Starting phenix.real_space_refine
on Wed Mar  4 03:19:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7q6z_13860/03_2026/7q6z_13860_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7q6z_13860/03_2026/7q6z_13860.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7q6z_13860/03_2026/7q6z_13860_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7q6z_13860/03_2026/7q6z_13860_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7q6z_13860/03_2026/7q6z_13860.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7q6z_13860/03_2026/7q6z_13860.map"
  }
  resolution = 3.59
  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=   0.001 sd=   0.068
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
     S      36      5.16       5
     C    3291      2.51       5
     N     802      2.21       5
     O     840      1.98       5
     H    4784      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9754
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7919
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 485, 7919
          Classifications: {'peptide': 485}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 469}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 1722
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 4, 'TRANS': 107}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 113
          Unusual residues: {'9V3': 1, 'CLR': 1, 'HEM': 1, 'PLM': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5233  SG  CYS A 324      40.122  50.446  63.748  1.00 36.18           S

  Time building chain proxies: 1.71, per 1000 atoms: 0.18
  Number of scatterers: 9754
  At special positions: 0
  Unit cell: (83.1, 84.208, 98.612, 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)
     Fe      1     26.01
     S      36     16.00
     O     840      8.00
     N     802      7.00
     C    3291      6.00
     H    4784      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 816 " - pdb=" SG  CYS B 889 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 378.0 milliseconds
  

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1110

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 4 sheets defined
      72.5% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 32
    Processing helix  chain 'A' and resid 32 through 41
    Processing helix  chain 'A' and resid 58 through 70
    Processing helix  chain 'A' and resid 70 through 89
    Processing helix  chain 'A' and resid 92 through 110
    Processing helix  chain 'A' and resid 110 through 130
      removed outlier: 3.502A  pdb=" N   VAL A 114 " --> pdb=" O   GLY A 110 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   MET A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   PHE A 130 " --> pdb=" O   CYS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 149
    Processing helix  chain 'A' and resid 149 through 160
      removed outlier: 3.714A  pdb=" N   TRP A 159 " --> pdb=" O   VAL A 155 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   TYR A 160 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 188
      removed outlier: 3.709A  pdb=" N   TYR A 166 " --> pdb=" O   THR A 162 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU A 178 " --> pdb=" O   THR A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 209
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 221 through 230
    Processing helix  chain 'A' and resid 236 through 265
    Processing helix  chain 'A' and resid 266 through 273
    Processing helix  chain 'A' and resid 273 through 278
    Processing helix  chain 'A' and resid 281 through 314
      removed outlier: 3.836A  pdb=" N   PHE A 304 " --> pdb=" O   TYR A 300 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   VAL A 306 " --> pdb=" O   VAL A 302 " (cutoff:3.500A)
      Proline residue:  A 307  - end of helix
    Processing helix  chain 'A' and resid 330 through 337
    Processing helix  chain 'A' and resid 339 through 349
    Processing helix  chain 'A' and resid 350 through 355
      removed outlier: 4.030A  pdb=" N   VAL A 354 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 380
      removed outlier: 3.701A  pdb=" N   GLY A 380 " --> pdb=" O   SER A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 408
    Processing helix  chain 'A' and resid 408 through 419
    Processing helix  chain 'A' and resid 420 through 449
      removed outlier: 3.729A  pdb=" N   ARG A 426 " --> pdb=" O   GLN A 422 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   CYS A 434 " --> pdb=" O   ALA A 430 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU A 441 " --> pdb=" O   SER A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 461
    Processing helix  chain 'A' and resid 467 through 488
    Processing helix  chain 'B' and resid 855 through 858
    Processing helix  chain 'B' and resid 880 through 884
      removed outlier: 3.758A  pdb=" N   THR B 884 " --> pdb=" O   PRO B 881 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44
    Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 30
      removed outlier: 3.855A  pdb=" N   GLN B  26 " --> pdb=" O   SER B 819 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   VAL B  28 " --> pdb=" O   THR B 817 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER B  30 " --> pdb=" O   SER B 815 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   SER B 815 " --> pdb=" O   SER B  30 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU B 812 " --> pdb=" O   MET B 876 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 851 through 853
      removed outlier: 6.802A  pdb=" N   TRP B 830 " --> pdb=" O   VAL B 842 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   ILE B 844 " --> pdb=" O   VAL B 828 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   VAL B 828 " --> pdb=" O   ILE B 844 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLY B 892 " --> pdb=" O   ASP B 827 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA B 891 " --> pdb=" O   TYR B 903 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 851 through 853
      removed outlier: 6.802A  pdb=" N   TRP B 830 " --> pdb=" O   VAL B 842 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   ILE B 844 " --> pdb=" O   VAL B 828 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   VAL B 828 " --> pdb=" O   ILE B 844 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLY B 892 " --> pdb=" O   ASP B 827 " (cutoff:3.500A)

    354 hydrogen bonds defined for protein.
    1023 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.22

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        0.84 -     1.09: 4771
        1.09 -     1.34: 1451
        1.34 -     1.58: 3635
        1.58 -     1.83: 55
        1.83 -     2.08: 5
  Bond restraints: 9917
  Sorted by residual:
  bond pdb=" C8  9V3 A 603 "
       pdb=" S   9V3 A 603 "
    ideal  model  delta    sigma   weight residual
    1.720  1.967 -0.247 2.00e-02 2.50e+03 1.52e+02
  bond pdb=" C8  9V3 A 603 "
       pdb=" C9  9V3 A 603 "
    ideal  model  delta    sigma   weight residual
    1.359  1.549 -0.190 2.00e-02 2.50e+03 8.99e+01
  bond pdb=" C10 9V3 A 603 "
       pdb=" C11 9V3 A 603 "
    ideal  model  delta    sigma   weight residual
    1.358  1.229  0.129 2.00e-02 2.50e+03 4.13e+01
  bond pdb=" C5  9V3 A 603 "
       pdb=" N1  9V3 A 603 "
    ideal  model  delta    sigma   weight residual
    1.358  1.475 -0.117 2.00e-02 2.50e+03 3.44e+01
  bond pdb=" C7  9V3 A 603 "
       pdb=" C8  9V3 A 603 "
    ideal  model  delta    sigma   weight residual
    1.489  1.394  0.095 2.00e-02 2.50e+03 2.25e+01
  ... (remaining 9912 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.15: 17768
        7.15 -    14.31: 7
       14.31 -    21.46: 0
       21.46 -    28.62: 0
       28.62 -    35.77: 6
  Bond angle restraints: 17781
  Sorted by residual:
  angle pdb=" N   MET A   1 "
        pdb=" CA  MET A   1 "
        pdb=" HA  MET A   1 "
      ideal   model   delta    sigma   weight residual
     110.00   74.23   35.77 3.00e+00 1.11e-01 1.42e+02
  angle pdb=" C   MET A   1 "
        pdb=" CA  MET A   1 "
        pdb=" HA  MET A   1 "
      ideal   model   delta    sigma   weight residual
     110.00   74.41   35.59 3.00e+00 1.11e-01 1.41e+02
  angle pdb=" CB  THR A 332 "
        pdb=" CA  THR A 332 "
        pdb=" HA  THR A 332 "
      ideal   model   delta    sigma   weight residual
     109.00   74.03   34.97 3.00e+00 1.11e-01 1.36e+02
  angle pdb=" N   THR A 332 "
        pdb=" CA  THR A 332 "
        pdb=" HA  THR A 332 "
      ideal   model   delta    sigma   weight residual
     110.00   75.32   34.68 3.00e+00 1.11e-01 1.34e+02
  angle pdb=" C   THR A 332 "
        pdb=" CA  THR A 332 "
        pdb=" HA  THR A 332 "
      ideal   model   delta    sigma   weight residual
     109.00   74.95   34.05 3.00e+00 1.11e-01 1.29e+02
  ... (remaining 17776 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4288
       17.96 -    35.92: 319
       35.92 -    53.88: 105
       53.88 -    71.84: 20
       71.84 -    89.80: 6
  Dihedral angle restraints: 4738
    sinusoidal: 2490
      harmonic: 2248
  Sorted by residual:
  dihedral pdb=" C2B HEM A 602 "
           pdb=" C3B HEM A 602 "
           pdb=" CAB HEM A 602 "
           pdb=" CBB HEM A 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   46.64  -46.64     2      1.00e+01 1.00e-02 2.54e+01
  dihedral pdb=" CA  MET A 334 "
           pdb=" C   MET A 334 "
           pdb=" N   TRP A 335 "
           pdb=" CA  TRP A 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.98   19.02     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  TYR A 300 "
           pdb=" C   TYR A 300 "
           pdb=" N   LEU A 301 "
           pdb=" CA  LEU A 301 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.59   18.41     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 4735 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 727
       0.093 -    0.186: 21
       0.186 -    0.279: 0
       0.279 -    0.372: 2
       0.372 -    0.465: 1
  Chirality restraints: 751
  Sorted by residual:
  chirality pdb=" CA  MET A   1 "
            pdb=" N   MET A   1 "
            pdb=" C   MET A   1 "
            pdb=" CB  MET A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.10    0.46 2.00e-01 2.50e+01 5.40e+00
  chirality pdb=" CA  THR A 332 "
            pdb=" N   THR A 332 "
            pdb=" C   THR A 332 "
            pdb=" CB  THR A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.17    0.36 2.00e-01 2.50e+01 3.24e+00
  chirality pdb=" C12 9V3 A 603 "
            pdb=" C13 9V3 A 603 "
            pdb=" C9  9V3 A 603 "
            pdb=" N1  9V3 A 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.68    0.32 2.00e-01 2.50e+01 2.59e+00
  ... (remaining 748 not shown)

  Planarity restraints: 1413
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 113 "   -0.009 2.00e-02 2.50e+03   1.78e-02 3.15e+00
        pdb=" C   GLY A 113 "    0.031 2.00e-02 2.50e+03
        pdb=" O   GLY A 113 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   VAL A 114 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 306 "   -0.022 5.00e-02 4.00e+02   3.31e-02 1.75e+00
        pdb=" N   PRO A 307 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 307 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 307 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  17 "   -0.012 2.00e-02 2.50e+03   6.51e-03 1.27e+00
        pdb=" CG  PHE A  17 "    0.011 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  17 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  17 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  17 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  17 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  17 "    0.001 2.00e-02 2.50e+03
        pdb=" HD1 PHE A  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD2 PHE A  17 "    0.001 2.00e-02 2.50e+03
        pdb=" HE1 PHE A  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE2 PHE A  17 "   -0.002 2.00e-02 2.50e+03
        pdb=" HZ  PHE A  17 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1410 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 396
        2.18 -     2.78: 18718
        2.78 -     3.39: 27645
        3.39 -     3.99: 34634
        3.99 -     4.60: 54177
  Nonbonded interactions: 135570
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 349 "
            pdb=" H   TYR A 351 "
     model   vdw
     1.569 2.450
  nonbonded pdb=" O   SER A  14 "
            pdb=" HD1 HIS A  18 "
     model   vdw
     1.662 2.450
  nonbonded pdb=" OE1 GLU B 882 "
            pdb=" H   GLU B 882 "
     model   vdw
     1.663 2.450
  nonbonded pdb=" HA  MET A   1 "
            pdb=" HB2 MET A   1 "
     model   vdw
     1.688 1.952
  nonbonded pdb=" O   THR B 846 "
            pdb="HH11 ARG B 865 "
     model   vdw
     1.695 2.450
  ... (remaining 135565 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:             2.280
  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:             0.050
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.720
  Find NCS groups from input model:        0.020
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
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      :  0.008   0.247   5135  Z= 0.374
  Angle     :  0.688  13.229   7006  Z= 0.345
  Chirality :  0.043   0.465    751
  Planarity :  0.003   0.033    839
  Dihedral  : 14.584  89.798   1837
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.36), residues: 589
  helix:  2.24 (0.27), residues: 381
  sheet: -1.00 (0.83), residues: 52
  loop : -1.10 (0.49), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 847 
 TYR   0.014   0.002   TYR A 166 
 PHE   0.012   0.002   PHE A  17 
 TRP   0.010   0.001   TRP A 388 
 HIS   0.006   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00781 ( 5133)
  covalent geometry    : angle       0.68781 ( 7004)
  SS BOND              : bond        0.00180 (    1)
  SS BOND              : angle       0.51118 (    2)
  hydrogen bonds       : bond        0.15397 (  342)
  hydrogen bonds       : angle       7.51231 ( 1023)
  Misc. bond           : bond        0.00665 (    1)

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

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

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LEU cc_start: 0.7902 (tp) cc_final: 0.7303 (mt)
REVERT: A  334 MET cc_start: 0.7452 (tmm) cc_final: 0.7151 (tmm)
REVERT: A  370 MET cc_start: 0.6733 (tpp) cc_final: 0.5853 (tpt)
REVERT: B  866 ASP cc_start: 0.7230 (t0) cc_final: 0.6975 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1373
  time to fit residues: 16.5133
Evaluate side-chains
  83 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.1980
   chunk 25 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.167136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.131884 restraints weight = 15671.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.137945 restraints weight = 8937.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.141964 restraints weight = 6249.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.144678 restraints weight = 4936.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.146663 restraints weight = 4173.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
moved from start:          0.0934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   5135  Z= 0.205
  Angle     :  0.575  10.060   7006  Z= 0.301
  Chirality :  0.041   0.452    751
  Planarity :  0.004   0.038    839
  Dihedral  :  7.652  78.605    766
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  6.20 %
    Favored  : 93.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.36), residues: 589
  helix:  2.27 (0.26), residues: 391
  sheet: -1.05 (0.79), residues: 52
  loop : -1.26 (0.49), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 847 
 TYR   0.017   0.002   TYR A 180 
 PHE   0.021   0.002   PHE A  17 
 TRP   0.008   0.001   TRP A  63 
 HIS   0.004   0.001   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 5133)
  covalent geometry    : angle       0.57469 ( 7004)
  SS BOND              : bond        0.00127 (    1)
  SS BOND              : angle       0.79505 (    2)
  hydrogen bonds       : bond        0.05038 (  342)
  hydrogen bonds       : angle       5.63320 ( 1023)
  Misc. bond           : bond        0.01639 (    1)

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

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

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LEU cc_start: 0.7875 (tp) cc_final: 0.7311 (mt)
REVERT: A  179 TYR cc_start: 0.8569 (m-80) cc_final: 0.8280 (m-10)
REVERT: A  334 MET cc_start: 0.7679 (tmm) cc_final: 0.7458 (tmm)
REVERT: A  370 MET cc_start: 0.6713 (tpp) cc_final: 0.5854 (tpt)
REVERT: B  865 ARG cc_start: 0.7991 (ptm160) cc_final: 0.7643 (ptm160)
  outliers start: 4
  outliers final: 4
  residues processed: 89
  average time/residue: 0.1376
  time to fit residues: 16.1235
Evaluate side-chains
  87 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain B residue  840 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.164942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.130253 restraints weight = 15850.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.136076 restraints weight = 9142.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.140005 restraints weight = 6449.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.142556 restraints weight = 5115.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.143898 restraints weight = 4353.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.1180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   5135  Z= 0.234
  Angle     :  0.589  10.100   7006  Z= 0.306
  Chirality :  0.041   0.450    751
  Planarity :  0.004   0.039    839
  Dihedral  :  7.332  72.741    766
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  8.14 %
    Favored  : 90.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.36), residues: 589
  helix:  2.22 (0.26), residues: 391
  sheet: -1.24 (0.74), residues: 52
  loop : -1.49 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 847 
 TYR   0.015   0.002   TYR A 166 
 PHE   0.016   0.002   PHE A 125 
 TRP   0.010   0.001   TRP A  63 
 HIS   0.005   0.001   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 ( 5133)
  covalent geometry    : angle       0.58918 ( 7004)
  SS BOND              : bond        0.00200 (    1)
  SS BOND              : angle       0.64694 (    2)
  hydrogen bonds       : bond        0.04852 (  342)
  hydrogen bonds       : angle       5.35126 ( 1023)
  Misc. bond           : bond        0.02340 (    1)

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

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

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 MET cc_start: 0.7719 (mmm) cc_final: 0.7368 (mtp)
REVERT: A  138 LEU cc_start: 0.7899 (tp) cc_final: 0.7326 (mt)
REVERT: A  229 MET cc_start: 0.8256 (mtt) cc_final: 0.8044 (mtp)
REVERT: A  370 MET cc_start: 0.6718 (tpp) cc_final: 0.5879 (tpt)
  outliers start: 6
  outliers final: 5
  residues processed: 86
  average time/residue: 0.1436
  time to fit residues: 16.2745
Evaluate side-chains
  87 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain B residue  840 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0060
   chunk 28 optimal weight:    0.0970
   chunk 41 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.167800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.132238 restraints weight = 15715.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.138428 restraints weight = 8868.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.142631 restraints weight = 6170.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.145383 restraints weight = 4831.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.147551 restraints weight = 4072.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6900
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5135  Z= 0.140
  Angle     :  0.513  10.409   7006  Z= 0.264
  Chirality :  0.039   0.455    751
  Planarity :  0.004   0.037    839
  Dihedral  :  6.997  70.919    766
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.30 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.36), residues: 589
  helix:  2.44 (0.26), residues: 391
  sheet: -1.28 (0.70), residues: 52
  loop : -1.36 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 176 
 TYR   0.016   0.001   TYR A 180 
 PHE   0.013   0.001   PHE A  17 
 TRP   0.006   0.001   TRP A  63 
 HIS   0.003   0.001   HIS A  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 5133)
  covalent geometry    : angle       0.51297 ( 7004)
  SS BOND              : bond        0.00232 (    1)
  SS BOND              : angle       0.48298 (    2)
  hydrogen bonds       : bond        0.04265 (  342)
  hydrogen bonds       : angle       4.95086 ( 1023)
  Misc. bond           : bond        0.00420 (    1)

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

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

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 MET cc_start: 0.7722 (mmm) cc_final: 0.7293 (mtp)
REVERT: A  138 LEU cc_start: 0.7883 (tp) cc_final: 0.7301 (mt)
REVERT: A  172 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7572 (m)
REVERT: A  186 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6503 (tp30)
REVERT: A  229 MET cc_start: 0.8275 (mtt) cc_final: 0.7990 (mtp)
REVERT: A  370 MET cc_start: 0.6635 (tpp) cc_final: 0.5825 (tpt)
  outliers start: 6
  outliers final: 5
  residues processed: 88
  average time/residue: 0.1547
  time to fit residues: 17.8887
Evaluate side-chains
  86 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain B residue  840 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0970
   chunk 55 optimal weight:    0.8980
   chunk 43 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 51 optimal weight:    0.2980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
A 292 GLN
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.167820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.132974 restraints weight = 15551.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.139111 restraints weight = 8904.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.143256 restraints weight = 6209.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.146084 restraints weight = 4874.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.147974 restraints weight = 4095.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6895
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5135  Z= 0.143
  Angle     :  0.509  10.177   7006  Z= 0.261
  Chirality :  0.039   0.452    751
  Planarity :  0.003   0.035    839
  Dihedral  :  6.785  66.895    766
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.85 %
    Favored  : 87.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.36), residues: 589
  helix:  2.49 (0.26), residues: 397
  sheet: -1.46 (0.68), residues: 52
  loop : -1.06 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 847 
 TYR   0.016   0.001   TYR A 180 
 PHE   0.012   0.001   PHE A 183 
 TRP   0.006   0.001   TRP A  63 
 HIS   0.003   0.001   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5133)
  covalent geometry    : angle       0.50932 ( 7004)
  SS BOND              : bond        0.00271 (    1)
  SS BOND              : angle       0.44662 (    2)
  hydrogen bonds       : bond        0.04082 (  342)
  hydrogen bonds       : angle       4.76642 ( 1023)
  Misc. bond           : bond        0.00774 (    1)

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

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

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 MET cc_start: 0.7733 (mmm) cc_final: 0.7262 (mtp)
REVERT: A  138 LEU cc_start: 0.7907 (tp) cc_final: 0.7340 (mt)
REVERT: A  172 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7576 (m)
REVERT: A  292 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7225 (mm-40)
REVERT: A  370 MET cc_start: 0.6598 (tpp) cc_final: 0.5793 (tpt)
REVERT: A  393 TRP cc_start: 0.8254 (t60) cc_final: 0.8013 (t60)
  outliers start: 9
  outliers final: 5
  residues processed: 88
  average time/residue: 0.1439
  time to fit residues: 16.8777
Evaluate side-chains
  88 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  292 GLN
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain B residue  840 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 28 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 17 optimal weight:    0.1980
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.169101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.132940 restraints weight = 15701.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.139207 restraints weight = 8988.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.143418 restraints weight = 6321.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.146261 restraints weight = 4980.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.148253 restraints weight = 4193.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6931
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5135  Z= 0.172
  Angle     :  0.533  10.555   7006  Z= 0.276
  Chirality :  0.040   0.464    751
  Planarity :  0.004   0.035    839
  Dihedral  :  6.808  65.375    766
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 11.24 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.36), residues: 589
  helix:  2.47 (0.26), residues: 397
  sheet: -1.54 (0.67), residues: 52
  loop : -1.00 (0.51), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 847 
 TYR   0.014   0.002   TYR A 351 
 PHE   0.010   0.001   PHE A 374 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.004   0.000   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 5133)
  covalent geometry    : angle       0.53329 ( 7004)
  SS BOND              : bond        0.00256 (    1)
  SS BOND              : angle       0.50098 (    2)
  hydrogen bonds       : bond        0.04125 (  342)
  hydrogen bonds       : angle       4.77942 ( 1023)
  Misc. bond           : bond        0.01331 (    1)

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

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

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 MET cc_start: 0.7769 (mmm) cc_final: 0.7287 (mtp)
REVERT: A  138 LEU cc_start: 0.7927 (tp) cc_final: 0.7358 (mt)
REVERT: A  172 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7638 (m)
REVERT: A  370 MET cc_start: 0.6623 (tpp) cc_final: 0.5813 (tpt)
REVERT: B  865 ARG cc_start: 0.7973 (ptm160) cc_final: 0.7366 (ptm160)
  outliers start: 8
  outliers final: 6
  residues processed: 88
  average time/residue: 0.1376
  time to fit residues: 16.2091
Evaluate side-chains
  90 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  261 MET
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  481 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0270
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.167972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.132368 restraints weight = 15641.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.138463 restraints weight = 9043.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.142618 restraints weight = 6349.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.145303 restraints weight = 4999.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.147431 restraints weight = 4243.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5135  Z= 0.187
  Angle     :  0.543  10.074   7006  Z= 0.281
  Chirality :  0.040   0.455    751
  Planarity :  0.004   0.035    839
  Dihedral  :  6.885  63.596    766
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 11.82 %
    Favored  : 86.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.36), residues: 589
  helix:  2.46 (0.26), residues: 397
  sheet: -1.49 (0.68), residues: 52
  loop : -1.01 (0.51), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 157 
 TYR   0.013   0.002   TYR A 166 
 PHE   0.011   0.001   PHE A 374 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.004   0.001   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 5133)
  covalent geometry    : angle       0.54330 ( 7004)
  SS BOND              : bond        0.00221 (    1)
  SS BOND              : angle       0.56527 (    2)
  hydrogen bonds       : bond        0.04221 (  342)
  hydrogen bonds       : angle       4.77001 ( 1023)
  Misc. bond           : bond        0.01564 (    1)

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

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

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 MET cc_start: 0.7777 (mmm) cc_final: 0.7288 (mtp)
REVERT: A  138 LEU cc_start: 0.7930 (tp) cc_final: 0.7363 (mt)
REVERT: A  172 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7638 (m)
REVERT: A  370 MET cc_start: 0.6622 (tpp) cc_final: 0.5816 (tpt)
REVERT: B  865 ARG cc_start: 0.7941 (ptm160) cc_final: 0.7514 (ptm160)
  outliers start: 8
  outliers final: 6
  residues processed: 87
  average time/residue: 0.1395
  time to fit residues: 16.1885
Evaluate side-chains
  89 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  481 HIS
Chi-restraints excluded: chain B residue  840 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0770
   chunk 35 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    0.1980
   chunk 28 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.168464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.133341 restraints weight = 15691.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.139370 restraints weight = 9119.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.143490 restraints weight = 6435.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.145996 restraints weight = 5067.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.148119 restraints weight = 4315.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6930
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      :  0.004   0.045   5135  Z= 0.164
  Angle     :  0.536  10.204   7006  Z= 0.274
  Chirality :  0.040   0.459    751
  Planarity :  0.004   0.036    839
  Dihedral  :  6.824  61.830    766
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.24 %
    Favored  : 87.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.36), residues: 589
  helix:  2.57 (0.26), residues: 391
  sheet: -1.49 (0.68), residues: 52
  loop : -1.19 (0.51), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 847 
 TYR   0.014   0.002   TYR A 180 
 PHE   0.011   0.001   PHE A 374 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.004   0.000   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 5133)
  covalent geometry    : angle       0.53622 ( 7004)
  SS BOND              : bond        0.00228 (    1)
  SS BOND              : angle       0.47830 (    2)
  hydrogen bonds       : bond        0.04119 (  342)
  hydrogen bonds       : angle       4.68873 ( 1023)
  Misc. bond           : bond        0.01091 (    1)

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

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

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 MET cc_start: 0.7774 (mmm) cc_final: 0.7251 (mtp)
REVERT: A  138 LEU cc_start: 0.7942 (tp) cc_final: 0.7360 (mt)
REVERT: A  172 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7626 (m)
REVERT: A  370 MET cc_start: 0.6591 (tpp) cc_final: 0.5824 (tpt)
REVERT: B  865 ARG cc_start: 0.7915 (ptm160) cc_final: 0.7482 (ptm160)
REVERT: B  875 GLN cc_start: 0.6820 (tp-100) cc_final: 0.6484 (tt0)
  outliers start: 9
  outliers final: 6
  residues processed: 90
  average time/residue: 0.1311
  time to fit residues: 15.9190
Evaluate side-chains
  88 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  481 HIS
Chi-restraints excluded: chain B residue  840 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 9 optimal weight:    0.2980
   chunk 54 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 15 optimal weight:    0.4980
   chunk 31 optimal weight:    0.4980
   chunk 36 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.168729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.133913 restraints weight = 15574.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.140055 restraints weight = 8977.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.143927 restraints weight = 6332.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.146892 restraints weight = 5014.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.148804 restraints weight = 4224.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5135  Z= 0.161
  Angle     :  0.546  10.470   7006  Z= 0.277
  Chirality :  0.040   0.468    751
  Planarity :  0.004   0.035    839
  Dihedral  :  6.788  60.050    766
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 12.21 %
    Favored  : 86.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.36), residues: 589
  helix:  2.57 (0.26), residues: 391
  sheet: -1.50 (0.68), residues: 52
  loop : -1.15 (0.51), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 847 
 TYR   0.014   0.001   TYR A 180 
 PHE   0.013   0.001   PHE A 183 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.003   0.000   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 5133)
  covalent geometry    : angle       0.54647 ( 7004)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       0.48063 (    2)
  hydrogen bonds       : bond        0.04087 (  342)
  hydrogen bonds       : angle       4.64811 ( 1023)
  Misc. bond           : bond        0.00892 (    1)

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

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

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.6425 (t-90)
REVERT: A  102 MET cc_start: 0.7761 (mmm) cc_final: 0.7245 (mtp)
REVERT: A  138 LEU cc_start: 0.7943 (tp) cc_final: 0.7369 (mt)
REVERT: A  172 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7617 (m)
REVERT: A  370 MET cc_start: 0.6561 (tpp) cc_final: 0.5798 (tpt)
REVERT: B  865 ARG cc_start: 0.7932 (ptm160) cc_final: 0.7469 (ptm160)
REVERT: B  875 GLN cc_start: 0.6818 (tp-100) cc_final: 0.6495 (tt0)
  outliers start: 8
  outliers final: 6
  residues processed: 87
  average time/residue: 0.1347
  time to fit residues: 15.5268
Evaluate side-chains
  88 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue   18 HIS
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  481 HIS
Chi-restraints excluded: chain B residue  840 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.167828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.132808 restraints weight = 15607.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.138823 restraints weight = 9142.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.142791 restraints weight = 6468.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.145698 restraints weight = 5107.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.147624 restraints weight = 4317.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5135  Z= 0.193
  Angle     :  0.562  10.454   7006  Z= 0.288
  Chirality :  0.041   0.466    751
  Planarity :  0.004   0.035    839
  Dihedral  :  6.902  59.209    766
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 12.21 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.36), residues: 589
  helix:  2.52 (0.26), residues: 391
  sheet: -1.54 (0.68), residues: 52
  loop : -1.29 (0.49), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 847 
 TYR   0.013   0.002   TYR A 166 
 PHE   0.011   0.001   PHE A 331 
 TRP   0.008   0.001   TRP A  63 
 HIS   0.004   0.001   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 5133)
  covalent geometry    : angle       0.56164 ( 7004)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       0.58713 (    2)
  hydrogen bonds       : bond        0.04218 (  342)
  hydrogen bonds       : angle       4.69617 ( 1023)
  Misc. bond           : bond        0.01616 (    1)

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

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

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1178 Ramachandran restraints generated.
    589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 MET cc_start: 0.7773 (mmm) cc_final: 0.7259 (mtp)
REVERT: A  138 LEU cc_start: 0.7968 (tp) cc_final: 0.7390 (mt)
REVERT: A  172 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7681 (m)
REVERT: A  370 MET cc_start: 0.6599 (tpp) cc_final: 0.5822 (tpt)
REVERT: B  865 ARG cc_start: 0.7944 (ptm160) cc_final: 0.7485 (ptm160)
REVERT: B  875 GLN cc_start: 0.6835 (tp-100) cc_final: 0.6463 (tt0)
  outliers start: 7
  outliers final: 6
  residues processed: 86
  average time/residue: 0.1193
  time to fit residues: 13.8573
Evaluate side-chains
  89 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   17 PHE
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  481 HIS
Chi-restraints excluded: chain B residue  840 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 46 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 26 optimal weight:    0.4980
   chunk 55 optimal weight:    0.1980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.168291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.133866 restraints weight = 15591.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.139935 restraints weight = 9039.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.144055 restraints weight = 6342.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.146937 restraints weight = 4987.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.148851 restraints weight = 4167.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5135  Z= 0.154
  Angle     :  0.536  10.505   7006  Z= 0.273
  Chirality :  0.040   0.467    751
  Planarity :  0.004   0.035    839
  Dihedral  :  6.791  57.295    766
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 12.40 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.36), residues: 589
  helix:  2.58 (0.26), residues: 391
  sheet: -1.52 (0.68), residues: 52
  loop : -1.30 (0.49), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 847 
 TYR   0.015   0.001   TYR A 180 
 PHE   0.012   0.001   PHE A 183 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.004   0.000   HIS A  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 5133)
  covalent geometry    : angle       0.53619 ( 7004)
  SS BOND              : bond        0.00221 (    1)
  SS BOND              : angle       0.48433 (    2)
  hydrogen bonds       : bond        0.04074 (  342)
  hydrogen bonds       : angle       4.58464 ( 1023)
  Misc. bond           : bond        0.00746 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1976.67 seconds
wall clock time: 34 minutes 14.44 seconds (2054.44 seconds total)