Starting phenix.real_space_refine
on Sun Sep 13 05:29:23 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6me0_9105/09_2026/6me0_9105.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6me0_9105/09_2026/6me0_9105.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6me0_9105/09_2026/6me0_9105.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6me0_9105/09_2026/6me0_9105.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6me0_9105/09_2026/6me0_9105.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6me0_9105/09_2026/6me0_9105.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6me0_9105/09_2026/6me0_9105.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6me0_9105/09_2026/6me0_9105.cif"
  }
  resolution = 3.6
  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=   0.003
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: 7
    Type Number    sf(0)   Gaussians
     P     845      5.49       5
     Mg     32      5.21       5
     S       8      5.16       5
     Na      1      4.78       5
     C   10256      2.51       5
     N    3976      2.21       5
     O    6421      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 21539
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 17776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 829, 17776
          Classifications: {'RNAv2': 829}
          Modifications used: {'rna2p_pur': 55, 'rna2p_pyr': 33, 'rna3p_pur': 414, 'rna3p_pyr': 327}
          Link IDs: {'rna2p': 88, 'rna3p': 740}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 337
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "C"
      Number of atoms: 3393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 414, 3393
          Classifications: {'peptide': 414}
          Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 398}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 33
          Unusual residues: {' MG': 32, ' NA': 1}
          Classifications: {'undetermined': 33}
          Link IDs: {None: 32}
  Time building chain proxies: 4.10, per 1000 atoms: 0.19
  Number of scatterers: 21539
  At special positions: 0
  Unit cell: (111.39, 160.37, 233.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S       8     16.00
     P     845     15.00
     Mg     32     11.99
     Na      1     11.00
     O    6421      8.00
     N    3976      7.00
     C   10256      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.56
  Conformation dependent library (CDL) restraints added in 279.0 milliseconds
  

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  776

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 4 sheets defined
      54.1% alpha, 7.2% beta
      291 base pairs and 472 stacking pairs defined.
    Time for finding SS restraints: 3.78
  Creating SS restraints...
    Processing helix  chain 'C' and resid 27 through 47
      removed outlier: 3.791A  pdb=" N   ASN C  32 " --> pdb=" O   TRP C  28 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   ARG C  33 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL C  35 " --> pdb=" O   ALA C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 63
    Processing helix  chain 'C' and resid 64 through 77
    Processing helix  chain 'C' and resid 93 through 105
      removed outlier: 3.702A  pdb=" N   LEU C 104 " --> pdb=" O   ALA C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 154
      Proline residue:  C 149  - end of helix
      removed outlier: 3.768A  pdb=" N   THR C 153 " --> pdb=" O   PRO C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 179
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 212 through 222
      removed outlier: 3.534A  pdb=" N   SER C 222 " --> pdb=" O   LYS C 218 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 251
    Processing helix  chain 'C' and resid 254 through 259
    Processing helix  chain 'C' and resid 285 through 301
      removed outlier: 3.750A  pdb=" N   GLU C 300 " --> pdb=" O   GLU C 296 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   ARG C 301 " --> pdb=" O   PHE C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 338 through 356
      removed outlier: 3.661A  pdb=" N   LYS C 343 " --> pdb=" O   LYS C 339 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ALA C 344 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   PHE C 345 " --> pdb=" O   ASN C 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 360 through 379
      Proline residue:  C 370  - end of helix
      removed outlier: 3.880A  pdb=" N   HIS C 379 " --> pdb=" O   TRP C 375 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 384 through 407
      removed outlier: 3.898A  pdb=" N   HIS C 407 " --> pdb=" O   ALA C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 411 through 419
      removed outlier: 3.805A  pdb=" N   THR C 415 " --> pdb=" O   PRO C 411 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 452
    Processing sheet with id=AA1, first strand: chain 'C' and resid 115 through 119
      removed outlier: 3.621A  pdb=" N   VAL C 117 " --> pdb=" O   LEU C 129 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE C 119 " --> pdb=" O   ARG C 127 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 270 through 273
    Processing sheet with id=AA3, first strand: chain 'C' and resid 319 through 321
    Processing sheet with id=AA4, first strand: chain 'C' and resid 420 through 421

    165 hydrogen bonds defined for protein.
    462 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      755 hydrogen bonds
      1294 hydrogen bond angles
      0 basepair planarities
      291 basepair parallelities
      472 stacking parallelities
  Total time for adding SS restraints: 8.06

  Time building geometry restraints manager: 2.20 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2097
        1.32 -     1.44: 11238
        1.44 -     1.56: 8713
        1.56 -     1.67: 1688
        1.67 -     1.79: 12
  Bond restraints: 23748
  Sorted by residual:
  bond pdb=" O3'   U A   1 "
       pdb=" P     U A   2 "
    ideal  model  delta    sigma   weight residual
    1.607  1.460  0.147 1.20e-02 6.94e+03 1.51e+02
  bond pdb=" C3'  DG B   7 "
       pdb=" O3'  DG B   7 "
    ideal  model  delta    sigma   weight residual
    1.435  1.365  0.070 1.30e-02 5.92e+03 2.93e+01
  bond pdb=" CA  HIS C 379 "
       pdb=" CB  HIS C 379 "
    ideal  model  delta    sigma   weight residual
    1.526  1.444  0.082 1.76e-02 3.23e+03 2.19e+01
  bond pdb=" N7   DA B  11 "
       pdb=" C5   DA B  11 "
    ideal  model  delta    sigma   weight residual
    1.388  1.361  0.027 6.00e-03 2.78e+04 2.07e+01
  bond pdb=" C3'  DG B   6 "
       pdb=" O3'  DG B   6 "
    ideal  model  delta    sigma   weight residual
    1.435  1.379  0.056 1.30e-02 5.92e+03 1.88e+01
  ... (remaining 23743 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.61: 33685
        2.61 -     5.22: 2351
        5.22 -     7.83: 226
        7.83 -    10.44: 24
       10.44 -    13.04: 6
  Bond angle restraints: 36292
  Sorted by residual:
  angle pdb=" C3'   U A 477 "
        pdb=" O3'   U A 477 "
        pdb=" P     G A 478 "
      ideal   model   delta    sigma   weight residual
     119.70  128.07   -8.37 1.20e+00 6.94e-01 4.86e+01
  angle pdb=" N   ILE C  89 "
        pdb=" CA  ILE C  89 "
        pdb=" C   ILE C  89 "
      ideal   model   delta    sigma   weight residual
     112.12  106.27    5.85 8.40e-01 1.42e+00 4.84e+01
  angle pdb=" C3'   U A 545 "
        pdb=" O3'   U A 545 "
        pdb=" P     C A 546 "
      ideal   model   delta    sigma   weight residual
     119.70  127.72   -8.02 1.20e+00 6.94e-01 4.46e+01
  angle pdb=" C   GLN C 228 "
        pdb=" N   GLN C 229 "
        pdb=" CA  GLN C 229 "
      ideal   model   delta    sigma   weight residual
     121.94  132.47  -10.53 1.76e+00 3.23e-01 3.58e+01
  angle pdb=" O4'  DG B  12 "
        pdb=" C4'  DG B  12 "
        pdb=" C3'  DG B  12 "
      ideal   model   delta    sigma   weight residual
     106.00  102.44    3.56 6.00e-01 2.78e+00 3.53e+01
  ... (remaining 36287 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.60: 10449
       34.60 -    69.20: 1646
       69.20 -   103.81: 98
      103.81 -   138.41: 4
      138.41 -   173.01: 6
  Dihedral angle restraints: 12203
    sinusoidal: 11005
      harmonic: 1198
  Sorted by residual:
  dihedral pdb=" C4'   U A 498 "
           pdb=" C3'   U A 498 "
           pdb=" C2'   U A 498 "
           pdb=" C1'   U A 498 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -41.27   77.62     1      3.10e+00 1.04e-01 7.85e+02
  dihedral pdb=" C4'   A A 770 "
           pdb=" C3'   A A 770 "
           pdb=" C2'   A A 770 "
           pdb=" C1'   A A 770 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -40.37   76.71     1      3.10e+00 1.04e-01 7.69e+02
  dihedral pdb=" C4'   A A 150 "
           pdb=" C3'   A A 150 "
           pdb=" C2'   A A 150 "
           pdb=" C1'   A A 150 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -39.64   75.98     1      3.10e+00 1.04e-01 7.57e+02
  ... (remaining 12200 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 3477
       0.110 -    0.219: 720
       0.219 -    0.329: 489
       0.329 -    0.439: 21
       0.439 -    0.548: 1
  Chirality restraints: 4708
  Sorted by residual:
  chirality pdb=" P     G A 478 "
            pdb=" OP1   G A 478 "
            pdb=" OP2   G A 478 "
            pdb=" O5'   G A 478 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.72   -0.55 2.00e-01 2.50e+01 7.52e+00
  chirality pdb=" P     G A 249 "
            pdb=" OP1   G A 249 "
            pdb=" OP2   G A 249 "
            pdb=" O5'   G A 249 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.59   -0.42 2.00e-01 2.50e+01 4.41e+00
  chirality pdb=" P     C A 861 "
            pdb=" OP1   C A 861 "
            pdb=" OP2   C A 861 "
            pdb=" O5'   C A 861 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.57   -0.39 2.00e-01 2.50e+01 3.89e+00
  ... (remaining 4705 not shown)

  Planarity restraints: 1430
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A  56 "   -0.011 2.00e-02 2.50e+03   2.73e-02 2.24e+01
        pdb=" N9    G A  56 "    0.004 2.00e-02 2.50e+03
        pdb=" C8    G A  56 "    0.007 2.00e-02 2.50e+03
        pdb=" N7    G A  56 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    G A  56 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    G A  56 "    0.023 2.00e-02 2.50e+03
        pdb=" O6    G A  56 "   -0.021 2.00e-02 2.50e+03
        pdb=" N1    G A  56 "   -0.009 2.00e-02 2.50e+03
        pdb=" C2    G A  56 "    0.075 2.00e-02 2.50e+03
        pdb=" N2    G A  56 "   -0.045 2.00e-02 2.50e+03
        pdb=" N3    G A  56 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    G A  56 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 113 "   -0.044 2.00e-02 2.50e+03   1.93e-02 1.12e+01
        pdb=" N9    G A 113 "    0.042 2.00e-02 2.50e+03
        pdb=" C8    G A 113 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G A 113 "    0.006 2.00e-02 2.50e+03
        pdb=" C5    G A 113 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G A 113 "   -0.020 2.00e-02 2.50e+03
        pdb=" O6    G A 113 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    G A 113 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G A 113 "    0.004 2.00e-02 2.50e+03
        pdb=" N2    G A 113 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    G A 113 "    0.016 2.00e-02 2.50e+03
        pdb=" C4    G A 113 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A A 262 "    0.043 2.00e-02 2.50e+03   1.84e-02 9.28e+00
        pdb=" N9    A A 262 "   -0.031 2.00e-02 2.50e+03
        pdb=" C8    A A 262 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7    A A 262 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    A A 262 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6    A A 262 "    0.000 2.00e-02 2.50e+03
        pdb=" N6    A A 262 "    0.024 2.00e-02 2.50e+03
        pdb=" N1    A A 262 "    0.004 2.00e-02 2.50e+03
        pdb=" C2    A A 262 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3    A A 262 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    A A 262 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1427 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.20: 30
        2.20 -     2.88: 7348
        2.88 -     3.55: 34573
        3.55 -     4.23: 69641
        4.23 -     4.90: 86898
  Nonbonded interactions: 198490
  Sorted by model distance:
  nonbonded pdb=" P     U A   1 "
            pdb=" O2'   A A 860 "
     model   vdw
     1.531 3.400
  nonbonded pdb=" O   LEU C 356 "
            pdb=" CH2 TRP C 402 "
     model   vdw
     1.616 3.340
  nonbonded pdb=" CZ2 TRP C  28 "
            pdb=" CD  LYS C  73 "
     model   vdw
     1.671 3.740
  nonbonded pdb=" OD1 ASP C 366 "
            pdb=" NH2 ARG C 444 "
     model   vdw
     1.693 3.120
  nonbonded pdb=" O2    U A   1 "
            pdb=" N1    G A 865 "
     model   vdw
     1.696 3.120
  ... (remaining 198485 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:             5.560
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     24.720
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
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      :  0.010   0.344  23749  Z= 0.574
  Angle     :  1.388  13.045  36292  Z= 0.585
  Chirality :  0.118   0.548   4708
  Planarity :  0.007   0.070   1430
  Dihedral  : 22.619 173.012  11427
  Min Nonbonded Distance : 1.531

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 1.26 %

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: -5.11 (0.30), residues: 408
  helix: -2.85 (0.24), residues: 212
  sheet: -2.47 (0.72), residues: 36
  loop : -4.27 (0.38), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARG C 163 
 TYR   0.035   0.004   TYR C 378 
 PHE   0.039   0.005   PHE C 231 
 TRP   0.042   0.005   TRP C 204 
 HIS   0.016   0.004   HIS C 346 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00995 /  0.53 (23748)
  covalent geometry    : angle       1.38798 /  0.59 (36292)
  hydrogen bonds       : bond        0.13169 /  7.01 (  920)
  hydrogen bonds       : angle       4.23243 /  1.73 ( 1756)
  Misc. bond           : bond        0.34354 / 17.18 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 LYS cc_start: 0.7923 (ptpt) cc_final: 0.7721 (ptpt)
REVERT: C   65 PHE cc_start: 0.8403 (t80) cc_final: 0.8201 (t80)
REVERT: C  118 TYR cc_start: 0.8201 (m-80) cc_final: 0.7976 (m-80)
REVERT: C  276 ASP cc_start: 0.7764 (m-30) cc_final: 0.7361 (m-30)
REVERT: C  429 VAL cc_start: 0.9186 (t) cc_final: 0.8923 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.2438
  time to fit residues: 31.2665
Evaluate side-chains
  54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.5980
   chunk 123 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  32 ASN
C 202 HIS
C 262 HIS
C 269 ASN
C 314 HIS
C 346 HIS
C 369 ASN
C 377 ASN
C 407 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.098719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.076323 restraints weight = 73710.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.078088 restraints weight = 29511.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.079247 restraints weight = 18162.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.079681 restraints weight = 13906.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.079956 restraints weight = 12448.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  23749  Z= 0.294
  Angle     :  1.673  21.366  36292  Z= 0.665
  Chirality :  0.140   1.523   4708
  Planarity :  0.006   0.067   1430
  Dihedral  : 20.952 176.875  10564
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  7.04 %
    Favored  : 90.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.50 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.84 (0.35), residues: 408
  helix: -1.43 (0.30), residues: 214
  sheet: -2.30 (0.73), residues: 36
  loop : -4.23 (0.41), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C 264 
 TYR   0.017   0.003   TYR C  66 
 PHE   0.034   0.003   PHE C 231 
 TRP   0.038   0.003   TRP C 396 
 HIS   0.009   0.002   HIS C 346 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00581 /  0.29 (23748)
  covalent geometry    : angle       1.67308 /  0.66 (36292)
  hydrogen bonds       : bond        0.08433 /  4.39 (  920)
  hydrogen bonds       : angle       3.35984 /  1.34 ( 1756)
  Misc. bond           : bond        0.03498 /  1.75 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: C   51 TRP cc_start: 0.8843 (m100) cc_final: 0.8578 (m-10)
REVERT: C   65 PHE cc_start: 0.8140 (t80) cc_final: 0.7753 (t80)
REVERT: C   66 TYR cc_start: 0.7499 (m-80) cc_final: 0.6334 (m-80)
REVERT: C  118 TYR cc_start: 0.8222 (m-80) cc_final: 0.7408 (m-80)
REVERT: C  246 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7602 (mpp)
  outliers start: 9
  outliers final: 5
  residues processed: 62
  average time/residue: 0.2259
  time to fit residues: 19.4093
Evaluate side-chains
  52 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  264 ARG
Chi-restraints excluded: chain C residue  284 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 9 optimal weight:    7.9990
   chunk 80 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 57 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   chunk 122 optimal weight:    2.9990
   chunk 46 optimal weight:    8.9990
   overall best weight:    3.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  58 GLN
C  63 HIS
C 262 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.097294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.074615 restraints weight = 74687.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.076420 restraints weight = 30457.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.077433 restraints weight = 18755.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.078239 restraints weight = 14401.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.078384 restraints weight = 12669.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.171  23749  Z= 0.358
  Angle     :  1.430  17.473  36292  Z= 0.567
  Chirality :  0.105   0.955   4708
  Planarity :  0.006   0.090   1430
  Dihedral  : 21.243 179.613  10564
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 19.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.78 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  :  7.04 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.41 (0.37), residues: 408
  helix: -0.80 (0.33), residues: 216
  sheet: -2.57 (0.73), residues: 36
  loop : -4.38 (0.39), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.029   0.001   ARG C 116 
 TYR   0.025   0.004   TYR C 143 
 PHE   0.024   0.003   PHE C 231 
 TRP   0.041   0.003   TRP C 226 
 HIS   0.008   0.002   HIS C 346 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00732 /  0.36 (23748)
  covalent geometry    : angle       1.42959 /  0.57 (36292)
  hydrogen bonds       : bond        0.08547 /  4.47 (  920)
  hydrogen bonds       : angle       3.32703 /  1.30 ( 1756)
  Misc. bond           : bond        0.00601 /  0.30 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   51 TRP cc_start: 0.8904 (m100) cc_final: 0.8422 (m-10)
REVERT: C   65 PHE cc_start: 0.8080 (t80) cc_final: 0.7670 (t80)
REVERT: C  110 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8607 (tppt)
REVERT: C  118 TYR cc_start: 0.8079 (m-80) cc_final: 0.7837 (m-80)
REVERT: C  246 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7331 (mpp)
REVERT: C  250 MET cc_start: 0.8825 (mmm) cc_final: 0.8592 (mmm)
REVERT: C  397 HIS cc_start: 0.7936 (t-90) cc_final: 0.7690 (t-90)
  outliers start: 16
  outliers final: 9
  residues processed: 63
  average time/residue: 0.1688
  time to fit residues: 15.6309
Evaluate side-chains
  51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  264 ARG
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  284 LYS
Chi-restraints excluded: chain C residue  314 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 113 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 63 optimal weight:    8.9990
   chunk 98 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 74 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  58 GLN

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 = 0.098932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.076347 restraints weight = 74359.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.078143 restraints weight = 30199.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.079403 restraints weight = 18478.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.079750 restraints weight = 13894.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.080108 restraints weight = 12611.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  23749  Z= 0.254
  Angle     :  1.260  14.434  36292  Z= 0.503
  Chirality :  0.095   0.873   4708
  Planarity :  0.006   0.082   1430
  Dihedral  : 20.950 177.598  10564
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  :  9.58 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.03 (0.38), residues: 408
  helix: -0.49 (0.34), residues: 217
  sheet: -2.35 (0.78), residues: 36
  loop : -4.24 (0.40), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.060   0.002   ARG C 116 
 TYR   0.016   0.003   TYR C 378 
 PHE   0.021   0.002   PHE C 231 
 TRP   0.081   0.004   TRP C 226 
 HIS   0.005   0.002   HIS C 346 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00509 /  0.25 (23748)
  covalent geometry    : angle       1.26025 /  0.50 (36292)
  hydrogen bonds       : bond        0.07621 /  3.96 (  920)
  hydrogen bonds       : angle       3.01398 /  1.19 ( 1756)
  Misc. bond           : bond        0.00491 /  0.25 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   65 PHE cc_start: 0.8073 (t80) cc_final: 0.7730 (t80)
REVERT: C  110 LYS cc_start: 0.8840 (mmmt) cc_final: 0.8576 (tppt)
REVERT: C  246 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7334 (mpp)
REVERT: C  317 GLU cc_start: 0.7252 (tm-30) cc_final: 0.7015 (tm-30)
REVERT: C  397 HIS cc_start: 0.7918 (t-90) cc_final: 0.7638 (t-90)
  outliers start: 15
  outliers final: 10
  residues processed: 58
  average time/residue: 0.1853
  time to fit residues: 15.5956
Evaluate side-chains
  55 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   99 GLN
Chi-restraints excluded: chain C residue  116 ARG
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  264 ARG
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  284 LYS
Chi-restraints excluded: chain C residue  314 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 81 optimal weight:    9.9990
   chunk 91 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    3.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.097297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.074554 restraints weight = 74495.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.076316 restraints weight = 30799.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.077430 restraints weight = 19098.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.077959 restraints weight = 14584.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.078186 restraints weight = 13135.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056  23749  Z= 0.354
  Angle     :  1.321  15.260  36292  Z= 0.521
  Chirality :  0.095   0.856   4708
  Planarity :  0.008   0.229   1430
  Dihedral  : 21.046 177.940  10564
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 19.34
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 12.50 %
    Favored  : 87.25 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 10.70 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.97 (0.39), residues: 408
  helix: -0.54 (0.33), residues: 219
  sheet: -2.05 (0.84), residues: 36
  loop : -4.18 (0.42), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.030   0.001   ARG C 116 
 TYR   0.024   0.003   TYR C 378 
 PHE   0.022   0.002   PHE C 231 
 TRP   0.083   0.004   TRP C 226 
 HIS   0.006   0.002   HIS C 346 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00714 /  0.35 (23748)
  covalent geometry    : angle       1.32059 /  0.52 (36292)
  hydrogen bonds       : bond        0.08320 /  4.35 (  920)
  hydrogen bonds       : angle       3.17373 /  1.25 ( 1756)
  Misc. bond           : bond        0.04161 /  2.08 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 43
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: C   65 PHE cc_start: 0.8139 (t80) cc_final: 0.7767 (t80)
REVERT: C  110 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8659 (tppt)
REVERT: C  216 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9209 (tp)
REVERT: C  246 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7432 (mpp)
REVERT: C  317 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7136 (tm-30)
REVERT: C  397 HIS cc_start: 0.7981 (t-90) cc_final: 0.7670 (t-90)
  outliers start: 17
  outliers final: 11
  residues processed: 56
  average time/residue: 0.1730
  time to fit residues: 14.3794
Evaluate side-chains
  55 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   99 GLN
Chi-restraints excluded: chain C residue  116 ARG
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  264 ARG
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  284 LYS
Chi-restraints excluded: chain C residue  314 HIS
Chi-restraints excluded: chain C residue  349 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 88 optimal weight:    7.9990
   chunk 68 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 66 optimal weight:    9.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.095509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.072677 restraints weight = 75080.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.074407 restraints weight = 31252.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.075671 restraints weight = 19437.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.076035 restraints weight = 14849.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.076268 restraints weight = 13323.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.066  23749  Z= 0.454
  Angle     :  1.445  16.208  36292  Z= 0.569
  Chirality :  0.101   0.939   4708
  Planarity :  0.009   0.234   1430
  Dihedral  : 21.153 177.941  10564
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 21.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.97 %
    Favored  : 86.03 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 14.37 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.15 (0.38), residues: 408
  helix: -0.71 (0.32), residues: 217
  sheet: -2.03 (0.83), residues: 34
  loop : -4.19 (0.43), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG C 116 
 TYR   0.026   0.004   TYR C 378 
 PHE   0.020   0.003   PHE C 231 
 TRP   0.068   0.004   TRP C 226 
 HIS   0.008   0.003   HIS C  63 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00919 /  0.45 (23748)
  covalent geometry    : angle       1.44512 /  0.57 (36292)
  hydrogen bonds       : bond        0.09341 /  4.89 (  920)
  hydrogen bonds       : angle       3.40878 /  1.34 ( 1756)
  Misc. bond           : bond        0.03566 /  1.78 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: C  246 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7435 (mpp)
  outliers start: 17
  outliers final: 12
  residues processed: 55
  average time/residue: 0.1778
  time to fit residues: 14.4699
Evaluate side-chains
  55 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   99 GLN
Chi-restraints excluded: chain C residue  116 ARG
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  264 ARG
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  314 HIS
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  445 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 81 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    2.1188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  58 GLN

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 = 0.098271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.075684 restraints weight = 74221.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.077429 restraints weight = 30367.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.078660 restraints weight = 18814.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.079025 restraints weight = 14374.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.079397 restraints weight = 12898.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  23749  Z= 0.258
  Angle     :  1.229  13.793  36292  Z= 0.486
  Chirality :  0.091   0.799   4708
  Planarity :  0.007   0.197   1430
  Dihedral  : 20.947 179.152  10564
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 18.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.25 %
    Favored  : 87.75 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 16.34 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.61 (0.40), residues: 408
  helix: -0.22 (0.34), residues: 215
  sheet: -1.84 (0.87), residues: 34
  loop : -3.94 (0.44), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.001   ARG C 116 
 TYR   0.017   0.003   TYR C 329 
 PHE   0.017   0.002   PHE C 231 
 TRP   0.058   0.003   TRP C 226 
 HIS   0.004   0.002   HIS C 397 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00519 /  0.26 (23748)
  covalent geometry    : angle       1.22906 /  0.49 (36292)
  hydrogen bonds       : bond        0.07920 /  4.10 (  920)
  hydrogen bonds       : angle       3.06336 /  1.21 ( 1756)
  Misc. bond           : bond        0.02135 /  1.07 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: C  246 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7431 (mpp)
REVERT: C  317 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7143 (tm-30)
REVERT: C  397 HIS cc_start: 0.7888 (t-90) cc_final: 0.7606 (t-90)
  outliers start: 15
  outliers final: 10
  residues processed: 55
  average time/residue: 0.2086
  time to fit residues: 16.4125
Evaluate side-chains
  53 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   99 GLN
Chi-restraints excluded: chain C residue  116 ARG
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  314 HIS
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  421 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 61 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 59 optimal weight:    6.9990
   chunk 117 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    4.9990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.095659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.072826 restraints weight = 74902.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.074483 restraints weight = 31293.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.075725 restraints weight = 19772.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.076074 restraints weight = 15141.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.076383 restraints weight = 13624.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.066  23749  Z= 0.464
  Angle     :  1.423  16.262  36292  Z= 0.559
  Chirality :  0.098   0.867   4708
  Planarity :  0.009   0.198   1430
  Dihedral  : 21.077 178.463  10564
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 22.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.46 %
    Favored  : 85.54 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 17.46 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.02 (0.39), residues: 408
  helix: -0.62 (0.33), residues: 218
  sheet: -1.87 (0.87), residues: 34
  loop : -4.13 (0.43), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.026   0.001   ARG C 116 
 TYR   0.023   0.003   TYR C 378 
 PHE   0.019   0.003   PHE C 231 
 TRP   0.058   0.003   TRP C 226 
 HIS   0.007   0.003   HIS C 346 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00941 /  0.46 (23748)
  covalent geometry    : angle       1.42310 /  0.56 (36292)
  hydrogen bonds       : bond        0.09221 /  4.81 (  920)
  hydrogen bonds       : angle       3.36562 /  1.32 ( 1756)
  Misc. bond           : bond        0.02271 /  1.14 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: C  216 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9203 (tp)
REVERT: C  246 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7515 (mpp)
REVERT: C  317 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7380 (tm-30)
  outliers start: 16
  outliers final: 10
  residues processed: 53
  average time/residue: 0.1989
  time to fit residues: 15.7035
Evaluate side-chains
  54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  116 ARG
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  314 HIS
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  360 THR
Chi-restraints excluded: chain C residue  421 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 120 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 50 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 54 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    2.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.098034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.075430 restraints weight = 73564.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.077234 restraints weight = 29566.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.078360 restraints weight = 18077.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.078919 restraints weight = 13734.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.079100 restraints weight = 12264.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  23749  Z= 0.273
  Angle     :  1.230  13.424  36292  Z= 0.487
  Chirality :  0.090   0.803   4708
  Planarity :  0.007   0.180   1430
  Dihedral  : 20.945 179.916  10564
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 18.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.25 %
    Favored  : 87.75 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 18.31 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.72 (0.40), residues: 408
  helix: -0.36 (0.34), residues: 217
  sheet: -1.74 (0.88), residues: 34
  loop : -4.01 (0.43), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.001   ARG C 116 
 TYR   0.023   0.003   TYR C 329 
 PHE   0.018   0.002   PHE C 231 
 TRP   0.053   0.003   TRP C 226 
 HIS   0.004   0.002   HIS C 397 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00550 /  0.27 (23748)
  covalent geometry    : angle       1.23008 /  0.49 (36292)
  hydrogen bonds       : bond        0.08019 /  4.16 (  920)
  hydrogen bonds       : angle       3.06502 /  1.21 ( 1756)
  Misc. bond           : bond        0.02045 /  1.02 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: C  246 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7463 (mpp)
REVERT: C  317 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7366 (tm-30)
REVERT: C  397 HIS cc_start: 0.7914 (t-90) cc_final: 0.7653 (t-90)
  outliers start: 15
  outliers final: 10
  residues processed: 54
  average time/residue: 0.1847
  time to fit residues: 15.0744
Evaluate side-chains
  53 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  116 ARG
Chi-restraints excluded: chain C residue  134 THR
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  314 HIS
Chi-restraints excluded: chain C residue  360 THR
Chi-restraints excluded: chain C residue  421 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 98 optimal weight:    0.7980
   chunk 70 optimal weight:    6.9990
   chunk 123 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 108 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 118 optimal weight:    0.7980
   overall best weight:    2.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.098909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.076463 restraints weight = 74365.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.078269 restraints weight = 31756.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.079202 restraints weight = 19568.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.080032 restraints weight = 15179.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.080176 restraints weight = 13396.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  23749  Z= 0.245
  Angle     :  1.192  13.748  36292  Z= 0.474
  Chirality :  0.087   0.891   4708
  Planarity :  0.007   0.176   1430
  Dihedral  : 20.879 179.960  10564
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 17.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.75 %
    Favored  : 87.25 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.44 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.53 (0.41), residues: 408
  helix: -0.22 (0.35), residues: 218
  sheet: -1.60 (0.93), residues: 34
  loop : -3.94 (0.43), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.001   ARG C 116 
 TYR   0.029   0.003   TYR C 329 
 PHE   0.016   0.002   PHE C 231 
 TRP   0.051   0.003   TRP C 226 
 HIS   0.003   0.001   HIS C 346 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00494 /  0.24 (23748)
  covalent geometry    : angle       1.19237 /  0.47 (36292)
  hydrogen bonds       : bond        0.07772 /  4.02 (  920)
  hydrogen bonds       : angle       2.95840 /  1.16 ( 1756)
  Misc. bond           : bond        0.02038 /  1.02 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  246 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7512 (mpp)
REVERT: C  317 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7145 (tm-30)
REVERT: C  397 HIS cc_start: 0.7881 (t-90) cc_final: 0.7551 (t-90)
  outliers start: 12
  outliers final: 10
  residues processed: 52
  average time/residue: 0.1886
  time to fit residues: 14.5662
Evaluate side-chains
  54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  116 ARG
Chi-restraints excluded: chain C residue  134 THR
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  314 HIS
Chi-restraints excluded: chain C residue  360 THR
Chi-restraints excluded: chain C residue  421 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 89 optimal weight:    6.9990
   chunk 54 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 94 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   overall best weight:    4.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.096607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.073978 restraints weight = 74927.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.075589 restraints weight = 32242.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.076584 restraints weight = 20650.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.077490 restraints weight = 15978.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.077645 restraints weight = 13747.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.058  23749  Z= 0.415
  Angle     :  1.341  15.652  36292  Z= 0.529
  Chirality :  0.093   0.821   4708
  Planarity :  0.008   0.183   1430
  Dihedral  : 20.987 179.964  10564
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 20.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.95 %
    Favored  : 85.05 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 19.15 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.94 (0.39), residues: 408
  helix: -0.66 (0.33), residues: 221
  sheet: -1.55 (0.92), residues: 34
  loop : -4.07 (0.43), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.026   0.001   ARG C 116 
 TYR   0.031   0.004   TYR C 329 
 PHE   0.018   0.003   PHE C 231 
 TRP   0.051   0.003   TRP C 226 
 HIS   0.005   0.002   HIS C 346 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00842 /  0.41 (23748)
  covalent geometry    : angle       1.34150 /  0.53 (36292)
  hydrogen bonds       : bond        0.08775 /  4.56 (  920)
  hydrogen bonds       : angle       3.21555 /  1.26 ( 1756)
  Misc. bond           : bond        0.02319 /  1.16 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3539.39 seconds
wall clock time: 62 minutes 47.40 seconds (3767.40 seconds total)