Starting phenix.real_space_refine
on Fri Aug 22 14:12:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hn1_34906/08_2025/8hn1_34906.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hn1_34906/08_2025/8hn1_34906.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hn1_34906/08_2025/8hn1_34906.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hn1_34906/08_2025/8hn1_34906.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hn1_34906/08_2025/8hn1_34906.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hn1_34906/08_2025/8hn1_34906.map"
  }
  resolution = 2.9
  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=   0.111
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 505 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    2314      2.51       5
     N     593      2.21       5
     O     626      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3560
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 510
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 65, 505
          Classifications: {'peptide': 65}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 60}
      Conformer: "B"
        Number of residues, atoms: 65, 505
          Classifications: {'peptide': 65}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 60}
          bond proxies already assigned to first conformer: 509
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2217
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 14, 'TRANS': 265}
    Chain: "D"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 833
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 1, 'TRANS': 109}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 16
  Time building chain proxies: 1.39, per 1000 atoms: 0.39
  Number of scatterers: 3560
  At special positions: 0
  Unit cell: (88.765, 84.435, 102.837, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O     626      8.00
     N     593      7.00
     C    2314      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C   3 " - pdb=" SG  CYS C  24 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  17 " - pdb=" SG  CYS C  42 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  46 " - pdb=" SG  CYS C  57 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  58 " - pdb=" SG  CYS C  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  99 " - pdb=" SG  CYS A 176 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  24 " - pdb=" SG  CYS D  97 " 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=0, symmetry=0
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 163.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  842

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 5 sheets defined
      54.4% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 53
    Processing helix  chain 'A' and resid 59 through 79
      removed outlier: 3.551A  pdb=" N   TYR A  64 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ILE A  65 " --> pdb=" O   THR A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 90
    Processing helix  chain 'A' and resid 94 through 130
      removed outlier: 4.123A  pdb=" N   PHE A  98 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE A 101 " --> pdb=" O   VAL A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 138
    Processing helix  chain 'A' and resid 139 through 160
    Processing helix  chain 'A' and resid 160 through 165
    Processing helix  chain 'A' and resid 181 through 193
    Processing helix  chain 'A' and resid 193 through 214
      removed outlier: 3.611A  pdb=" N   ALA A 198 " --> pdb=" O   TYR A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 298
      removed outlier: 3.686A  pdb=" N   ALA A 270 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
      Proline residue:  A 287  - end of helix
      Proline residue:  A 293  - end of helix
    Processing helix  chain 'A' and resid 304 through 317
      removed outlier: 3.590A  pdb=" N   PHE A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 330
      Proline residue:  A 323  - end of helix
      Proline residue:  A 327  - end of helix
    Processing helix  chain 'A' and resid 331 through 343
      removed outlier: 3.870A  pdb=" N   ILE A 343 " --> pdb=" O   ASN A 339 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 3
      removed outlier: 3.612A  pdb=" N   GLU C  15 " --> pdb=" O   CYS C   3 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 8
    Processing sheet with id=AA3, first strand: chain 'C' and resid 23 through 32
      removed outlier: 3.768A  pdb=" N   GLY C  41 " --> pdb=" O   PHE C  25 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   ILE C  35 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 5 through 6
      removed outlier: 3.759A  pdb=" N   THR D  79 " --> pdb=" O   ASP D  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 59 through 61
      removed outlier: 3.591A  pdb=" N   ALA D  51 " --> pdb=" O   TRP D  38 " (cutoff:3.500A)
      removed outlier: 5.770A  pdb=" N   LEU D  33 " --> pdb=" O   ARG D 102 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   ARG D 102 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ASP D  35 " --> pdb=" O   GLU D 100 " (cutoff:3.500A)

    212 hydrogen bonds defined for protein.
    618 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.51

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1111
        1.34 -     1.46: 897
        1.46 -     1.58: 1606
        1.58 -     1.70: 0
        1.70 -     1.81: 32
  Bond restraints: 3646
  Sorted by residual:
  bond pdb=" CE2 PHE A  86 "
       pdb=" CZ  PHE A  86 "
    ideal  model  delta    sigma   weight residual
    1.382  1.353  0.029 3.00e-02 1.11e+03 9.13e-01
  bond pdb=" CE1 PHE A  86 "
       pdb=" CZ  PHE A  86 "
    ideal  model  delta    sigma   weight residual
    1.382  1.355  0.027 3.00e-02 1.11e+03 8.33e-01
  bond pdb=" CA  ILE C  48 "
       pdb=" CB  ILE C  48 "
    ideal  model  delta    sigma   weight residual
    1.526  1.539 -0.013 1.55e-02 4.16e+03 7.22e-01
  bond pdb=" C   GLN A 167 "
       pdb=" N   PRO A 168 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.020 2.34e-02 1.83e+03 7.00e-01
  bond pdb=" CG  PRO A 196 "
       pdb=" CD  PRO A 196 "
    ideal  model  delta    sigma   weight residual
    1.503  1.477  0.026 3.40e-02 8.65e+02 5.92e-01
  ... (remaining 3641 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 4686
        1.06 -     2.12: 216
        2.12 -     3.18: 36
        3.18 -     4.24: 15
        4.24 -     5.30: 7
  Bond angle restraints: 4960
  Sorted by residual:
  angle pdb=" N   GLY D  37 "
        pdb=" CA  GLY D  37 "
        pdb=" C   GLY D  37 "
      ideal   model   delta    sigma   weight residual
     110.18  114.00   -3.82 1.56e+00 4.11e-01 6.00e+00
  angle pdb=" N   ALA A 169 "
        pdb=" CA  ALA A 169 "
        pdb=" C   ALA A 169 "
      ideal   model   delta    sigma   weight residual
     109.81  115.11   -5.30 2.21e+00 2.05e-01 5.74e+00
  angle pdb=" N   PRO C  33 "
        pdb=" CA  PRO C  33 "
        pdb=" C   PRO C  33 "
      ideal   model   delta    sigma   weight residual
     112.47  117.22   -4.75 2.06e+00 2.36e-01 5.32e+00
  angle pdb=" CA  ALA A 169 "
        pdb=" C   ALA A 169 "
        pdb=" N   PRO A 170 "
      ideal   model   delta    sigma   weight residual
     118.44  121.83   -3.39 1.59e+00 3.96e-01 4.54e+00
  angle pdb=" N   VAL A 207 "
        pdb=" CA  VAL A 207 "
        pdb=" C   VAL A 207 "
      ideal   model   delta    sigma   weight residual
     110.62  108.52    2.10 1.02e+00 9.61e-01 4.22e+00
  ... (remaining 4955 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 1984
       17.41 -    34.82: 147
       34.82 -    52.23: 13
       52.23 -    69.64: 4
       69.64 -    87.05: 3
  Dihedral angle restraints: 2151
    sinusoidal: 833
      harmonic: 1318
  Sorted by residual:
  dihedral pdb=" CA  GLN A 167 "
           pdb=" C   GLN A 167 "
           pdb=" N   PRO A 168 "
           pdb=" CA  PRO A 168 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.46  -23.54     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  ALA A 169 "
           pdb=" C   ALA A 169 "
           pdb=" N   PRO A 170 "
           pdb=" CA  PRO A 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.31  -17.69     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  ASP A 172 "
           pdb=" CB  ASP A 172 "
           pdb=" CG  ASP A 172 "
           pdb=" OD1 ASP A 172 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.98   59.98     1      2.00e+01 2.50e-03 1.20e+01
  ... (remaining 2148 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 418
       0.042 -    0.083: 118
       0.083 -    0.125: 32
       0.125 -    0.166: 1
       0.166 -    0.208: 1
  Chirality restraints: 570
  Sorted by residual:
  chirality pdb=" CA  PRO C  33 "
            pdb=" N   PRO C  33 "
            pdb=" C   PRO C  33 "
            pdb=" CB  PRO C  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  PRO A 168 "
            pdb=" N   PRO A 168 "
            pdb=" C   PRO A 168 "
            pdb=" CB  PRO A 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  VAL C  32 "
            pdb=" N   VAL C  32 "
            pdb=" C   VAL C  32 "
            pdb=" CB  VAL C  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.61e-01
  ... (remaining 567 not shown)

  Planarity restraints: 616
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C  32 "   -0.029 5.00e-02 4.00e+02   4.35e-02 3.03e+00
        pdb=" N   PRO C  33 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO C  33 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C  33 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 298 "   -0.028 5.00e-02 4.00e+02   4.30e-02 2.96e+00
        pdb=" N   PRO A 299 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 299 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 299 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  86 "    0.014 2.00e-02 2.50e+03   1.20e-02 2.51e+00
        pdb=" CG  PHE A  86 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  86 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  86 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  86 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  86 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  86 "    0.003 2.00e-02 2.50e+03
  ... (remaining 613 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 23
        2.57 -     3.15: 2954
        3.15 -     3.74: 5332
        3.74 -     4.32: 7471
        4.32 -     4.90: 12587
  Nonbonded interactions: 28367
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 103 "
            pdb=" OE1 GLU D 107 "
     model   vdw
     1.991 3.040
  nonbonded pdb=" O   ARG D  68 "
            pdb=" OG  SER D  85 "
     model   vdw
     2.027 3.040
  nonbonded pdb=" NH2 ARG D  68 "
            pdb=" O   SER D  86 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" OD2 ASP D  74 "
            pdb=" NZ  LYS D  77 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" O   THR C   5 "
            pdb=" OG  SER C   6 "
     model   vdw
     2.299 3.040
  ... (remaining 28362 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=0.42 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             0.620
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.870
  Find NCS groups from input model:        0.010
  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:6.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3652  Z= 0.146
  Angle     :  0.578   5.296   4972  Z= 0.325
  Chirality :  0.040   0.208    570
  Planarity :  0.004   0.044    616
  Dihedral  : 12.060  87.052   1291
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.40), residues: 449
  helix:  1.35 (0.35), residues: 217
  sheet: -2.36 (0.60), residues: 72
  loop : -2.02 (0.46), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  55 
 TYR   0.006   0.001   TYR A 204 
 PHE   0.027   0.001   PHE A  86 
 TRP   0.019   0.001   TRP A 165 
 HIS   0.002   0.000   HIS C  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 3646)
  covalent geometry    : angle       0.57756 ( 4960)
  SS BOND              : bond        0.00147 (    6)
  SS BOND              : angle       0.67889 (   12)
  hydrogen bonds       : bond        0.20403 (  212)
  hydrogen bonds       : angle       7.64056 (  618)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: D  108 GLU cc_start: 0.8247 (pt0) cc_final: 0.7832 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.3452
  time to fit residues: 24.6435
Evaluate side-chains
  55 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0770
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    7.9990
   overall best weight:    0.6738

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.191905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.115718 restraints weight = 5528.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.80
r_work: 0.3122 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2962
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3652  Z= 0.147
  Angle     :  0.622   6.993   4972  Z= 0.323
  Chirality :  0.044   0.180    570
  Planarity :  0.005   0.038    616
  Dihedral  :  4.321  23.126    502
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  8.81 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.41), residues: 449
  helix:  1.70 (0.35), residues: 230
  sheet: -1.90 (0.58), residues: 82
  loop : -2.34 (0.46), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 213 
 TYR   0.011   0.001   TYR A 316 
 PHE   0.011   0.001   PHE A 308 
 TRP   0.016   0.001   TRP A 165 
 HIS   0.001   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3646)
  covalent geometry    : angle       0.62031 ( 4960)
  SS BOND              : bond        0.00490 (    6)
  SS BOND              : angle       1.19140 (   12)
  hydrogen bonds       : bond        0.04845 (  212)
  hydrogen bonds       : angle       5.08753 (  618)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7576 (mt) cc_final: 0.7309 (mp)
REVERT: D  108 GLU cc_start: 0.8177 (pt0) cc_final: 0.7738 (pt0)
  outliers start: 9
  outliers final: 5
  residues processed: 58
  average time/residue: 0.3843
  time to fit residues: 23.3295
Evaluate side-chains
  56 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  321 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 8 optimal weight:    0.2980
   chunk 38 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    0.2980
   chunk 36 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 39 optimal weight:    6.9990
   chunk 27 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 322 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.190536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.111322 restraints weight = 9795.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 3.49
r_work: 0.2931 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2938
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2938
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3652  Z= 0.145
  Angle     :  0.593   7.166   4972  Z= 0.305
  Chirality :  0.044   0.197    570
  Planarity :  0.004   0.034    616
  Dihedral  :  4.156  21.517    502
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.36 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.41), residues: 449
  helix:  1.81 (0.35), residues: 231
  sheet: -1.67 (0.59), residues: 82
  loop : -2.21 (0.47), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 213 
 TYR   0.010   0.001   TYR A 316 
 PHE   0.008   0.001   PHE D  69 
 TRP   0.021   0.001   TRP A 165 
 HIS   0.002   0.000   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 3646)
  covalent geometry    : angle       0.59264 ( 4960)
  SS BOND              : bond        0.00258 (    6)
  SS BOND              : angle       0.80758 (   12)
  hydrogen bonds       : bond        0.04673 (  212)
  hydrogen bonds       : angle       4.80587 (  618)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.5983 (tpm170)
REVERT: A  144 LEU cc_start: 0.7509 (mt) cc_final: 0.7295 (mp)
REVERT: A  179 ASN cc_start: 0.7954 (m-40) cc_final: 0.7494 (t0)
REVERT: D  108 GLU cc_start: 0.8223 (pt0) cc_final: 0.7848 (pt0)
  outliers start: 8
  outliers final: 6
  residues processed: 56
  average time/residue: 0.3855
  time to fit residues: 22.4182
Evaluate side-chains
  57 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  321 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 12 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.186543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.109861 restraints weight = 5487.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 2.78
r_work: 0.3026 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2749
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2749 r_free = 0.2749    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2749 r_free = 0.2749    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2749
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3652  Z= 0.212
  Angle     :  0.648   7.584   4972  Z= 0.334
  Chirality :  0.047   0.234    570
  Planarity :  0.005   0.041    616
  Dihedral  :  4.308  21.002    502
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  :  9.59 %
    Favored  : 86.53 %
  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 aren not related in a simple way.
  whole: -0.29 (0.40), residues: 449
  helix:  1.53 (0.34), residues: 231
  sheet: -1.65 (0.58), residues: 83
  loop : -2.27 (0.47), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 213 
 TYR   0.012   0.001   TYR A 316 
 PHE   0.011   0.002   PHE A 289 
 TRP   0.028   0.002   TRP A 165 
 HIS   0.002   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 3646)
  covalent geometry    : angle       0.64700 ( 4960)
  SS BOND              : bond        0.00224 (    6)
  SS BOND              : angle       0.83059 (   12)
  hydrogen bonds       : bond        0.05515 (  212)
  hydrogen bonds       : angle       4.88728 (  618)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   50 GLU cc_start: 0.7371 (tt0) cc_final: 0.6889 (pt0)
REVERT: A  179 ASN cc_start: 0.7939 (m-40) cc_final: 0.7385 (t0)
REVERT: D   36 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7151 (mtm)
REVERT: D  108 GLU cc_start: 0.8257 (pt0) cc_final: 0.7945 (pt0)
  outliers start: 15
  outliers final: 9
  residues processed: 59
  average time/residue: 0.3947
  time to fit residues: 24.2316
Evaluate side-chains
  61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain D residue   36 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 29 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 4 optimal weight:    8.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.189652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.117790 restraints weight = 12155.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 4.54
r_work: 0.2981 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3652  Z= 0.139
  Angle     :  0.577   7.276   4972  Z= 0.298
  Chirality :  0.043   0.198    570
  Planarity :  0.004   0.038    616
  Dihedral  :  4.094  21.647    502
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.92 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.41), residues: 449
  helix:  1.92 (0.35), residues: 231
  sheet: -1.47 (0.58), residues: 83
  loop : -2.15 (0.48), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 213 
 TYR   0.011   0.001   TYR A 316 
 PHE   0.007   0.001   PHE A 312 
 TRP   0.023   0.001   TRP A 165 
 HIS   0.002   0.000   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3646)
  covalent geometry    : angle       0.57679 ( 4960)
  SS BOND              : bond        0.00209 (    6)
  SS BOND              : angle       0.74549 (   12)
  hydrogen bonds       : bond        0.04533 (  212)
  hydrogen bonds       : angle       4.61778 (  618)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   50 GLU cc_start: 0.7273 (tt0) cc_final: 0.6833 (pt0)
REVERT: A   28 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7084 (tt)
REVERT: A  144 LEU cc_start: 0.7295 (mt) cc_final: 0.7087 (mp)
REVERT: A  179 ASN cc_start: 0.7832 (m-40) cc_final: 0.7300 (t0)
REVERT: A  213 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.7402 (ttp-170)
REVERT: D  108 GLU cc_start: 0.8274 (pt0) cc_final: 0.8040 (pt0)
  outliers start: 9
  outliers final: 7
  residues processed: 56
  average time/residue: 0.4226
  time to fit residues: 24.6674
Evaluate side-chains
  58 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  321 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 38 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 39 optimal weight:    7.9990
   chunk 24 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.188631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.110605 restraints weight = 7223.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 3.10
r_work: 0.2972 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2904
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2904
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3652  Z= 0.154
  Angle     :  0.591   7.358   4972  Z= 0.304
  Chirality :  0.044   0.211    570
  Planarity :  0.004   0.038    616
  Dihedral  :  4.047  21.449    502
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 12.44 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.41), residues: 449
  helix:  1.92 (0.34), residues: 231
  sheet: -1.37 (0.59), residues: 83
  loop : -2.11 (0.49), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 213 
 TYR   0.010   0.001   TYR A 316 
 PHE   0.008   0.001   PHE A 289 
 TRP   0.024   0.001   TRP A 165 
 HIS   0.002   0.000   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 3646)
  covalent geometry    : angle       0.59053 ( 4960)
  SS BOND              : bond        0.00191 (    6)
  SS BOND              : angle       0.73855 (   12)
  hydrogen bonds       : bond        0.04737 (  212)
  hydrogen bonds       : angle       4.60970 (  618)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7051 (tt)
REVERT: A  179 ASN cc_start: 0.7803 (m-40) cc_final: 0.7246 (t0)
REVERT: A  213 ARG cc_start: 0.7792 (ttp-110) cc_final: 0.7356 (ttp-170)
REVERT: D   36 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7354 (mtm)
  outliers start: 12
  outliers final: 9
  residues processed: 58
  average time/residue: 0.3905
  time to fit residues: 23.6586
Evaluate side-chains
  61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain D residue   36 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 38 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 42 optimal weight:    9.9990
   chunk 36 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    1.0382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.188418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.110412 restraints weight = 6981.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 3.06
r_work: 0.2958 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3026
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3026
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3652  Z= 0.160
  Angle     :  0.598   7.222   4972  Z= 0.307
  Chirality :  0.044   0.214    570
  Planarity :  0.004   0.039    616
  Dihedral  :  4.043  21.435    502
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 11.92 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.41), residues: 449
  helix:  1.93 (0.34), residues: 231
  sheet: -1.23 (0.63), residues: 74
  loop : -2.05 (0.48), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 102 
 TYR   0.010   0.001   TYR A 316 
 PHE   0.009   0.001   PHE A 289 
 TRP   0.024   0.001   TRP A 165 
 HIS   0.001   0.000   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 3646)
  covalent geometry    : angle       0.59723 ( 4960)
  SS BOND              : bond        0.00186 (    6)
  SS BOND              : angle       0.75691 (   12)
  hydrogen bonds       : bond        0.04808 (  212)
  hydrogen bonds       : angle       4.61499 (  618)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 51
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   50 GLU cc_start: 0.7290 (tt0) cc_final: 0.6868 (pt0)
REVERT: A   28 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.6974 (tt)
REVERT: A  179 ASN cc_start: 0.7786 (m-40) cc_final: 0.7243 (t0)
REVERT: A  213 ARG cc_start: 0.7801 (ttp-110) cc_final: 0.7362 (ttp-170)
  outliers start: 17
  outliers final: 12
  residues processed: 61
  average time/residue: 0.3789
  time to fit residues: 24.1035
Evaluate side-chains
  64 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  321 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 44 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    0.2980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.190810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.111994 restraints weight = 9044.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 3.39
r_work: 0.3006 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3037
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3037
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3652  Z= 0.129
  Angle     :  0.567   7.107   4972  Z= 0.291
  Chirality :  0.043   0.195    570
  Planarity :  0.004   0.036    616
  Dihedral  :  3.895  21.195    502
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 13.73 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.41), residues: 449
  helix:  2.18 (0.34), residues: 232
  sheet: -1.05 (0.63), residues: 73
  loop : -1.88 (0.49), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  28 
 TYR   0.010   0.001   TYR A 316 
 PHE   0.008   0.001   PHE A 312 
 TRP   0.020   0.001   TRP A 165 
 HIS   0.002   0.000   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3646)
  covalent geometry    : angle       0.56615 ( 4960)
  SS BOND              : bond        0.00183 (    6)
  SS BOND              : angle       0.73818 (   12)
  hydrogen bonds       : bond        0.04273 (  212)
  hydrogen bonds       : angle       4.45668 (  618)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   50 GLU cc_start: 0.7218 (tt0) cc_final: 0.6816 (pt0)
REVERT: A   28 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.6976 (tt)
REVERT: A  179 ASN cc_start: 0.7723 (m-40) cc_final: 0.7152 (t0)
REVERT: A  213 ARG cc_start: 0.7810 (ttp-110) cc_final: 0.7349 (ttp-170)
  outliers start: 12
  outliers final: 10
  residues processed: 64
  average time/residue: 0.3702
  time to fit residues: 24.8839
Evaluate side-chains
  63 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  321 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 27 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.7182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.190254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.115646 restraints weight = 3961.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.46
r_work: 0.3076 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2970
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2970
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3652  Z= 0.134
  Angle     :  0.574   6.993   4972  Z= 0.294
  Chirality :  0.043   0.201    570
  Planarity :  0.004   0.036    616
  Dihedral  :  3.885  21.301    502
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 15.03 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.41), residues: 449
  helix:  2.20 (0.34), residues: 232
  sheet: -1.00 (0.63), residues: 75
  loop : -1.77 (0.51), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 213 
 TYR   0.009   0.001   TYR A 316 
 PHE   0.008   0.001   PHE A 312 
 TRP   0.020   0.001   TRP A 165 
 HIS   0.002   0.000   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3646)
  covalent geometry    : angle       0.57335 ( 4960)
  SS BOND              : bond        0.00190 (    6)
  SS BOND              : angle       0.80296 (   12)
  hydrogen bonds       : bond        0.04372 (  212)
  hydrogen bonds       : angle       4.44143 (  618)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   50 GLU cc_start: 0.7385 (tt0) cc_final: 0.6971 (pt0)
REVERT: A   28 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7000 (tt)
REVERT: A  179 ASN cc_start: 0.7733 (m-40) cc_final: 0.7268 (t0)
REVERT: A  213 ARG cc_start: 0.7905 (ttp-110) cc_final: 0.7455 (ttp-170)
REVERT: D   36 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7251 (mtm)
  outliers start: 14
  outliers final: 11
  residues processed: 60
  average time/residue: 0.4049
  time to fit residues: 25.4395
Evaluate side-chains
  64 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain D residue   36 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0270
   chunk 39 optimal weight:   20.0000
   chunk 42 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 35 optimal weight:   30.0000
   chunk 32 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.6238

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.190819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.113111 restraints weight = 8948.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 3.29
r_work: 0.2938 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2913
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2913
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3652  Z= 0.127
  Angle     :  0.566   7.046   4972  Z= 0.290
  Chirality :  0.042   0.194    570
  Planarity :  0.004   0.036    616
  Dihedral  :  3.825  20.907    502
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.80 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.42), residues: 449
  helix:  2.29 (0.34), residues: 232
  sheet: -0.79 (0.65), residues: 73
  loop : -1.76 (0.50), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  32 
 TYR   0.010   0.001   TYR A 316 
 PHE   0.008   0.001   PHE A 312 
 TRP   0.019   0.001   TRP A 165 
 HIS   0.002   0.000   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 3646)
  covalent geometry    : angle       0.56514 ( 4960)
  SS BOND              : bond        0.00180 (    6)
  SS BOND              : angle       0.76522 (   12)
  hydrogen bonds       : bond        0.04191 (  212)
  hydrogen bonds       : angle       4.38578 (  618)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   50 GLU cc_start: 0.7292 (tt0) cc_final: 0.6898 (pt0)
REVERT: A   28 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7010 (tt)
REVERT: A  179 ASN cc_start: 0.7823 (m-40) cc_final: 0.7317 (t0)
REVERT: A  213 ARG cc_start: 0.7795 (ttp-110) cc_final: 0.7328 (ttp-170)
  outliers start: 11
  outliers final: 9
  residues processed: 60
  average time/residue: 0.3675
  time to fit residues: 23.0757
Evaluate side-chains
  61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  321 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0970
   chunk 27 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 31 optimal weight:    0.3980
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 30 optimal weight:    0.4980
   overall best weight:    0.4978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.192325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.116039 restraints weight = 7128.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 3.02
r_work: 0.3105 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3107
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3652  Z= 0.117
  Angle     :  0.553   7.116   4972  Z= 0.282
  Chirality :  0.042   0.187    570
  Planarity :  0.004   0.035    616
  Dihedral  :  3.765  21.157    502
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 15.28 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.42), residues: 449
  helix:  2.45 (0.34), residues: 232
  sheet: -0.70 (0.66), residues: 73
  loop : -1.69 (0.50), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  32 
 TYR   0.010   0.001   TYR A 316 
 PHE   0.008   0.001   PHE A 312 
 TRP   0.016   0.001   TRP A 165 
 HIS   0.002   0.000   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 3646)
  covalent geometry    : angle       0.55245 ( 4960)
  SS BOND              : bond        0.00171 (    6)
  SS BOND              : angle       0.72192 (   12)
  hydrogen bonds       : bond        0.03922 (  212)
  hydrogen bonds       : angle       4.30479 (  618)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1773.83 seconds
wall clock time: 30 minutes 54.27 seconds (1854.27 seconds total)