Starting phenix.real_space_refine
on Sat Aug 23 01:59:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tq2_41499/08_2025/8tq2_41499_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tq2_41499/08_2025/8tq2_41499.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tq2_41499/08_2025/8tq2_41499_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tq2_41499/08_2025/8tq2_41499_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tq2_41499/08_2025/8tq2_41499.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tq2_41499/08_2025/8tq2_41499.map"
  }
  resolution = 3.8
  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=   0.002
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 4357 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      36      5.16       5
     C    3569      2.51       5
     N     931      2.21       5
     O     969      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5505
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 639
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 8, 'TRANS': 73}
    Chain: "D"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 120
          Classifications: {'peptide': 16}
          Link IDs: {'PTRANS': 1, 'TRANS': 14}
    Chain: "A"
      Number of atoms: 2561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2561
          Classifications: {'peptide': 313}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 294}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 2185
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 261, 2178
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 12, 'TRANS': 248}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 261, 2178
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 12, 'TRANS': 248}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2226
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AVAL B 163 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CG2BVAL B 163 " occ=0.50
  Time building chain proxies: 2.00, per 1000 atoms: 0.36
  Number of scatterers: 5505
  At special positions: 0
  Unit cell: (81.3276, 101.659, 82.3977, 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      36     16.00
     O     969      8.00
     N     931      7.00
     C    3569      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 277.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1292

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 3 sheets defined
      52.5% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'C' and resid 37 through 44
      removed outlier: 3.546A  pdb=" N   LYS C  42 " --> pdb=" O   ALA C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 84
    Processing helix  chain 'D' and resid 1619 through 1623
      removed outlier: 3.693A  pdb=" N   VAL D1622 " --> pdb=" O   ARG D1619 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLY D1623 " --> pdb=" O   ASP D1620 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 1619 through 1623'
    Processing helix  chain 'A' and resid 2 through 13
    Processing helix  chain 'A' and resid 60 through 71
    Processing helix  chain 'A' and resid 104 through 111
    Processing helix  chain 'A' and resid 124 through 145
      removed outlier: 3.629A  pdb=" N   VAL A 128 " --> pdb=" O   PRO A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 155
      No H-bonds generated for 'chain 'A' and resid 153 through 155'
    Processing helix  chain 'A' and resid 201 through 206
    Processing helix  chain 'A' and resid 214 through 230
    Processing helix  chain 'A' and resid 251 through 260
      removed outlier: 3.750A  pdb=" N   MET A 259 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 300
      removed outlier: 3.714A  pdb=" N   HIS A 300 " --> pdb=" O   TYR A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 316
      removed outlier: 3.949A  pdb=" N   HIS A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 332
      removed outlier: 3.600A  pdb=" N   ALA A 329 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   MET A 330 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLN A 331 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 13
    Processing helix  chain 'B' and resid 17 through 25
    Processing helix  chain 'B' and resid 25 through 30
    Processing helix  chain 'B' and resid 33 through 55
    Processing helix  chain 'B' and resid 58 through 70
      removed outlier: 3.914A  pdb=" N   ILE B  62 " --> pdb=" O   ARG B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 75
    Processing helix  chain 'B' and resid 82 through 98
      Proline residue:  B  88  - end of helix
    Processing helix  chain 'B' and resid 104 through 120
      removed outlier: 3.512A  pdb=" N   PHE B 120 " --> pdb=" O   LEU B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 146
    Processing helix  chain 'B' and resid 155 through 167
    Processing helix  chain 'B' and resid 172 through 183
    Processing helix  chain 'B' and resid 184 through 186
      No H-bonds generated for 'chain 'B' and resid 184 through 186'
    Processing helix  chain 'B' and resid 187 through 192
    Processing helix  chain 'B' and resid 193 through 209
      removed outlier: 3.535A  pdb=" N   ILE B 197 " --> pdb=" O   PRO B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 220
      removed outlier: 3.793A  pdb=" N   GLU B 219 " --> pdb=" O   GLN B 215 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU B 220 " --> pdb=" O   TRP B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 241
    Processing helix  chain 'B' and resid 242 through 244
      No H-bonds generated for 'chain 'B' and resid 242 through 244'
    Processing helix  chain 'B' and resid 245 through 256
      removed outlier: 3.619A  pdb=" N   GLU B 249 " --> pdb=" O   ASP B 245 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   ALA B 251 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   THR B 252 " --> pdb=" O   LYS B 248 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29
      removed outlier: 6.584A  pdb=" N   LYS A  26 " --> pdb=" O   LYS A  37 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LYS A  37 " --> pdb=" O   LYS A  26 " (cutoff:3.500A)
      removed outlier: 5.143A  pdb=" N   VAL A  93 " --> pdb=" O   ILE A  54 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   LYS A  92 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   LEU A  86 " --> pdb=" O   LYS A  92 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   TRP A  94 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   VAL A  84 " --> pdb=" O   TRP A  94 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   LEU A  96 " --> pdb=" O   GLN A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103
      removed outlier: 4.430A  pdb=" N   MET A 160 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   ARG A 168 " --> pdb=" O   MET A 160 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 148

    230 hydrogen bonds defined for protein.
    679 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: 0.82

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1743
        1.35 -     1.46: 1291
        1.46 -     1.58: 2552
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 5644
  Sorted by residual:
  bond pdb=" C   MET A 273 "
       pdb=" N   PRO A 274 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.022 2.34e-02 1.83e+03 9.03e-01
  bond pdb=" CB  GLU B  98 "
       pdb=" CG  GLU B  98 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.99e-01
  bond pdb=" CG  GLU B  98 "
       pdb=" CD  GLU B  98 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 2.50e-02 1.60e+03 6.59e-01
  bond pdb=" CA  ASP A 137 "
       pdb=" CB  ASP A 137 "
    ideal  model  delta    sigma   weight residual
    1.528  1.541 -0.013 1.59e-02 3.96e+03 6.43e-01
  bond pdb=" N   PRO B 193 "
       pdb=" CA  PRO B 193 "
    ideal  model  delta    sigma   weight residual
    1.457  1.467 -0.010 1.31e-02 5.83e+03 6.20e-01
  ... (remaining 5639 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 7458
        1.53 -     3.05: 125
        3.05 -     4.58: 32
        4.58 -     6.10: 7
        6.10 -     7.63: 3
  Bond angle restraints: 7625
  Sorted by residual:
  angle pdb=" CB  MET B 250 "
        pdb=" CG  MET B 250 "
        pdb=" SD  MET B 250 "
      ideal   model   delta    sigma   weight residual
     112.70  120.33   -7.63 3.00e+00 1.11e-01 6.47e+00
  angle pdb=" CB  MET B  86 "
        pdb=" CG  MET B  86 "
        pdb=" SD  MET B  86 "
      ideal   model   delta    sigma   weight residual
     112.70  120.32   -7.62 3.00e+00 1.11e-01 6.46e+00
  angle pdb=" CA  MET A 174 "
        pdb=" CB  MET A 174 "
        pdb=" CG  MET A 174 "
      ideal   model   delta    sigma   weight residual
     114.10  118.42   -4.32 2.00e+00 2.50e-01 4.67e+00
  angle pdb=" C   LEU A  69 "
        pdb=" N   LEU A  70 "
        pdb=" CA  LEU A  70 "
      ideal   model   delta    sigma   weight residual
     121.94  117.69    4.25 2.00e+00 2.50e-01 4.52e+00
  angle pdb=" C   LYS C  15 "
        pdb=" N   ARG C  16 "
        pdb=" CA  ARG C  16 "
      ideal   model   delta    sigma   weight residual
     120.58  123.32   -2.74 1.32e+00 5.74e-01 4.29e+00
  ... (remaining 7620 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.18: 2991
       16.18 -    32.35: 337
       32.35 -    48.53: 71
       48.53 -    64.70: 10
       64.70 -    80.88: 7
  Dihedral angle restraints: 3416
    sinusoidal: 1431
      harmonic: 1985
  Sorted by residual:
  dihedral pdb=" CA  ASP B  20 "
           pdb=" CB  ASP B  20 "
           pdb=" CG  ASP B  20 "
           pdb=" OD1 ASP B  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.65   51.65     1      2.00e+01 2.50e-03 9.11e+00
  dihedral pdb=" CG  ARG B  58 "
           pdb=" CD  ARG B  58 "
           pdb=" NE  ARG B  58 "
           pdb=" CZ  ARG B  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  139.55   40.45     2      1.50e+01 4.44e-03 8.98e+00
  dihedral pdb=" CB  GLU A 101 "
           pdb=" CG  GLU A 101 "
           pdb=" CD  GLU A 101 "
           pdb=" OE1 GLU A 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   80.88  -80.88     1      3.00e+01 1.11e-03 8.98e+00
  ... (remaining 3413 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 481
       0.028 -    0.057: 204
       0.057 -    0.085: 90
       0.085 -    0.113: 47
       0.113 -    0.141: 5
  Chirality restraints: 827
  Sorted by residual:
  chirality pdb=" CA  VAL B 222 "
            pdb=" N   VAL B 222 "
            pdb=" C   VAL B 222 "
            pdb=" CB  VAL B 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.00e-01
  chirality pdb=" CA  LEU A  70 "
            pdb=" N   LEU A  70 "
            pdb=" C   LEU A  70 "
            pdb=" CB  LEU A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.16e-01
  chirality pdb=" CA  VAL A 195 "
            pdb=" N   VAL A 195 "
            pdb=" C   VAL A 195 "
            pdb=" CB  VAL A 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.69e-01
  ... (remaining 824 not shown)

  Planarity restraints: 964
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C  25 "    0.027 5.00e-02 4.00e+02   4.11e-02 2.70e+00
        pdb=" N   PRO C  26 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO C  26 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C  26 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 340 "    0.021 5.00e-02 4.00e+02   3.19e-02 1.63e+00
        pdb=" N   PRO A 341 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 341 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 341 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  28 "    0.019 5.00e-02 4.00e+02   2.86e-02 1.31e+00
        pdb=" N   PRO C  29 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO C  29 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C  29 "    0.016 5.00e-02 4.00e+02
  ... (remaining 961 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1376
        2.80 -     3.33: 5197
        3.33 -     3.85: 8567
        3.85 -     4.38: 9625
        4.38 -     4.90: 16927
  Nonbonded interactions: 41692
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 203 "
            pdb=" NH2 ARG A 323 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" O   LYS B  70 "
            pdb=" N   PHE B  72 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O   THR B 252 "
            pdb=" OG  SER B 255 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   ILE A  59 "
            pdb=" NZ  LYS B  96 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" NE2 GLN C  27 "
            pdb=" O   HIS A 143 "
     model   vdw
     2.332 3.120
  ... (remaining 41687 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=0.00 max=1.00 mean=0.98
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:             3.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.060
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
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      :  0.002   0.031   5644  Z= 0.104
  Angle     :  0.551   7.630   7625  Z= 0.276
  Chirality :  0.041   0.141    827
  Planarity :  0.004   0.041    964
  Dihedral  : 14.159  80.877   2124
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.72 (0.33), residues: 655
  helix:  1.66 (0.31), residues: 311
  sheet:  1.88 (1.30), residues: 13
  loop : -0.75 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 209 
 TYR   0.007   0.001   TYR C  25 
 PHE   0.011   0.001   PHE B 140 
 TRP   0.011   0.001   TRP B  38 
 HIS   0.001   0.000   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 5644)
  covalent geometry    : angle       0.55073 ( 7625)
  hydrogen bonds       : bond        0.14502 (  230)
  hydrogen bonds       : angle       4.90312 (  679)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.228 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.5644 (mmp) cc_final: 0.4255 (tmm)
REVERT: A   61 MET cc_start: 0.7989 (mmm) cc_final: 0.7777 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0762
  time to fit residues: 9.8026
Evaluate side-chains
  67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0040
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.6792

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.113677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.092950 restraints weight = 24785.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.097086 restraints weight = 12066.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.100574 restraints weight = 6505.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.100621 restraints weight = 4936.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.101358 restraints weight = 4024.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3370
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       80 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3369
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5644  Z= 0.120
  Angle     :  0.552  11.192   7625  Z= 0.274
  Chirality :  0.042   0.136    827
  Planarity :  0.004   0.030    964
  Dihedral  :  3.629  15.670    728
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  7.64 %
    Favored  : 91.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.83 (0.33), residues: 655
  helix:  1.59 (0.30), residues: 317
  sheet: -0.31 (0.97), residues: 25
  loop : -0.43 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 323 
 TYR   0.009   0.001   TYR B 184 
 PHE   0.010   0.001   PHE A 180 
 TRP   0.012   0.001   TRP B  38 
 HIS   0.007   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 5644)
  covalent geometry    : angle       0.55242 ( 7625)
  hydrogen bonds       : bond        0.04011 (  230)
  hydrogen bonds       : angle       4.30690 (  679)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.209 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.5698 (mmp) cc_final: 0.4317 (tmm)
REVERT: A  330 MET cc_start: 0.7047 (mtm) cc_final: 0.6837 (mtm)
REVERT: B  138 CYS cc_start: 0.8977 (t) cc_final: 0.8705 (t)
  outliers start: 3
  outliers final: 2
  residues processed: 76
  average time/residue: 0.0562
  time to fit residues: 6.2551
Evaluate side-chains
  70 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain B residue   47 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    0.3980
   chunk 58 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3532 r_free = 0.3532 target = 0.110098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.089704 restraints weight = 29912.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.094709 restraints weight = 14615.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.095103 restraints weight = 8673.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.096035 restraints weight = 6333.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.096776 restraints weight = 5402.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3303
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3303
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5644  Z= 0.162
  Angle     :  0.577   7.795   7625  Z= 0.286
  Chirality :  0.043   0.148    827
  Planarity :  0.004   0.032    964
  Dihedral  :  3.902  16.225    728
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  9.14 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.70 (0.32), residues: 655
  helix:  1.39 (0.29), residues: 319
  sheet: -0.33 (0.91), residues: 25
  loop : -0.40 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  16 
 TYR   0.013   0.001   TYR B 184 
 PHE   0.010   0.001   PHE A 180 
 TRP   0.013   0.002   TRP B  38 
 HIS   0.004   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 5644)
  covalent geometry    : angle       0.57684 ( 7625)
  hydrogen bonds       : bond        0.04129 (  230)
  hydrogen bonds       : angle       4.27022 (  679)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.229 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6037 (mmp) cc_final: 0.4359 (tmm)
REVERT: A  107 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.9138 (mm)
REVERT: A  151 ASP cc_start: 0.7777 (t0) cc_final: 0.7572 (t0)
REVERT: A  330 MET cc_start: 0.7360 (mtm) cc_final: 0.7141 (mtm)
  outliers start: 8
  outliers final: 4
  residues processed: 70
  average time/residue: 0.0574
  time to fit residues: 5.9113
Evaluate side-chains
  65 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue   47 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 26 optimal weight:    0.4980
   chunk 55 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
C  40 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.109399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.089296 restraints weight = 35666.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.093963 restraints weight = 18787.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.096048 restraints weight = 8719.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.096488 restraints weight = 6157.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.099356 restraints weight = 5303.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5644  Z= 0.154
  Angle     :  0.555   7.542   7625  Z= 0.277
  Chirality :  0.043   0.147    827
  Planarity :  0.004   0.044    964
  Dihedral  :  3.935  15.387    728
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.96 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 (0.32), residues: 655
  helix:  1.23 (0.29), residues: 320
  sheet: -0.27 (0.92), residues: 25
  loop : -0.37 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 178 
 TYR   0.011   0.001   TYR B 184 
 PHE   0.010   0.001   PHE B  44 
 TRP   0.013   0.002   TRP B  38 
 HIS   0.004   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 5644)
  covalent geometry    : angle       0.55545 ( 7625)
  hydrogen bonds       : bond        0.03937 (  230)
  hydrogen bonds       : angle       4.21013 (  679)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.256 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6029 (mmp) cc_final: 0.4407 (tmm)
REVERT: A  107 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9139 (mm)
REVERT: A  330 MET cc_start: 0.7228 (mtm) cc_final: 0.6995 (mtm)
REVERT: B  132 MET cc_start: 0.7653 (tpt) cc_final: 0.7315 (tpp)
  outliers start: 11
  outliers final: 6
  residues processed: 71
  average time/residue: 0.0594
  time to fit residues: 6.2198
Evaluate side-chains
  68 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  328 GLN
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  252 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0670
   chunk 10 optimal weight:    0.0870
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.3544 r_free = 0.3544 target = 0.111054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.090122 restraints weight = 24628.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.094491 restraints weight = 12309.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.098302 restraints weight = 6121.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.098062 restraints weight = 3859.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.098316 restraints weight = 3780.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3331
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3331
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5644  Z= 0.108
  Angle     :  0.518   6.728   7625  Z= 0.258
  Chirality :  0.041   0.138    827
  Planarity :  0.004   0.043    964
  Dihedral  :  3.853  19.138    728
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 12.46 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.71 (0.33), residues: 655
  helix:  1.33 (0.29), residues: 320
  sheet: -0.16 (0.94), residues: 25
  loop : -0.32 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 323 
 TYR   0.008   0.001   TYR B  76 
 PHE   0.010   0.001   PHE B  44 
 TRP   0.012   0.001   TRP B  38 
 HIS   0.004   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 5644)
  covalent geometry    : angle       0.51766 ( 7625)
  hydrogen bonds       : bond        0.03407 (  230)
  hydrogen bonds       : angle       4.04899 (  679)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.185 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6066 (mmp) cc_final: 0.4431 (ppp)
REVERT: A  107 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9159 (mm)
REVERT: B  250 MET cc_start: 0.7962 (mmm) cc_final: 0.7647 (mmm)
  outliers start: 6
  outliers final: 4
  residues processed: 72
  average time/residue: 0.0591
  time to fit residues: 6.2570
Evaluate side-chains
  67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain B residue   47 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 54 optimal weight:    0.2980
   chunk 41 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.3524 r_free = 0.3524 target = 0.109650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.089181 restraints weight = 32908.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.094495 restraints weight = 15152.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.094962 restraints weight = 8462.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.095790 restraints weight = 6328.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.096838 restraints weight = 5471.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3304
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3304 r_free = 0.3304    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3304 r_free = 0.3304    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3304
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5644  Z= 0.140
  Angle     :  0.545   7.672   7625  Z= 0.270
  Chirality :  0.042   0.156    827
  Planarity :  0.004   0.043    964
  Dihedral  :  3.891  18.936    728
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.79 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.65 (0.33), residues: 655
  helix:  1.24 (0.29), residues: 320
  sheet: -0.14 (0.95), residues: 25
  loop : -0.31 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 178 
 TYR   0.010   0.001   TYR B 184 
 PHE   0.009   0.001   PHE B  44 
 TRP   0.013   0.001   TRP B  38 
 HIS   0.003   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 5644)
  covalent geometry    : angle       0.54520 ( 7625)
  hydrogen bonds       : bond        0.03693 (  230)
  hydrogen bonds       : angle       4.10000 (  679)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.213 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6260 (mmp) cc_final: 0.4560 (tmm)
REVERT: A    1 MET cc_start: 0.6515 (tpt) cc_final: 0.6213 (tpp)
REVERT: A  107 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9132 (mm)
REVERT: B  132 MET cc_start: 0.7668 (tpt) cc_final: 0.7312 (tpp)
REVERT: B  250 MET cc_start: 0.8083 (mmm) cc_final: 0.7773 (mmm)
  outliers start: 11
  outliers final: 8
  residues processed: 72
  average time/residue: 0.0570
  time to fit residues: 5.9076
Evaluate side-chains
  72 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 ASN
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue   47 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3530 r_free = 0.3530 target = 0.110132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.089522 restraints weight = 26131.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.094316 restraints weight = 12091.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.097446 restraints weight = 6112.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.097609 restraints weight = 4466.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.098000 restraints weight = 3781.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3311
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3311
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5644  Z= 0.125
  Angle     :  0.544   9.277   7625  Z= 0.269
  Chirality :  0.042   0.155    827
  Planarity :  0.004   0.043    964
  Dihedral  :  3.867  17.634    728
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 13.29 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.71 (0.33), residues: 655
  helix:  1.31 (0.29), residues: 320
  sheet: -0.09 (0.98), residues: 25
  loop : -0.31 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D1619 
 TYR   0.009   0.001   TYR B  76 
 PHE   0.009   0.001   PHE B  44 
 TRP   0.013   0.001   TRP B  38 
 HIS   0.002   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 5644)
  covalent geometry    : angle       0.54432 ( 7625)
  hydrogen bonds       : bond        0.03496 (  230)
  hydrogen bonds       : angle       4.04565 (  679)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.237 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6127 (mmp) cc_final: 0.4491 (ppp)
REVERT: A  107 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9158 (mm)
REVERT: B  132 MET cc_start: 0.7660 (tpt) cc_final: 0.7290 (tpp)
REVERT: B  246 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6986 (mm-30)
REVERT: B  250 MET cc_start: 0.8100 (mmm) cc_final: 0.7738 (mmm)
  outliers start: 14
  outliers final: 9
  residues processed: 74
  average time/residue: 0.0556
  time to fit residues: 6.0972
Evaluate side-chains
  74 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 ASN
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  171 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3511 r_free = 0.3511 target = 0.108883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.089060 restraints weight = 15880.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.092064 restraints weight = 8495.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.094114 restraints weight = 5562.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.095431 restraints weight = 4150.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.096428 restraints weight = 3403.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3313
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3313
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5644  Z= 0.158
  Angle     :  0.573   7.760   7625  Z= 0.286
  Chirality :  0.043   0.173    827
  Planarity :  0.004   0.043    964
  Dihedral  :  3.985  18.384    728
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.95 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.55 (0.33), residues: 655
  helix:  1.12 (0.29), residues: 326
  sheet: -0.15 (1.00), residues: 25
  loop : -0.35 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 178 
 TYR   0.010   0.001   TYR B 184 
 PHE   0.029   0.001   PHE A 261 
 TRP   0.013   0.002   TRP B  38 
 HIS   0.002   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 5644)
  covalent geometry    : angle       0.57304 ( 7625)
  hydrogen bonds       : bond        0.03856 (  230)
  hydrogen bonds       : angle       4.13783 (  679)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.245 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6101 (mmp) cc_final: 0.4359 (ppp)
REVERT: A  107 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9169 (mm)
REVERT: B  132 MET cc_start: 0.7683 (tpt) cc_final: 0.7301 (tpp)
REVERT: B  220 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7558 (pp)
  outliers start: 13
  outliers final: 7
  residues processed: 66
  average time/residue: 0.0552
  time to fit residues: 5.3881
Evaluate side-chains
  68 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  171 MET
Chi-restraints excluded: chain B residue  220 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 11 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0770
   chunk 24 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.9742

-------------------------------------------------------------------------------
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 = 0.3515 r_free = 0.3515 target = 0.109289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.088689 restraints weight = 33165.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.093797 restraints weight = 14660.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.094817 restraints weight = 7952.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.095577 restraints weight = 6238.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.096307 restraints weight = 5336.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3284
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5644  Z= 0.135
  Angle     :  0.568   9.960   7625  Z= 0.280
  Chirality :  0.043   0.171    827
  Planarity :  0.004   0.043    964
  Dihedral  :  3.948  17.719    728
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.29 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.56 (0.33), residues: 655
  helix:  1.14 (0.29), residues: 326
  sheet: -0.10 (1.04), residues: 25
  loop : -0.37 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D1619 
 TYR   0.009   0.001   TYR B  76 
 PHE   0.025   0.001   PHE A 261 
 TRP   0.014   0.001   TRP B  38 
 HIS   0.002   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5644)
  covalent geometry    : angle       0.56833 ( 7625)
  hydrogen bonds       : bond        0.03593 (  230)
  hydrogen bonds       : angle       4.07484 (  679)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.243 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6459 (mmp) cc_final: 0.4452 (ppp)
REVERT: A  107 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9128 (mm)
REVERT: B  132 MET cc_start: 0.7680 (tpt) cc_final: 0.7304 (tpp)
REVERT: B  220 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7587 (pp)
REVERT: B  246 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6893 (mm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 70
  average time/residue: 0.0571
  time to fit residues: 5.9370
Evaluate side-chains
  70 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  171 MET
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  220 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 54 optimal weight:    0.2980
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3529 r_free = 0.3529 target = 0.110132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.089399 restraints weight = 26485.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.094409 restraints weight = 12213.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.097829 restraints weight = 5754.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.097914 restraints weight = 4337.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.098116 restraints weight = 3630.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3321
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3321
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5644  Z= 0.115
  Angle     :  0.548   9.854   7625  Z= 0.271
  Chirality :  0.042   0.152    827
  Planarity :  0.004   0.042    964
  Dihedral  :  3.855  18.314    728
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.95 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.66 (0.33), residues: 655
  helix:  1.23 (0.29), residues: 326
  sheet:  0.02 (1.04), residues: 25
  loop : -0.33 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D1619 
 TYR   0.008   0.001   TYR B  76 
 PHE   0.027   0.001   PHE A 261 
 TRP   0.014   0.001   TRP B  38 
 HIS   0.002   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 5644)
  covalent geometry    : angle       0.54849 ( 7625)
  hydrogen bonds       : bond        0.03319 (  230)
  hydrogen bonds       : angle       3.98808 (  679)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.236 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6311 (mmp) cc_final: 0.4434 (ppp)
REVERT: A  107 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9177 (mm)
REVERT: B  137 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6725 (tm-30)
REVERT: B  141 TYR cc_start: 0.8107 (m-10) cc_final: 0.7645 (m-10)
REVERT: B  220 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7614 (pp)
  outliers start: 9
  outliers final: 7
  residues processed: 72
  average time/residue: 0.0594
  time to fit residues: 6.2069
Evaluate side-chains
  71 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  171 MET
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  220 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 54 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   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 = 0.3525 r_free = 0.3525 target = 0.109927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.089462 restraints weight = 24974.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.093054 restraints weight = 13048.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.095777 restraints weight = 6999.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.096843 restraints weight = 5128.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.097336 restraints weight = 4571.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3313
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3313
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5644  Z= 0.122
  Angle     :  0.559   9.728   7625  Z= 0.276
  Chirality :  0.042   0.152    827
  Planarity :  0.004   0.042    964
  Dihedral  :  3.854  17.123    728
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.29 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.66 (0.33), residues: 655
  helix:  1.24 (0.29), residues: 326
  sheet:  0.08 (1.04), residues: 25
  loop : -0.34 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 178 
 TYR   0.009   0.001   TYR B  76 
 PHE   0.025   0.001   PHE A 261 
 TRP   0.014   0.001   TRP B  38 
 HIS   0.002   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5644)
  covalent geometry    : angle       0.55889 ( 7625)
  hydrogen bonds       : bond        0.03383 (  230)
  hydrogen bonds       : angle       3.97821 (  679)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1070.14 seconds
wall clock time: 19 minutes 11.94 seconds (1151.94 seconds total)