Starting phenix.real_space_refine
on Fri Aug 22 16:42:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jfw_36218/08_2025/8jfw_36218.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jfw_36218/08_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_36218/08_2025/8jfw_36218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jfw_36218/08_2025/8jfw_36218.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jfw_36218/08_2025/8jfw_36218.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jfw_36218/08_2025/8jfw_36218.cif"
  }
  resolution = 3.64
  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: 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.31, per 1000 atoms: 0.22
  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: 0.51
  Conformation dependent library (CDL) restraints added in 289.4 milliseconds
  
  Enol-peptide restraints added in 0.0 nanoseconds
  
  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: 0.24
  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: 1.02

  Time building geometry restraints manager: 0.68 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:             1.150
  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:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.260
  Find NCS groups from input model:        0.030
  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:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.680
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.000   ARG D 440 
 TYR   0.006   0.001   TYR D 394 
 PHE   0.010   0.001   PHE D 535 
 TRP   0.011   0.001   TRP D  15 
 HIS   0.002   0.000   HIS D 271 

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

*********************** 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  : 0.178 
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: 0.0690
  time to fit residues: 8.0448
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  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0270
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7242

-------------------------------------------------------------------------------
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 = 0.4236 r_free = 0.4236 target = 0.204141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.152608 restraints weight = 6828.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.151179 restraints weight = 8126.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.152717 restraints weight = 7883.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.153427 restraints weight = 4398.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.154804 restraints weight = 3976.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.0918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6188  Z= 0.120
  Angle     :  0.512   8.058   8348  Z= 0.274
  Chirality :  0.041   0.214    912
  Planarity :  0.003   0.031   1099
  Dihedral  :  4.130  21.142    823
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.62 %
    Favored  : 84.72 %
  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 aren not related in a simple way.
  whole:  1.32 (0.32), residues: 750
  helix:  1.70 (0.27), residues: 397
  sheet:  0.14 (0.78), residues: 51
  loop : -0.01 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 440 
 TYR   0.010   0.001   TYR D 254 
 PHE   0.010   0.001   PHE D 347 
 TRP   0.010   0.001   TRP D  15 
 HIS   0.003   0.001   HIS D 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6187)
  covalent geometry    : angle       0.51223 ( 8348)
  hydrogen bonds       : bond        0.04418 (  311)
  hydrogen bonds       : angle       4.35586 (  906)
  metal coordination   : bond        0.00340 (    1)

*********************** 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: 11
    poor density    : 84
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6217 (mtm)
REVERT: D   47 GLU cc_start: 0.8181 (pp20) cc_final: 0.7974 (pp20)
  outliers start: 11
  outliers final: 5
  residues processed: 86
  average time/residue: 0.0695
  time to fit residues: 8.1418
Evaluate side-chains
  85 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
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  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 71 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 3 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 61 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0070
   chunk 15 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7602

-------------------------------------------------------------------------------
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 = 0.4265 r_free = 0.4265 target = 0.207713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.153216 restraints weight = 6896.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.149858 restraints weight = 6975.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.151280 restraints weight = 7619.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.152217 restraints weight = 4344.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.157250 restraints weight = 3876.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6188  Z= 0.113
  Angle     :  0.485   8.149   8348  Z= 0.258
  Chirality :  0.040   0.215    912
  Planarity :  0.003   0.025   1099
  Dihedral  :  4.053  18.418    823
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 13.62 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.31), residues: 750
  helix:  1.68 (0.27), residues: 398
  sheet:  0.27 (0.75), residues: 56
  loop : -0.11 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 440 
 TYR   0.011   0.001   TYR D 394 
 PHE   0.011   0.001   PHE D 347 
 TRP   0.011   0.001   TRP D  15 
 HIS   0.004   0.001   HIS D 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6187)
  covalent geometry    : angle       0.48462 ( 8348)
  hydrogen bonds       : bond        0.04037 (  311)
  hydrogen bonds       : angle       4.13543 (  906)
  metal coordination   : bond        0.00248 (    1)

*********************** 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
  91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.5996 (mtm)
REVERT: D   47 GLU cc_start: 0.8255 (pp20) cc_final: 0.7949 (pp20)
REVERT: D  470 MET cc_start: 0.8830 (tpp) cc_final: 0.8607 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 86
  average time/residue: 0.0680
  time to fit residues: 8.2495
Evaluate side-chains
  83 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
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 64 optimal weight:    0.0040
   chunk 3 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 63 optimal weight:    0.4980
   chunk 70 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.8998

-------------------------------------------------------------------------------
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 = 0.203470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.151116 restraints weight = 6876.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.152505 restraints weight = 8138.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.152578 restraints weight = 6482.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.152696 restraints weight = 3599.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.153725 restraints weight = 3421.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1363

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= 0.120
  Angle     :  0.486   7.310   8348  Z= 0.257
  Chirality :  0.040   0.218    912
  Planarity :  0.003   0.032   1099
  Dihedral  :  4.052  18.184    823
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.22 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.31), residues: 750
  helix:  1.69 (0.27), residues: 398
  sheet:  0.01 (0.71), residues: 62
  loop : -0.22 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 440 
 TYR   0.011   0.001   TYR D 394 
 PHE   0.012   0.001   PHE D 347 
 TRP   0.008   0.001   TRP D  15 
 HIS   0.004   0.001   HIS D 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6187)
  covalent geometry    : angle       0.48579 ( 8348)
  hydrogen bonds       : bond        0.03921 (  311)
  hydrogen bonds       : angle       4.05832 (  906)
  metal coordination   : bond        0.00343 (    1)

*********************** 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
  94 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6113 (mtm)
REVERT: D   47 GLU cc_start: 0.8266 (pp20) cc_final: 0.7912 (pp20)
REVERT: D  470 MET cc_start: 0.8883 (tpp) cc_final: 0.8646 (mmm)
REVERT: D  521 MET cc_start: 0.6125 (mtp) cc_final: 0.5691 (mmm)
  outliers start: 10
  outliers final: 6
  residues processed: 90
  average time/residue: 0.0678
  time to fit residues: 8.3641
Evaluate side-chains
  88 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  110 MET
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 65 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0970
   chunk 45 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0970
   chunk 11 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   chunk 61 optimal weight:    8.9990
   chunk 18 optimal weight:    0.5980
   chunk 60 optimal weight:    0.4980
   overall best weight:    0.3776

-------------------------------------------------------------------------------
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 = 0.4282 r_free = 0.4282 target = 0.209428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.154910 restraints weight = 6921.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.150362 restraints weight = 6407.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.152781 restraints weight = 6929.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.153261 restraints weight = 4234.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.154360 restraints weight = 3939.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1483

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= 0.092
  Angle     :  0.453   6.639   8348  Z= 0.240
  Chirality :  0.040   0.213    912
  Planarity :  0.003   0.032   1099
  Dihedral  :  3.860  18.008    823
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.52 %
    Favored  : 83.66 %
  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 aren not related in a simple way.
  whole:  1.34 (0.31), residues: 750
  helix:  1.80 (0.27), residues: 397
  sheet:  0.20 (0.77), residues: 56
  loop : -0.15 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 440 
 TYR   0.010   0.001   TYR D 394 
 PHE   0.010   0.001   PHE D 535 
 TRP   0.011   0.001   TRP D  15 
 HIS   0.002   0.000   HIS D 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 ( 6187)
  covalent geometry    : angle       0.45346 ( 8348)
  hydrogen bonds       : bond        0.03429 (  311)
  hydrogen bonds       : angle       3.93044 (  906)
  metal coordination   : bond        0.00223 (    1)

*********************** 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
  100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8131 (tpp)
REVERT: A  110 MET cc_start: 0.6681 (OUTLIER) cc_final: 0.6161 (mtm)
REVERT: D  470 MET cc_start: 0.8859 (tpp) cc_final: 0.8570 (mmm)
REVERT: D  521 MET cc_start: 0.6158 (mtp) cc_final: 0.5704 (mmm)
  outliers start: 12
  outliers final: 6
  residues processed: 94
  average time/residue: 0.0630
  time to fit residues: 8.2443
Evaluate side-chains
  93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
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  305 LEU
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 29 optimal weight:    0.0570
   chunk 28 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.6698

-------------------------------------------------------------------------------
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 = 0.4246 r_free = 0.4246 target = 0.204886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.151964 restraints weight = 6870.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.149987 restraints weight = 7224.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.151560 restraints weight = 7276.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.152167 restraints weight = 4215.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.153280 restraints weight = 3837.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1618

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= 0.104
  Angle     :  0.469   8.164   8348  Z= 0.247
  Chirality :  0.040   0.215    912
  Planarity :  0.003   0.035   1099
  Dihedral  :  3.864  17.643    823
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.98 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.31), residues: 750
  helix:  1.81 (0.27), residues: 398
  sheet:  0.18 (0.76), residues: 56
  loop : -0.12 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 440 
 TYR   0.010   0.001   TYR D 394 
 PHE   0.010   0.001   PHE D 347 
 TRP   0.010   0.001   TRP D  15 
 HIS   0.003   0.001   HIS D 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 6187)
  covalent geometry    : angle       0.46939 ( 8348)
  hydrogen bonds       : bond        0.03559 (  311)
  hydrogen bonds       : angle       3.90607 (  906)
  metal coordination   : bond        0.00245 (    1)

*********************** 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: 13
    poor density    : 85
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.6199 (mtm)
REVERT: D  470 MET cc_start: 0.8862 (tpp) cc_final: 0.8637 (mmm)
REVERT: D  521 MET cc_start: 0.6155 (mtp) cc_final: 0.5725 (mmm)
  outliers start: 13
  outliers final: 7
  residues processed: 92
  average time/residue: 0.0595
  time to fit residues: 7.5804
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  : 0.214 
-------------------------------------------------------------------------------
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  305 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 74 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0030
   chunk 13 optimal weight:    0.1980
   overall best weight:    0.5592

-------------------------------------------------------------------------------
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 = 0.4249 r_free = 0.4249 target = 0.205283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.152588 restraints weight = 6830.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.150691 restraints weight = 7451.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.151321 restraints weight = 8088.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.152512 restraints weight = 4314.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.153144 restraints weight = 3773.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.1667

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= 0.098
  Angle     :  0.474   8.783   8348  Z= 0.246
  Chirality :  0.040   0.226    912
  Planarity :  0.003   0.035   1099
  Dihedral  :  3.822  19.780    823
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 15.28 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.31), residues: 750
  helix:  1.82 (0.27), residues: 399
  sheet:  0.20 (0.76), residues: 56
  loop : -0.12 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 440 
 TYR   0.010   0.001   TYR D 394 
 PHE   0.008   0.001   PHE D 347 
 TRP   0.011   0.001   TRP D  15 
 HIS   0.003   0.000   HIS D 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 6187)
  covalent geometry    : angle       0.47434 ( 8348)
  hydrogen bonds       : bond        0.03370 (  311)
  hydrogen bonds       : angle       3.86486 (  906)
  metal coordination   : bond        0.00239 (    1)

*********************** 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
  99 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 MET cc_start: 0.7257 (mtt) cc_final: 0.6691 (mtt)
REVERT: A   72 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7793 (tpp)
REVERT: A  110 MET cc_start: 0.6391 (OUTLIER) cc_final: 0.6184 (mtm)
REVERT: D  470 MET cc_start: 0.8837 (tpp) cc_final: 0.8614 (mmm)
  outliers start: 13
  outliers final: 9
  residues processed: 93
  average time/residue: 0.0571
  time to fit residues: 7.4251
Evaluate side-chains
  95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
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  110 MET
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain D residue  178 SER
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  432 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 28 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   chunk 35 optimal weight:    0.0670
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 45 optimal weight:    0.4980
   chunk 56 optimal weight:    0.7980
   chunk 20 optimal weight:    9.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 = 0.4256 r_free = 0.4256 target = 0.206012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.152837 restraints weight = 6840.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.149714 restraints weight = 7556.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.151338 restraints weight = 7864.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.152424 restraints weight = 4372.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.153657 restraints weight = 3843.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1783

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= 0.100
  Angle     :  0.482   9.915   8348  Z= 0.248
  Chirality :  0.040   0.217    912
  Planarity :  0.003   0.036   1099
  Dihedral  :  3.796  19.516    823
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 15.43 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.32), residues: 750
  helix:  1.88 (0.27), residues: 398
  sheet:  0.17 (0.76), residues: 56
  loop : -0.13 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 440 
 TYR   0.010   0.001   TYR D 394 
 PHE   0.010   0.001   PHE A 142 
 TRP   0.009   0.001   TRP D  15 
 HIS   0.003   0.000   HIS D 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 6187)
  covalent geometry    : angle       0.48162 ( 8348)
  hydrogen bonds       : bond        0.03378 (  311)
  hydrogen bonds       : angle       3.84294 (  906)
  metal coordination   : bond        0.00245 (    1)

*********************** 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
  96 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 MET cc_start: 0.7269 (mtt) cc_final: 0.6641 (mtt)
REVERT: A   72 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7789 (tpp)
REVERT: A   73 MET cc_start: 0.8156 (mmm) cc_final: 0.7790 (tpt)
REVERT: A  139 TYR cc_start: 0.7922 (p90) cc_final: 0.7391 (p90)
REVERT: D  470 MET cc_start: 0.8835 (tpp) cc_final: 0.8618 (mmm)
  outliers start: 13
  outliers final: 8
  residues processed: 91
  average time/residue: 0.0601
  time to fit residues: 7.7647
Evaluate side-chains
  91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
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  178 SER
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  432 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 7 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0970
   chunk 62 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.4254 r_free = 0.4254 target = 0.206051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.153791 restraints weight = 6943.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.153769 restraints weight = 7810.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.153780 restraints weight = 7156.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.154666 restraints weight = 3826.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.155513 restraints weight = 3424.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1823

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= 0.103
  Angle     :  0.510  10.759   8348  Z= 0.258
  Chirality :  0.040   0.210    912
  Planarity :  0.003   0.036   1099
  Dihedral  :  3.840  19.550    823
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.31), residues: 750
  helix:  1.90 (0.27), residues: 398
  sheet:  0.16 (0.75), residues: 56
  loop : -0.11 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 440 
 TYR   0.010   0.001   TYR D 394 
 PHE   0.011   0.001   PHE A 142 
 TRP   0.008   0.001   TRP D  15 
 HIS   0.003   0.000   HIS D 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 6187)
  covalent geometry    : angle       0.51042 ( 8348)
  hydrogen bonds       : bond        0.03337 (  311)
  hydrogen bonds       : angle       3.82241 (  906)
  metal coordination   : bond        0.00244 (    1)

*********************** 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
  92 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8301 (tpp)
REVERT: A   73 MET cc_start: 0.8127 (mmm) cc_final: 0.7773 (tpt)
REVERT: A  139 TYR cc_start: 0.7906 (p90) cc_final: 0.7454 (p90)
REVERT: D  470 MET cc_start: 0.8843 (tpp) cc_final: 0.8627 (mmm)
  outliers start: 9
  outliers final: 8
  residues processed: 89
  average time/residue: 0.0611
  time to fit residues: 7.5954
Evaluate side-chains
  91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
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  122 VAL
Chi-restraints excluded: chain D residue  178 SER
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  432 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 39 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 66 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0670
   chunk 45 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 8 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 = 0.4256 r_free = 0.4256 target = 0.206124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.152016 restraints weight = 6889.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.149819 restraints weight = 7119.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.150625 restraints weight = 7279.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.151390 restraints weight = 3897.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.152985 restraints weight = 3462.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1895

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= 0.102
  Angle     :  0.514  12.463   8348  Z= 0.258
  Chirality :  0.040   0.210    912
  Planarity :  0.003   0.035   1099
  Dihedral  :  3.828  19.640    823
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 16.49 %
    Favored  : 82.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.31), residues: 750
  helix:  1.88 (0.27), residues: 398
  sheet:  0.12 (0.75), residues: 56
  loop : -0.15 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 440 
 TYR   0.010   0.001   TYR D 394 
 PHE   0.011   0.001   PHE A 142 
 TRP   0.009   0.001   TRP D  15 
 HIS   0.003   0.000   HIS D 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6187)
  covalent geometry    : angle       0.51417 ( 8348)
  hydrogen bonds       : bond        0.03324 (  311)
  hydrogen bonds       : angle       3.81224 (  906)
  metal coordination   : bond        0.00246 (    1)

********************** 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
  93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.8136 (mmm) cc_final: 0.7773 (tpt)
REVERT: A  139 TYR cc_start: 0.7992 (p90) cc_final: 0.7488 (p90)
REVERT: D  470 MET cc_start: 0.8841 (tpp) cc_final: 0.8604 (mmm)
  outliers start: 7
  outliers final: 7
  residues processed: 91
  average time/residue: 0.0664
  time to fit residues: 8.3607
Evaluate side-chains
  89 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain D residue  178 SER
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  432 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 45 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 61 optimal weight:   10.0000
   chunk 69 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.204245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.152326 restraints weight = 6887.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.150993 restraints weight = 8152.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.152186 restraints weight = 7465.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.152749 restraints weight = 4056.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.153957 restraints weight = 3726.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
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      :  0.003   0.033   6188  Z= 0.116
  Angle     :  0.528  11.903   8348  Z= 0.266
  Chirality :  0.041   0.215    912
  Planarity :  0.003   0.036   1099
  Dihedral  :  3.898  19.274    823
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.31), residues: 750
  helix:  1.88 (0.27), residues: 398
  sheet:  0.06 (0.75), residues: 56
  loop : -0.14 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 440 
 TYR   0.010   0.001   TYR D 394 
 PHE   0.010   0.001   PHE D 347 
 TRP   0.006   0.001   TRP D 318 
 HIS   0.003   0.001   HIS D 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6187)
  covalent geometry    : angle       0.52820 ( 8348)
  hydrogen bonds       : bond        0.03508 (  311)
  hydrogen bonds       : angle       3.85489 (  906)
  metal coordination   : bond        0.00328 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 929.79 seconds
wall clock time: 16 minutes 40.32 seconds (1000.32 seconds total)