: 3.858A  pdb=" N   ARG A  38 " --> pdb=" O   GLY A  34 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 65 through 77
    Processing helix  chain 'A' and resid 84 through 92
      removed outlier: 4.239A  pdb=" N   GLU A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ALA A  89 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 113
      removed outlier: 3.609A  pdb=" N   LEU A 106 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   MET A 110 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ASN A 112 " --> pdb=" O   HIS A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 129
      removed outlier: 3.736A  pdb=" N   VAL A 122 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 148
    Processing helix  chain 'D' and resid 2 through 46
    Processing helix  chain 'D' and resid 46 through 59
      removed outlier: 4.017A  pdb=" N   LYS D  50 " --> pdb=" O   ALA D  46 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LYS D  57 " --> pdb=" O   ASN D  53 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 114
      removed outlier: 3.739A  pdb=" N   ILE D 105 " --> pdb=" O   ARG D 101 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LYS D 114 " --> pdb=" O   ASP D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 137
      removed outlier: 3.645A  pdb=" N   LYS D 137 " --> pdb=" O   ALA D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 162 through 174
    Processing helix  chain 'D' and resid 194 through 209
      removed outlier: 3.711A  pdb=" N   VAL D 198 " --> pdb=" O   ARG D 194 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 227
      removed outlier: 3.677A  pdb=" N   ALA D 227 " --> pdb=" O   SER D 223 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 230 through 239
    Processing helix  chain 'D' and resid 242 through 256
      removed outlier: 3.566A  pdb=" N   ARG D 255 " --> pdb=" O   ASP D 251 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   TRP D 256 " --> pdb=" O   GLU D 252 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 279 through 284
    Processing helix  chain 'D' and resid 285 through 286
      No H-bonds generated for 'chain 'D' and resid 285 through 286'
    Processing helix  chain 'D' and resid 287 through 291
    Processing helix  chain 'D' and resid 306 through 319
      removed outlier: 3.834A  pdb=" N   TRP D 310 " --> pdb=" O   ASP D 306 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 340 through 352
    Processing helix  chain 'D' and resid 411 through 416
    Processing helix  chain 'D' and resid 419 through 440
      removed outlier: 3.928A  pdb=" N   VAL D 427 " --> pdb=" O   ARG D 423 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 442 through 453
    Processing helix  chain 'D' and resid 463 through 475
    Processing helix  chain 'D' and resid 479 through 482
    Processing helix  chain 'D' and resid 483 through 488
    Processing helix  chain 'D' and resid 498 through 506
      removed outlier: 3.618A  pdb=" N   LEU D 505 " --> pdb=" O   THR D 501 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 507 through 517
      removed outlier: 3.832A  pdb=" N   ASP D 516 " --> pdb=" O   GLU D 512 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLY D 517 " --> pdb=" O   ALA D 513 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 522 through 527
    Processing helix  chain 'D' and resid 527 through 538
      removed outlier: 3.783A  pdb=" N   LEU D 531 " --> pdb=" O   ASN D 527 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 547 through 562
      removed outlier: 3.550A  pdb=" N   HIS D 561 " --> pdb=" O   LEU D 557 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 569 through 579
    Processing helix  chain 'D' and resid 587 through 612
      removed outlier: 4.418A  pdb=" N   ALA D 594 " --> pdb=" O   GLU D 590 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   PHE D 595 " --> pdb=" O   PHE D 591 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29
    Processing sheet with id=AA2, first strand: chain 'D' and resid 142 through 145
      removed outlier: 6.905A  pdb=" N   LEU D 268 " --> pdb=" O   ILE D 357 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 213 through 215
    Processing sheet with id=AA4, first strand: chain 'D' and resid 320 through 321
    Processing sheet with id=AA5, first strand: chain 'D' and resid 460 through 462

    311 hydrogen bonds defined for protein.
    906 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: 1.78

  Time building geometry restraints manager: 1.61 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2069
        1.35 -     1.46: 1341
        1.46 -     1.58: 2717
        1.58 -     1.70: 1
        1.70 -     1.82: 59
  Bond restraints: 6187
  Sorted by residual:
  bond pdb=" CB  PRO D 329 "
       pdb=" CG  PRO D 329 "
    ideal  model  delta    sigma   weight residual
    1.492  1.600 -0.108 5.00e-02 4.00e+02 4.65e+00
  bond pdb=" CA  ASP D 190 "
       pdb=" CB  ASP D 190 "
    ideal  model  delta    sigma   weight residual
    1.532  1.548 -0.016 1.33e-02 5.65e+03 1.42e+00
  bond pdb=" N   ASP D 457 "
       pdb=" CA  ASP D 457 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.48e-01
  bond pdb=" CB  MET A 145 "
       pdb=" CG  MET A 145 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.36e-01
  bond pdb=" CB  GLU A 128 "
       pdb=" CG  GLU A 128 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.16e-01
  ... (remaining 6182 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 8253
        2.28 -     4.55: 85
        4.55 -     6.83: 5
        6.83 -     9.11: 2
        9.11 -    11.39: 3
  Bond angle restraints: 8348
  Sorted by residual:
  angle pdb=" CA  PRO D 329 "
        pdb=" N   PRO D 329 "
        pdb=" CD  PRO D 329 "
      ideal   model   delta    sigma   weight residual
     112.00  102.42    9.58 1.40e+00 5.10e-01 4.68e+01
  angle pdb=" CB  MET D 424 "
        pdb=" CG  MET D 424 "
        pdb=" SD  MET D 424 "
      ideal   model   delta    sigma   weight residual
     112.70  124.09  -11.39 3.00e+00 1.11e-01 1.44e+01
  angle pdb=" CB  MET A 145 "
        pdb=" CG  MET A 145 "
        pdb=" SD  MET A 145 "
      ideal   model   delta    sigma   weight residual
     112.70  123.21  -10.51 3.00e+00 1.11e-01 1.23e+01
  angle pdb=" N   ASN D 536 "
        pdb=" CA  ASN D 536 "
        pdb=" C   ASN D 536 "
      ideal   model   delta    sigma   weight residual
     113.41  109.66    3.75 1.22e+00 6.72e-01 9.44e+00
  angle pdb=" CA  MET A 145 "
        pdb=" CB  MET A 145 "
        pdb=" CG  MET A 145 "
      ideal   model   delta    sigma   weight residual
     114.10  120.14   -6.04 2.00e+00 2.50e-01 9.13e+00
  ... (remaining 8343 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3336
       17.96 -    35.93: 347
       35.93 -    53.89: 72
       53.89 -    71.86: 11
       71.86 -    89.82: 5
  Dihedral angle restraints: 3771
    sinusoidal: 1564
      harmonic: 2207
  Sorted by residual:
  dihedral pdb=" CA  PHE D 188 "
           pdb=" C   PHE D 188 "
           pdb=" N   VAL D 189 "
           pdb=" CA  VAL D 189 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.71  -21.29     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  VAL D 189 "
           pdb=" C   VAL D 189 "
           pdb=" N   ASP D 190 "
           pdb=" CA  ASP D 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.22   18.78     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  ILE A 126 "
           pdb=" C   ILE A 126 "
           pdb=" N   ARG A 127 "
           pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.53   17.47     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 3768 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 689
       0.040 -    0.081: 160
       0.081 -    0.121: 56
       0.121 -    0.161: 5
       0.161 -    0.201: 2
  Chirality restraints: 912
  Sorted by residual:
  chirality pdb=" CB  VAL D 189 "
            pdb=" CA  VAL D 189 "
            pdb=" CG1 VAL D 189 "
            pdb=" CG2 VAL D 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  ASP D 190 "
            pdb=" N   ASP D 190 "
            pdb=" C   ASP D 190 "
            pdb=" CB  ASP D 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.19e-01
  chirality pdb=" CA  PRO D 329 "
            pdb=" N   PRO D 329 "
            pdb=" C   PRO D 329 "
            pdb=" CB  PRO D 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.35e-01
  ... (remaining 909 not shown)

  Planarity restraints: 1099
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 328 "   -0.069 5.00e-02 4.00e+02   9.82e-02 1.54e+01
        pdb=" N   PRO D 329 "    0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO D 329 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO D 329 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 189 "   -0.006 2.00e-02 2.50e+03   1.24e-02 1.53e+00
        pdb=" C   VAL D 189 "    0.021 2.00e-02 2.50e+03
        pdb=" O   VAL D 189 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ASP D 190 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  43 "   -0.020 5.00e-02 4.00e+02   3.06e-02 1.50e+00
        pdb=" N   PRO A  44 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A  44 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A  44 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1096 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 57
        2.60 -     3.18: 5194
        3.18 -     3.75: 9274
        3.75 -     4.33: 11975
        4.33 -     4.90: 20400
  Nonbonded interactions: 46900
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN D 219 "
            pdb="ZN    ZN D 702 "
     model   vdw
     2.029 2.230
  nonbonded pdb=" OD2 ASP D 187 "
            pdb="ZN    ZN D 702 "
     model   vdw
     2.070 2.230
  nonbonded pdb=" OG1 THR D 547 "
            pdb=" OD1 ASP D 549 "
     model   vdw
     2.111 3.040
  nonbonded pdb=" OD2 ASP D 187 "
            pdb="FE    FE D 701 "
     model   vdw
     2.118 2.260
  nonbonded pdb=" NE2 HIS D 160 "
            pdb="FE    FE D 701 "
     model   vdw
     2.176 2.340
  ... (remaining 46895 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.040
  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:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.510
  Find NCS groups from input model:        0.380
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
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   0.108   6188  Z= 0.124
  Angle     :  0.603  11.386   8348  Z= 0.350
  Chirality :  0.040   0.201    912
  Planarity :  0.004   0.098   1099
  Dihedral  : 15.174  89.824   2339
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 14.67 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.31), residues: 750
  helix:  1.78 (0.27), residues: 379
  sheet: -0.09 (0.65), residues: 63
  loop : -0.01 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  15 
 HIS   0.002   0.000   HIS D 271 
 PHE   0.010   0.001   PHE D 535 
 TYR   0.006   0.001   TYR D 394 
 ARG   0.006   0.000   ARG D 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18857 (  311)
  hydrogen bonds       : angle       5.80065 (  906)
  metal coordination   : bond        0.00238 (    1)
  covalent geometry    : bond        0.00272 ( 6187)
  covalent geometry    : angle       0.60272 ( 8348)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.7873 (p90) cc_final: 0.7295 (p90)
REVERT: D  498 TYR cc_start: 0.7701 (p90) cc_final: 0.7253 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1671
  time to fit residues: 19.1831
Evaluate side-chains
  81 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 68 optimal weight:    4.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
D 104 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.201335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.147511 restraints weight = 6751.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.146239 restraints weight = 7243.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.146826 restraints weight = 7254.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6188  Z= 0.153
  Angle     :  0.537   7.929   8348  Z= 0.288
  Chirality :  0.042   0.220    912
  Planarity :  0.004   0.036   1099
  Dihedral  :  4.283  21.132    823
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.01 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.32), residues: 750
  helix:  1.54 (0.26), residues: 403
  sheet: -0.33 (0.83), residues: 46
  loop : -0.04 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 318 
 HIS   0.005   0.001   HIS D 271 
 PHE   0.014   0.001   PHE D 347 
 TYR   0.011   0.001   TYR D 254 
 ARG   0.004   0.000   ARG D 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04750 (  311)
  hydrogen bonds       : angle       4.38334 (  906)
  metal coordination   : bond        0.00459 (    1)
  covalent geometry    : bond        0.00354 ( 6187)
  covalent geometry    : angle       0.53721 ( 8348)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6257 (mtm)
REVERT: D   47 GLU cc_start: 0.8271 (pp20) cc_final: 0.8070 (pp20)
  outliers start: 14
  outliers final: 6
  residues processed: 85
  average time/residue: 0.1655
  time to fit residues: 19.2805
Evaluate side-chains
  86 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain D residue  577 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 61 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 19 optimal weight:    0.1980
   chunk 31 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0370
   overall best weight:    0.5260

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
D 104 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.203994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.151651 restraints weight = 6800.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.150018 restraints weight = 7811.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.151319 restraints weight = 7604.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6188  Z= 0.101
  Angle     :  0.477   8.071   8348  Z= 0.253
  Chirality :  0.040   0.212    912
  Planarity :  0.003   0.027   1099
  Dihedral  :  4.085  18.817    823
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 14.52 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.31), residues: 750
  helix:  1.67 (0.27), residues: 399
  sheet:  0.20 (0.76), residues: 56
  loop : -0.10 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  15 
 HIS   0.003   0.000   HIS D 271 
 PHE   0.010   0.001   PHE D 535 
 TYR   0.010   0.001   TYR D 394 
 ARG   0.003   0.000   ARG D 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  311)
  hydrogen bonds       : angle       4.13197 (  906)
  metal coordination   : bond        0.00255 (    1)
  covalent geometry    : bond        0.00219 ( 6187)
  covalent geometry    : angle       0.47655 ( 8348)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.5958 (mtm)
REVERT: D   47 GLU cc_start: 0.8213 (pp20) cc_final: 0.7895 (pp20)
  outliers start: 8
  outliers final: 4
  residues processed: 88
  average time/residue: 0.1572
  time to fit residues: 19.4395
Evaluate side-chains
  86 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain D residue  548 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 2 optimal weight:    0.4980
   chunk 20 optimal weight:    0.0020
   chunk 54 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.0592

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

Flipped N/Q/H residues before XYZ refinement:
D 104 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.202011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.149302 restraints weight = 6930.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.148058 restraints weight = 7865.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.148947 restraints weight = 7261.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6188  Z= 0.134
  Angle     :  0.501   8.446   8348  Z= 0.265
  Chirality :  0.041   0.219    912
  Planarity :  0.003   0.032   1099
  Dihedral  :  4.117  18.769    823
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.07 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.31), residues: 750
  helix:  1.63 (0.26), residues: 402
  sheet:  0.04 (0.77), residues: 56
  loop : -0.27 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  15 
 HIS   0.005   0.001   HIS D 271 
 PHE   0.014   0.001   PHE D 347 
 TYR   0.012   0.001   TYR D 394 
 ARG   0.002   0.000   ARG D  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04089 (  311)
  hydrogen bonds       : angle       4.07889 (  906)
  metal coordination   : bond        0.00411 (    1)
  covalent geometry    : bond        0.00318 ( 6187)
  covalent geometry    : angle       0.50098 ( 8348)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8190 (tpp)
REVERT: A  110 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.6096 (mtm)
REVERT: D   47 GLU cc_start: 0.8279 (pp20) cc_final: 0.7937 (pp20)
REVERT: D  521 MET cc_start: 0.6251 (mtp) cc_final: 0.5830 (mmm)
  outliers start: 13
  outliers final: 8
  residues processed: 90
  average time/residue: 0.1658
  time to fit residues: 20.6770
Evaluate side-chains
  88 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain D residue  505 LEU
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  572 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 60 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 71 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 67 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0010
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
D 104 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.204294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.152445 restraints weight = 6863.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.150636 restraints weight = 8143.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.151689 restraints weight = 8292.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6188  Z= 0.101
  Angle     :  0.463   6.963   8348  Z= 0.244
  Chirality :  0.040   0.214    912
  Planarity :  0.003   0.033   1099
  Dihedral  :  3.935  19.029    823
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 15.13 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.31), residues: 750
  helix:  1.76 (0.27), residues: 397
  sheet:  0.07 (0.77), residues: 56
  loop : -0.22 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  15 
 HIS   0.003   0.000   HIS D 271 
 PHE   0.009   0.001   PHE D 535 
 TYR   0.010   0.001   TYR D 394 
 ARG   0.002   0.000   ARG D 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03592 (  311)
  hydrogen bonds       : angle       3.94687 (  906)
  metal coordination   : bond        0.00263 (    1)
  covalent geometry    : bond        0.00223 ( 6187)
  covalent geometry    : angle       0.46263 ( 8348)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7278 (mt-10)
REVERT: A  110 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.6178 (mtm)
REVERT: D  521 MET cc_start: 0.6177 (mtp) cc_final: 0.5770 (mmm)
  outliers start: 10
  outliers final: 6
  residues processed: 94
  average time/residue: 0.1686
  time to fit residues: 21.9858
Evaluate side-chains
  91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain D residue  178 SER
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  572 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 64 optimal weight:    7.9990
   chunk 19 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D 104 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.203982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.150290 restraints weight = 6735.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.146912 restraints weight = 6994.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.148576 restraints weight = 7512.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6188  Z= 0.107
  Angle     :  0.473   8.148   8348  Z= 0.249
  Chirality :  0.040   0.215    912
  Planarity :  0.003   0.035   1099
  Dihedral  :  3.927  18.393    823
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.98 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.31), residues: 750
  helix:  1.78 (0.27), residues: 397
  sheet:  0.01 (0.77), residues: 56
  loop : -0.17 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  15 
 HIS   0.004   0.001   HIS D 271 
 PHE   0.010   0.001   PHE D 347 
 TYR   0.010   0.001   TYR D 394 
 ARG   0.001   0.000   ARG D 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03634 (  311)
  hydrogen bonds       : angle       3.93424 (  906)
  metal coordination   : bond        0.00277 (    1)
  covalent geometry    : bond        0.00245 ( 6187)
  covalent geometry    : angle       0.47293 ( 8348)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7308 (mt-10)
REVERT: A   52 MET cc_start: 0.7319 (mtt) cc_final: 0.6695 (mtt)
REVERT: A   72 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7783 (tpp)
REVERT: D  251 ASP cc_start: 0.8015 (t70) cc_final: 0.7795 (t70)
REVERT: D  521 MET cc_start: 0.6245 (mtp) cc_final: 0.5827 (mmm)
  outliers start: 14
  outliers final: 8
  residues processed: 91
  average time/residue: 0.1623
  time to fit residues: 20.5852
Evaluate side-chains
  92 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  178 SER
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  572 LEU
Chi-restraints excluded: chain D residue  578 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 53 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.6980
   chunk 14 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 13 optimal weight:    9.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
D 104 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.200281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.147598 restraints weight = 6859.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.145507 restraints weight = 8102.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.146982 restraints weight = 8139.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6188  Z= 0.162
  Angle     :  0.526   8.969   8348  Z= 0.277
  Chirality :  0.041   0.226    912
  Planarity :  0.003   0.034   1099
  Dihedral  :  4.165  19.423    823
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.13 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.32), residues: 750
  helix:  1.61 (0.26), residues: 403
  sheet: -0.22 (0.75), residues: 56
  loop : -0.22 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 318 
 HIS   0.006   0.001   HIS D 271 
 PHE   0.017   0.001   PHE D 347 
 TYR   0.012   0.001   TYR D 394 
 ARG   0.003   0.000   ARG D  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04226 (  311)
  hydrogen bonds       : angle       4.06629 (  906)
  metal coordination   : bond        0.00548 (    1)
  covalent geometry    : bond        0.00391 ( 6187)
  covalent geometry    : angle       0.52605 ( 8348)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
REVERT: D   47 GLU cc_start: 0.8274 (pp20) cc_final: 0.7861 (pp20)
REVERT: D  251 ASP cc_start: 0.8092 (t70) cc_final: 0.7877 (t70)
REVERT: D  447 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8804 (tt0)
  outliers start: 15
  outliers final: 12
  residues processed: 88
  average time/residue: 0.1710
  time to fit residues: 20.9957
Evaluate side-chains
  91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  178 SER
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  447 GLU
Chi-restraints excluded: chain D residue  461 ILE
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain D residue  505 LEU
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  572 LEU
Chi-restraints excluded: chain D residue  578 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 73 optimal weight:   20.0000
   chunk 44 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 5 optimal weight:   20.0000
   chunk 47 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 12 optimal weight:    8.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
D 104 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.201538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.149720 restraints weight = 6795.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.148001 restraints weight = 8390.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.149445 restraints weight = 8002.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6188  Z= 0.133
  Angle     :  0.519   9.458   8348  Z= 0.268
  Chirality :  0.041   0.238    912
  Planarity :  0.003   0.035   1099
  Dihedral  :  4.127  20.739    823
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 15.73 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.31), residues: 750
  helix:  1.61 (0.26), residues: 403
  sheet: -0.30 (0.76), residues: 56
  loop : -0.28 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  15 
 HIS   0.005   0.001   HIS D 271 
 PHE   0.013   0.001   PHE D 347 
 TYR   0.011   0.001   TYR D 394 
 ARG   0.002   0.000   ARG D  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03924 (  311)
  hydrogen bonds       : angle       4.00649 (  906)
  metal coordination   : bond        0.00428 (    1)
  covalent geometry    : bond        0.00316 ( 6187)
  covalent geometry    : angle       0.51924 ( 8348)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8282 (tpp)
REVERT: A   73 MET cc_start: 0.8095 (mmm) cc_final: 0.7766 (tpt)
REVERT: D   47 GLU cc_start: 0.8281 (pp20) cc_final: 0.7851 (pp20)
REVERT: D  251 ASP cc_start: 0.8083 (t70) cc_final: 0.7868 (t70)
REVERT: D  541 ASP cc_start: 0.6218 (p0) cc_final: 0.5882 (p0)
  outliers start: 13
  outliers final: 11
  residues processed: 91
  average time/residue: 0.1630
  time to fit residues: 20.6591
Evaluate side-chains
  92 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  178 SER
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain D residue  505 LEU
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  572 LEU
Chi-restraints excluded: chain D residue  578 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 73 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   chunk 6 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
D 104 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.199791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.146886 restraints weight = 6881.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.143348 restraints weight = 7798.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.144791 restraints weight = 8323.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6188  Z= 0.166
  Angle     :  0.555  10.501   8348  Z= 0.286
  Chirality :  0.042   0.228    912
  Planarity :  0.003   0.035   1099
  Dihedral  :  4.242  20.697    823
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.19 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.31), residues: 750
  helix:  1.54 (0.26), residues: 404
  sheet: -0.64 (0.79), residues: 51
  loop : -0.31 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 318 
 HIS   0.006   0.001   HIS D 271 
 PHE   0.017   0.001   PHE D 347 
 TYR   0.012   0.001   TYR D 394 
 ARG   0.003   0.000   ARG D  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04239 (  311)
  hydrogen bonds       : angle       4.08118 (  906)
  metal coordination   : bond        0.00569 (    1)
  covalent geometry    : bond        0.00403 ( 6187)
  covalent geometry    : angle       0.55491 ( 8348)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
REVERT: D   47 GLU cc_start: 0.8280 (pp20) cc_final: 0.7876 (pp20)
REVERT: D  251 ASP cc_start: 0.8100 (t70) cc_final: 0.7885 (t70)
REVERT: D  447 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8841 (tt0)
  outliers start: 14
  outliers final: 11
  residues processed: 88
  average time/residue: 0.1876
  time to fit residues: 23.0216
Evaluate side-chains
  92 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  178 SER
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  447 GLU
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain D residue  505 LEU
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  572 LEU
Chi-restraints excluded: chain D residue  578 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 70 optimal weight:    8.9990
   chunk 29 optimal weight:    0.0980
   chunk 48 optimal weight:    0.2980
   chunk 54 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 51 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
D 104 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.203042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.151874 restraints weight = 6872.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.148781 restraints weight = 7851.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.150645 restraints weight = 7813.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6188  Z= 0.103
  Angle     :  0.502  10.950   8348  Z= 0.258
  Chirality :  0.041   0.217    912
  Planarity :  0.003   0.035   1099
  Dihedral  :  4.033  20.614    823
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 16.64 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.31), residues: 750
  helix:  1.70 (0.27), residues: 399
  sheet: -0.31 (0.80), residues: 53
  loop : -0.31 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 466 
 HIS   0.004   0.001   HIS D 271 
 PHE   0.008   0.001   PHE D 347 
 TYR   0.009   0.001   TYR D 394 
 ARG   0.002   0.000   ARG A 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03566 (  311)
  hydrogen bonds       : angle       3.94799 (  906)
  metal coordination   : bond        0.00190 (    1)
  covalent geometry    : bond        0.00232 ( 6187)
  covalent geometry    : angle       0.50161 ( 8348)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.8019 (mmm) cc_final: 0.7789 (tpt)
REVERT: D  251 ASP cc_start: 0.8027 (t70) cc_final: 0.7812 (t70)
  outliers start: 8
  outliers final: 6
  residues processed: 87
  average time/residue: 0.1655
  time to fit residues: 20.0704
Evaluate side-chains
  86 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  432 LEU
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  572 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 22 optimal weight:    0.0980
   chunk 4 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 52 optimal weight:    0.1980
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
D 104 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.203550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.152370 restraints weight = 6927.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.149387 restraints weight = 7856.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.151121 restraints weight = 7859.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6188  Z= 0.103
  Angle     :  0.498  11.389   8348  Z= 0.255
  Chirality :  0.040   0.215    912
  Planarity :  0.003   0.035   1099
  Dihedral  :  3.940  20.105    823
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 17.25 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.32), residues: 750
  helix:  1.74 (0.27), residues: 400
  sheet: -0.25 (0.80), residues: 53
  loop : -0.26 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 466 
 HIS   0.004   0.001   HIS D 271 
 PHE   0.012   0.001   PHE A  90 
 TYR   0.009   0.001   TYR D 394 
 ARG   0.001   0.000   ARG D  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03494 (  311)
  hydrogen bonds       : angle       3.90274 (  906)
  metal coordination   : bond        0.00255 (    1)
  covalent geometry    : bond        0.00234 ( 6187)
  covalent geometry    : angle       0.49782 ( 8348)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1944.69 seconds
wall clock time: 34 minutes 53.23 seconds (2093.23 seconds total)