Starting phenix.real_space_refine
on Tue Aug  4 21:57:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kqj_62506/08_2026/9kqj_62506.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kqj_62506/08_2026/9kqj_62506.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kqj_62506/08_2026/9kqj_62506.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kqj_62506/08_2026/9kqj_62506.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kqj_62506/08_2026/9kqj_62506.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kqj_62506/08_2026/9kqj_62506.cif"
  }
  resolution = 2.95
  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=   0.002 sd=   0.093
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     P      16      5.49       5
     S      40      5.16       5
     C    4818      2.51       5
     N    1016      2.21       5
     O    1164      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7056
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 3171
          Classifications: {'peptide': 377}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 364}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 3171
          Classifications: {'peptide': 377}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 364}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 357
          Unusual residues: {' CA': 1, 'C14': 1, 'D12': 1, 'LBN': 5, 'PSF': 2, 'T7X': 1}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 51
          Planarities with less than four sites: {'LBN:plan-3': 2}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 357
          Unusual residues: {' CA': 1, 'C14': 1, 'D12': 1, 'LBN': 5, 'PSF': 2, 'T7X': 1}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 51
          Planarities with less than four sites: {'LBN:plan-3': 2}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 1.44, per 1000 atoms: 0.20
  Number of scatterers: 7056
  At special positions: 0
  Unit cell: (94.95, 108.665, 71.74, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      2     19.99
     S      40     16.00
     P      16     15.00
     O    1164      8.00
     N    1016      7.00
     C    4818      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: 0.49
  Conformation dependent library (CDL) restraints added in 307.7 milliseconds
  

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1436

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 0 sheets defined
      77.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 22
      removed outlier: 3.559A  pdb=" N   LYS A  18 " --> pdb=" O   ASP A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 39
      removed outlier: 3.598A  pdb=" N   PHE A  37 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ARG A  39 " --> pdb=" O   PHE A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 59
    Processing helix  chain 'A' and resid 64 through 88
    Processing helix  chain 'A' and resid 97 through 119
      removed outlier: 4.017A  pdb=" N   TRP A 101 " --> pdb=" O   HIS A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 134
    Processing helix  chain 'A' and resid 135 through 139
    Processing helix  chain 'A' and resid 160 through 165
    Processing helix  chain 'A' and resid 166 through 184
    Processing helix  chain 'A' and resid 185 through 203
    Processing helix  chain 'A' and resid 213 through 220
      removed outlier: 4.316A  pdb=" N   GLN A 217 " --> pdb=" O   CYS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 242
    Processing helix  chain 'A' and resid 255 through 265
    Processing helix  chain 'A' and resid 266 through 268
      No H-bonds generated for 'chain 'A' and resid 266 through 268'
    Processing helix  chain 'A' and resid 283 through 311
      removed outlier: 3.619A  pdb=" N   LYS A 308 " --> pdb=" O   THR A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 344
      removed outlier: 3.785A  pdb=" N   ARG A 323 " --> pdb=" O   LEU A 319 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ALA A 332 " --> pdb=" O   GLY A 328 " (cutoff:3.500A)
      Proline residue:  A 333  - end of helix
    Processing helix  chain 'A' and resid 351 through 372
    Processing helix  chain 'A' and resid 381 through 408
      removed outlier: 3.677A  pdb=" N   VAL A 391 " --> pdb=" O   TRP A 387 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR A 394 " --> pdb=" O   CYS A 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 25
      removed outlier: 3.611A  pdb=" N   MET B  23 " --> pdb=" O   MET B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 59
    Processing helix  chain 'B' and resid 64 through 88
      removed outlier: 3.533A  pdb=" N   ILE B  69 " --> pdb=" O   PRO B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 119
      removed outlier: 4.066A  pdb=" N   TRP B 101 " --> pdb=" O   HIS B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 134
      removed outlier: 3.523A  pdb=" N   ASP B 134 " --> pdb=" O   MET B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 139
    Processing helix  chain 'B' and resid 160 through 165
    Processing helix  chain 'B' and resid 166 through 184
      removed outlier: 3.548A  pdb=" N   GLY B 171 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU B 182 " --> pdb=" O   MET B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 203
      removed outlier: 3.860A  pdb=" N   GLU B 197 " --> pdb=" O   SER B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 219
      removed outlier: 4.453A  pdb=" N   GLN B 217 " --> pdb=" O   CYS B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 224
    Processing helix  chain 'B' and resid 224 through 242
    Processing helix  chain 'B' and resid 255 through 265
    Processing helix  chain 'B' and resid 266 through 268
      No H-bonds generated for 'chain 'B' and resid 266 through 268'
    Processing helix  chain 'B' and resid 283 through 311
      removed outlier: 3.717A  pdb=" N   GLN B 298 " --> pdb=" O   MET B 294 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLU B 301 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU B 302 " --> pdb=" O   GLN B 298 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR B 304 " --> pdb=" O   THR B 300 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE B 305 " --> pdb=" O   GLU B 301 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   HIS B 309 " --> pdb=" O   PHE B 305 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE B 311 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 344
      removed outlier: 3.831A  pdb=" N   ARG B 323 " --> pdb=" O   LEU B 319 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA B 332 " --> pdb=" O   GLY B 328 " (cutoff:3.500A)
      Proline residue:  B 333  - end of helix
      removed outlier: 3.654A  pdb=" N   ARG B 336 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ALA B 340 " --> pdb=" O   ARG B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 372
      removed outlier: 3.847A  pdb=" N   ALA B 365 " --> pdb=" O   GLY B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 408
      removed outlier: 3.513A  pdb=" N   LEU B 389 " --> pdb=" O   VAL B 385 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL B 391 " --> pdb=" O   TRP B 387 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR B 394 " --> pdb=" O   CYS B 390 " (cutoff:3.500A)

    405 hydrogen bonds defined for protein.
    1200 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.03

  Time building geometry restraints manager: 0.64 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 976
        1.32 -     1.44: 2253
        1.44 -     1.56: 3941
        1.56 -     1.69: 32
        1.69 -     1.81: 62
  Bond restraints: 7264
  Sorted by residual:
  bond pdb=" CG1 ILE A 192 "
       pdb=" CD1 ILE A 192 "
    ideal  model  delta    sigma   weight residual
    1.513  1.464  0.049 3.90e-02 6.57e+02 1.56e+00
  bond pdb=" CG1 ILE B 192 "
       pdb=" CD1 ILE B 192 "
    ideal  model  delta    sigma   weight residual
    1.513  1.468  0.045 3.90e-02 6.57e+02 1.32e+00
  bond pdb=" CB  GLN B 298 "
       pdb=" CG  GLN B 298 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.23e+00
  bond pdb=" CG1 ILE B  50 "
       pdb=" CD1 ILE B  50 "
    ideal  model  delta    sigma   weight residual
    1.513  1.475  0.038 3.90e-02 6.57e+02 9.37e-01
  bond pdb=" CG  LEU B  46 "
       pdb=" CD2 LEU B  46 "
    ideal  model  delta    sigma   weight residual
    1.521  1.492  0.029 3.30e-02 9.18e+02 7.65e-01
  ... (remaining 7259 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.11: 9629
        2.11 -     4.23: 115
        4.23 -     6.34: 21
        6.34 -     8.45: 3
        8.45 -    10.56: 2
  Bond angle restraints: 9770
  Sorted by residual:
  angle pdb=" C   VAL A 218 "
        pdb=" N   ILE A 219 "
        pdb=" CA  ILE A 219 "
      ideal   model   delta    sigma   weight residual
     122.97  119.36    3.61 9.80e-01 1.04e+00 1.35e+01
  angle pdb=" CA  LEU A 386 "
        pdb=" CB  LEU A 386 "
        pdb=" CG  LEU A 386 "
      ideal   model   delta    sigma   weight residual
     116.30  126.86  -10.56 3.50e+00 8.16e-02 9.11e+00
  angle pdb=" CA  LEU B 386 "
        pdb=" CB  LEU B 386 "
        pdb=" CG  LEU B 386 "
      ideal   model   delta    sigma   weight residual
     116.30  125.89   -9.59 3.50e+00 8.16e-02 7.51e+00
  angle pdb=" CA  MET A  19 "
        pdb=" CB  MET A  19 "
        pdb=" CG  MET A  19 "
      ideal   model   delta    sigma   weight residual
     114.10  119.50   -5.40 2.00e+00 2.50e-01 7.29e+00
  angle pdb=" CB  MET A  19 "
        pdb=" CG  MET A  19 "
        pdb=" SD  MET A  19 "
      ideal   model   delta    sigma   weight residual
     112.70  120.39   -7.69 3.00e+00 1.11e-01 6.56e+00
  ... (remaining 9765 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.64: 3966
       35.64 -    71.29: 219
       71.29 -   106.93: 28
      106.93 -   142.58: 14
      142.58 -   178.22: 13
  Dihedral angle restraints: 4240
    sinusoidal: 2022
      harmonic: 2218
  Sorted by residual:
  dihedral pdb=" C1  LBN B 509 "
           pdb=" O1  LBN B 509 "
           pdb=" P1  LBN B 509 "
           pdb=" O3  LBN B 509 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -84.60   93.62 -178.22     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C1  LBN A 507 "
           pdb=" O1  LBN A 507 "
           pdb=" P1  LBN A 507 "
           pdb=" O3  LBN A 507 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -84.60   93.51 -178.11     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" O5  LBN A 503 "
           pdb=" C2  LBN A 503 "
           pdb=" C3  LBN A 503 "
           pdb=" O7  LBN A 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.67 -105.21  167.88     1      3.00e+01 1.11e-03 2.11e+01
  ... (remaining 4237 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 658
       0.038 -    0.076: 270
       0.076 -    0.113: 59
       0.113 -    0.151: 11
       0.151 -    0.189: 4
  Chirality restraints: 1002
  Sorted by residual:
  chirality pdb=" C4  T7X B 501 "
            pdb=" C3  T7X B 501 "
            pdb=" C5  T7X B 501 "
            pdb=" O4  T7X B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.33   -0.19 2.00e-01 2.50e+01 8.91e-01
  chirality pdb=" C4  T7X A 510 "
            pdb=" C3  T7X A 510 "
            pdb=" C5  T7X A 510 "
            pdb=" O4  T7X A 510 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.33   -0.19 2.00e-01 2.50e+01 8.70e-01
  chirality pdb=" C1  T7X B 501 "
            pdb=" C2  T7X B 501 "
            pdb=" C6  T7X B 501 "
            pdb=" O1  T7X B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -2.25   -0.16 2.00e-01 2.50e+01 6.77e-01
  ... (remaining 999 not shown)

  Planarity restraints: 1126
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  36 "    0.010 2.00e-02 2.50e+03   1.42e-02 3.51e+00
        pdb=" CG  PHE B  36 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  36 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  36 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  36 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  36 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  36 "   -0.009 2.00e-02 2.50e+03   1.42e-02 3.51e+00
        pdb=" CG  PHE A  36 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  36 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  36 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  36 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  36 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 317 "    0.024 5.00e-02 4.00e+02   3.69e-02 2.18e+00
        pdb=" N   PRO B 318 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 318 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 318 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1123 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 128
        2.66 -     3.22: 6339
        3.22 -     3.78: 10714
        3.78 -     4.34: 15572
        4.34 -     4.90: 25677
  Nonbonded interactions: 58430
  Sorted by model distance:
  nonbonded pdb=" O   TYR B  55 "
            pdb=" OG1 THR B  59 "
     model   vdw
     2.099 3.040
  nonbonded pdb=" O   TYR A  55 "
            pdb=" OG1 THR A  59 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" O   HIS B 246 "
            pdb=" ND1 HIS B 246 "
     model   vdw
     2.121 3.120
  nonbonded pdb=" O   HIS A 246 "
            pdb=" ND1 HIS A 246 "
     model   vdw
     2.129 3.120
  nonbonded pdb=" O   GLY B 289 "
            pdb=" OH  TYR B 338 "
     model   vdw
     2.178 3.040
  ... (remaining 58425 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 14 through 408)
  selection = (chain 'B' and resid 14 through 408)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.890
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
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      :  0.005   0.049   7264  Z= 0.201
  Angle     :  0.623  10.563   9770  Z= 0.298
  Chirality :  0.043   0.189   1002
  Planarity :  0.004   0.037   1126
  Dihedral  : 24.654 178.222   2804
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.65 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.30), residues: 746
  helix: -0.45 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.59 (0.44), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  22 
 TYR   0.015   0.001   TYR A  17 
 PHE   0.032   0.002   PHE B  36 
 TRP   0.013   0.001   TRP A 321 
 HIS   0.003   0.001   HIS A 309 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00490 /  0.20 ( 7264)
  covalent geometry    : angle       0.62347 /  0.30 ( 9770)
  hydrogen bonds       : bond        0.22037 / 14.12 (  405)
  hydrogen bonds       : angle       8.26990 /  6.20 ( 1200)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.223 
Fit side-chains
  outliers start: 22
  outliers final: 22
  residues processed: 92
  average time/residue: 0.5391
  time to fit residues: 52.0851
Evaluate side-chains
  92 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 70
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 HIS
Chi-restraints excluded: chain A residue   24 ILE
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain B residue   18 LYS
Chi-restraints excluded: chain B residue   20 HIS
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  122 ASN
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  395 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  41 HIS
A 125 GLN
A 205 HIS
A 346 GLN
B  41 HIS
B 125 GLN
B 205 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.168716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.138340 restraints weight = 7249.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 1.69
r_work: 0.3476 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3336 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7264  Z= 0.140
  Angle     :  0.592   8.098   9770  Z= 0.283
  Chirality :  0.043   0.210   1002
  Planarity :  0.004   0.032   1126
  Dihedral  : 25.276 178.619   1432
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 18.58 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.30), residues: 746
  helix:  0.71 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.72 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  22 
 TYR   0.012   0.001   TYR B 186 
 PHE   0.015   0.001   PHE A  36 
 TRP   0.016   0.001   TRP A 321 
 HIS   0.003   0.001   HIS B 172 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.14 ( 7264)
  covalent geometry    : angle       0.59177 /  0.28 ( 9770)
  hydrogen bonds       : bond        0.04290 /  2.81 (  405)
  hydrogen bonds       : angle       4.95838 /  3.61 ( 1200)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 71
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A   22 ARG cc_start: 0.7485 (ttm-80) cc_final: 0.7266 (ttm-80)
REVERT: A  162 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7585 (pp)
REVERT: A  170 PHE cc_start: 0.6594 (OUTLIER) cc_final: 0.6086 (t80)
REVERT: A  393 PHE cc_start: 0.6391 (t80) cc_final: 0.5751 (t80)
REVERT: B   22 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.7244 (ttm-80)
REVERT: B  162 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7661 (pp)
REVERT: B  308 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7343 (ttpt)
  outliers start: 29
  outliers final: 8
  residues processed: 89
  average time/residue: 0.4782
  time to fit residues: 44.8405
Evaluate side-chains
  75 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  402 MET
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  402 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 71 optimal weight:    0.0970
   chunk 36 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.9980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.168332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.138159 restraints weight = 7189.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 1.68
r_work: 0.3473 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7264  Z= 0.154
  Angle     :  0.583   8.568   9770  Z= 0.277
  Chirality :  0.044   0.221   1002
  Planarity :  0.004   0.030   1126
  Dihedral  : 24.502 179.657   1402
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 19.17 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.30), residues: 746
  helix:  1.07 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.76 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  22 
 TYR   0.010   0.001   TYR A  17 
 PHE   0.013   0.001   PHE B  21 
 TRP   0.016   0.001   TRP B 321 
 HIS   0.003   0.001   HIS B 172 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.15 ( 7264)
  covalent geometry    : angle       0.58308 /  0.28 ( 9770)
  hydrogen bonds       : bond        0.04149 /  2.71 (  405)
  hydrogen bonds       : angle       4.70125 /  3.41 ( 1200)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 65
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A   22 ARG cc_start: 0.7580 (ttm-80) cc_final: 0.7340 (ttm-80)
REVERT: A  170 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.6044 (t80)
REVERT: A  204 MET cc_start: 0.6688 (pp-130) cc_final: 0.6258 (ppp)
REVERT: A  309 HIS cc_start: 0.8016 (OUTLIER) cc_final: 0.7392 (m90)
REVERT: B   22 ARG cc_start: 0.7394 (ttm-80) cc_final: 0.7151 (ttm-80)
REVERT: B  308 LYS cc_start: 0.7848 (ttmt) cc_final: 0.7192 (ttpt)
  outliers start: 23
  outliers final: 8
  residues processed: 82
  average time/residue: 0.5267
  time to fit residues: 45.3880
Evaluate side-chains
  70 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  384 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.165991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.135437 restraints weight = 7262.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 1.70
r_work: 0.3438 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3297 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   7264  Z= 0.205
  Angle     :  0.625   7.520   9770  Z= 0.298
  Chirality :  0.046   0.239   1002
  Planarity :  0.004   0.032   1126
  Dihedral  : 24.290 178.163   1400
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 18.58 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.30), residues: 746
  helix:  1.06 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.82 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  22 
 TYR   0.012   0.001   TYR A  17 
 PHE   0.013   0.001   PHE B  21 
 TRP   0.016   0.002   TRP B 321 
 HIS   0.003   0.001   HIS B 172 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00506 /  0.21 ( 7264)
  covalent geometry    : angle       0.62502 /  0.30 ( 9770)
  hydrogen bonds       : bond        0.04411 /  2.90 (  405)
  hydrogen bonds       : angle       4.72081 /  3.41 ( 1200)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 67
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.7162 (ttm-80)
REVERT: A  162 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7644 (pp)
REVERT: A  204 MET cc_start: 0.6733 (pp-130) cc_final: 0.6164 (ppp)
REVERT: A  309 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7502 (m90)
REVERT: A  346 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7552 (mm110)
REVERT: A  393 PHE cc_start: 0.6564 (t80) cc_final: 0.5950 (t80)
REVERT: B   18 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.6259 (mtpp)
REVERT: B  308 LYS cc_start: 0.7796 (ttmt) cc_final: 0.7148 (ttpt)
  outliers start: 28
  outliers final: 16
  residues processed: 89
  average time/residue: 0.4610
  time to fit residues: 43.1993
Evaluate side-chains
  84 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain B residue   18 LYS
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  384 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 48 optimal weight:    0.2980
   chunk 15 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0370
   chunk 60 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 31 optimal weight:    0.3980
   overall best weight:    0.4258

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.171650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.142659 restraints weight = 7233.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 1.60
r_work: 0.3524 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3384 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7264  Z= 0.103
  Angle     :  0.528  11.647   9770  Z= 0.249
  Chirality :  0.041   0.215   1002
  Planarity :  0.003   0.029   1126
  Dihedral  : 22.978 179.845   1397
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 20.50 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.30), residues: 746
  helix:  1.52 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.79 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  22 
 TYR   0.008   0.001   TYR A  17 
 PHE   0.008   0.001   PHE B  21 
 TRP   0.018   0.001   TRP B 321 
 HIS   0.003   0.001   HIS B 172 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00227 /  0.10 ( 7264)
  covalent geometry    : angle       0.52805 /  0.25 ( 9770)
  hydrogen bonds       : bond        0.03398 /  2.22 (  405)
  hydrogen bonds       : angle       4.38408 /  3.16 ( 1200)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A   22 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.7309 (ttm-80)
REVERT: A  170 PHE cc_start: 0.6661 (OUTLIER) cc_final: 0.6076 (t80)
REVERT: A  309 HIS cc_start: 0.7838 (OUTLIER) cc_final: 0.7403 (m90)
REVERT: A  393 PHE cc_start: 0.6498 (t80) cc_final: 0.5902 (t80)
REVERT: B  308 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7398 (ttpp)
  outliers start: 19
  outliers final: 4
  residues processed: 77
  average time/residue: 0.4639
  time to fit residues: 37.6086
Evaluate side-chains
  63 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  384 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0270
   chunk 2 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.5438

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.171368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.142524 restraints weight = 7236.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 1.60
r_work: 0.3528 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3390 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7264  Z= 0.111
  Angle     :  0.537  10.501   9770  Z= 0.253
  Chirality :  0.042   0.210   1002
  Planarity :  0.003   0.028   1126
  Dihedral  : 22.638 178.471   1397
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 20.80 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.30), residues: 746
  helix:  1.65 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.74 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  22 
 TYR   0.014   0.001   TYR A 186 
 PHE   0.025   0.001   PHE B  36 
 TRP   0.017   0.001   TRP B 321 
 HIS   0.002   0.001   HIS B 172 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.11 ( 7264)
  covalent geometry    : angle       0.53674 /  0.25 ( 9770)
  hydrogen bonds       : bond        0.03429 /  2.26 (  405)
  hydrogen bonds       : angle       4.29953 /  3.10 ( 1200)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   22 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7314 (ttm-80)
REVERT: A  170 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.6126 (t80)
REVERT: A  309 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7427 (m90)
REVERT: A  393 PHE cc_start: 0.6436 (t80) cc_final: 0.5902 (t80)
REVERT: A  399 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6222 (mp)
REVERT: B  308 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7221 (ttpt)
  outliers start: 15
  outliers final: 9
  residues processed: 71
  average time/residue: 0.4567
  time to fit residues: 34.1750
Evaluate side-chains
  67 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  384 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 63 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.168444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.139138 restraints weight = 7219.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 1.59
r_work: 0.3481 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3345 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7264  Z= 0.159
  Angle     :  0.589  10.419   9770  Z= 0.278
  Chirality :  0.044   0.226   1002
  Planarity :  0.003   0.028   1126
  Dihedral  : 22.991 179.955   1396
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.35 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.30), residues: 746
  helix:  1.53 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.74 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 184 
 TYR   0.013   0.001   TYR A 186 
 PHE   0.023   0.001   PHE A  36 
 TRP   0.015   0.001   TRP B 321 
 HIS   0.002   0.001   HIS B 172 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.16 ( 7264)
  covalent geometry    : angle       0.58920 /  0.28 ( 9770)
  hydrogen bonds       : bond        0.03912 /  2.57 (  405)
  hydrogen bonds       : angle       4.40161 /  3.18 ( 1200)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A  170 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.6096 (t80)
REVERT: A  184 ARG cc_start: 0.7739 (tpt170) cc_final: 0.7425 (tmt-80)
REVERT: A  309 HIS cc_start: 0.8070 (OUTLIER) cc_final: 0.7517 (m90)
REVERT: A  393 PHE cc_start: 0.6418 (t80) cc_final: 0.5917 (t80)
REVERT: A  399 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6093 (mp)
REVERT: B   24 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8185 (tp)
REVERT: B  308 LYS cc_start: 0.7868 (ttmt) cc_final: 0.7209 (ttpt)
REVERT: B  399 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6098 (mp)
  outliers start: 21
  outliers final: 8
  residues processed: 73
  average time/residue: 0.4599
  time to fit residues: 35.2602
Evaluate side-chains
  68 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 38 optimal weight:    0.0060
   chunk 42 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 63 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.6998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.170370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.141235 restraints weight = 7310.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 1.61
r_work: 0.3504 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7264  Z= 0.121
  Angle     :  0.551  10.745   9770  Z= 0.259
  Chirality :  0.042   0.212   1002
  Planarity :  0.003   0.028   1126
  Dihedral  : 22.621 178.724   1396
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 21.24 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.30), residues: 746
  helix:  1.66 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.81 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 184 
 TYR   0.013   0.001   TYR A 186 
 PHE   0.028   0.001   PHE B  36 
 TRP   0.017   0.001   TRP B 321 
 HIS   0.002   0.001   HIS B 172 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.12 ( 7264)
  covalent geometry    : angle       0.55073 /  0.26 ( 9770)
  hydrogen bonds       : bond        0.03548 /  2.33 (  405)
  hydrogen bonds       : angle       4.29221 /  3.10 ( 1200)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 52
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  170 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.6060 (t80)
REVERT: A  184 ARG cc_start: 0.7750 (tpt170) cc_final: 0.7442 (tmt-80)
REVERT: A  309 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7498 (m90)
REVERT: A  393 PHE cc_start: 0.6376 (t80) cc_final: 0.5876 (t80)
REVERT: A  399 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6140 (mp)
REVERT: B  308 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7171 (ttpt)
REVERT: B  399 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6054 (mp)
  outliers start: 18
  outliers final: 11
  residues processed: 67
  average time/residue: 0.4175
  time to fit residues: 29.5297
Evaluate side-chains
  67 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 18 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 68 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.170336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.141337 restraints weight = 7228.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 1.58
r_work: 0.3504 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7264  Z= 0.126
  Angle     :  0.561  11.434   9770  Z= 0.263
  Chirality :  0.042   0.213   1002
  Planarity :  0.003   0.028   1126
  Dihedral  : 22.428 179.990   1396
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 21.09 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.30), residues: 746
  helix:  1.67 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.80 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 184 
 TYR   0.014   0.001   TYR A 186 
 PHE   0.009   0.001   PHE B  79 
 TRP   0.017   0.001   TRP A 321 
 HIS   0.002   0.001   HIS B 172 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 7264)
  covalent geometry    : angle       0.56091 /  0.26 ( 9770)
  hydrogen bonds       : bond        0.03583 /  2.35 (  405)
  hydrogen bonds       : angle       4.27980 /  3.09 ( 1200)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A  170 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.6113 (t80)
REVERT: A  184 ARG cc_start: 0.7713 (tpt170) cc_final: 0.7417 (tmt-80)
REVERT: A  309 HIS cc_start: 0.7936 (OUTLIER) cc_final: 0.7481 (m90)
REVERT: A  393 PHE cc_start: 0.6400 (t80) cc_final: 0.5902 (t80)
REVERT: A  399 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.5869 (mp)
REVERT: B  308 LYS cc_start: 0.7926 (ttmt) cc_final: 0.7164 (ttpt)
REVERT: B  399 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6015 (mp)
  outliers start: 19
  outliers final: 12
  residues processed: 69
  average time/residue: 0.4450
  time to fit residues: 32.5076
Evaluate side-chains
  68 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   36 PHE
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0870
   chunk 59 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 13 optimal weight:    9.9990
   chunk 71 optimal weight:    0.5980
   chunk 19 optimal weight:    5.9990
   overall best weight:    0.6158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.170860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.141136 restraints weight = 7227.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 1.65
r_work: 0.3509 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7264  Z= 0.117
  Angle     :  0.558  11.423   9770  Z= 0.261
  Chirality :  0.042   0.208   1002
  Planarity :  0.003   0.028   1126
  Dihedral  : 22.228 179.857   1396
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 21.83 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.30), residues: 746
  helix:  1.72 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.79 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 184 
 TYR   0.012   0.001   TYR A 186 
 PHE   0.008   0.001   PHE B  36 
 TRP   0.017   0.001   TRP A 321 
 HIS   0.002   0.001   HIS B 172 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 ( 7264)
  covalent geometry    : angle       0.55819 /  0.26 ( 9770)
  hydrogen bonds       : bond        0.03495 /  2.29 (  405)
  hydrogen bonds       : angle       4.25101 /  3.07 ( 1200)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 51
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A  170 PHE cc_start: 0.6625 (OUTLIER) cc_final: 0.6034 (t80)
REVERT: A  184 ARG cc_start: 0.7664 (tpt170) cc_final: 0.7369 (tmt-80)
REVERT: A  309 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7462 (m90)
REVERT: A  393 PHE cc_start: 0.6307 (t80) cc_final: 0.5816 (t80)
REVERT: A  399 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.5889 (mp)
REVERT: B   36 PHE cc_start: 0.7845 (t80) cc_final: 0.7621 (t80)
REVERT: B  308 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7052 (ttpt)
REVERT: B  399 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.5942 (mp)
  outliers start: 16
  outliers final: 11
  residues processed: 65
  average time/residue: 0.4950
  time to fit residues: 33.8813
Evaluate side-chains
  66 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 40 optimal weight:    0.3980
   chunk 69 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.167002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.136680 restraints weight = 7291.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 1.68
r_work: 0.3487 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7264  Z= 0.147
  Angle     :  0.587  10.844   9770  Z= 0.275
  Chirality :  0.043   0.219   1002
  Planarity :  0.003   0.031   1126
  Dihedral  : 22.388 179.728   1396
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 21.98 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.30), residues: 746
  helix:  1.60 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.78 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 184 
 TYR   0.013   0.001   TYR A 186 
 PHE   0.010   0.001   PHE B  79 
 TRP   0.015   0.001   TRP A 321 
 HIS   0.002   0.001   HIS B 172 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.15 ( 7264)
  covalent geometry    : angle       0.58651 /  0.28 ( 9770)
  hydrogen bonds       : bond        0.03786 /  2.49 (  405)
  hydrogen bonds       : angle       4.32263 /  3.13 ( 1200)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1807.79 seconds
wall clock time: 31 minutes 31.18 seconds (1891.18 seconds total)