Starting phenix.real_space_refine
on Mon Apr 28 05:29:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kqj_62506/04_2025/9kqj_62506.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kqj_62506/04_2025/9kqj_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_62506/04_2025/9kqj_62506.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kqj_62506/04_2025/9kqj_62506.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kqj_62506/04_2025/9kqj_62506.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kqj_62506/04_2025/9kqj_62506.cif"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.28, per 1000 atoms: 0.75
  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: 2.37
  Conformation dependent library (CDL) restraints added in 750.2 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: 0.59
  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: 1.67

  Time building geometry restraints manager: 2.57 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: 3998
       35.64 -    71.29: 239
       71.29 -   106.93: 44
      106.93 -   142.58: 20
      142.58 -   178.22: 13
  Dihedral angle restraints: 4314
    sinusoidal: 2096
      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 4311 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 658
       0.038 -    0.076: 271
       0.076 -    0.113: 58
       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 8.94e-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 8.73e-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: 0.03
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:             0.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.880
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  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:11.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
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  : 26.546 178.222   2878
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 9.36
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.013   0.001   TRP A 321 
 HIS   0.003   0.001   HIS A 309 
 PHE   0.032   0.002   PHE B  36 
 TYR   0.015   0.001   TYR A  17 
 ARG   0.009   0.001   ARG B  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22037 (  405)
  hydrogen bonds       : angle       8.26990 ( 1200)
  covalent geometry    : bond        0.00490 ( 7264)
  covalent geometry    : angle       0.62347 ( 9770)

*********************** 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  : 0.807 
Fit side-chains
  outliers start: 22
  outliers final: 22
  residues processed: 92
  average time/residue: 1.3685
  time to fit residues: 132.1931
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  : 0.704 
-------------------------------------------------------------------------------
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 62 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3881 r_free = 0.3881 target = 0.165840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.135073 restraints weight = 7185.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 1.69
r_work: 0.3463 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.1174

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= 0.150
  Angle     :  0.604   8.475   9770  Z= 0.291
  Chirality :  0.043   0.265   1002
  Planarity :  0.004   0.034   1126
  Dihedral  : 26.580 178.474   1506
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 19.03 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.30), residues: 746
  helix:  0.69 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.72 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 321 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.017   0.001   PHE B  36 
 TYR   0.011   0.001   TYR A  17 
 ARG   0.007   0.001   ARG B  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04465 (  405)
  hydrogen bonds       : angle       4.98259 ( 1200)
  covalent geometry    : bond        0.00350 ( 7264)
  covalent geometry    : angle       0.60416 ( 9770)

*********************** 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
  94 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A   24 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8297 (tp)
REVERT: A  162 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7595 (pp)
REVERT: A  170 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.6074 (t80)
REVERT: A  393 PHE cc_start: 0.6428 (t80) cc_final: 0.5799 (t80)
REVERT: B   22 ARG cc_start: 0.7578 (ttm-80) cc_final: 0.7245 (ttm-80)
REVERT: B  162 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7673 (pp)
REVERT: B  308 LYS cc_start: 0.7924 (ttmt) cc_final: 0.7325 (ttpt)
  outliers start: 26
  outliers final: 8
  residues processed: 84
  average time/residue: 1.1895
  time to fit residues: 105.7276
Evaluate side-chains
  75 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ILE
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  103 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 45 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.169746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.139462 restraints weight = 7218.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 1.69
r_work: 0.3487 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7264  Z= 0.128
  Angle     :  0.540   9.201   9770  Z= 0.259
  Chirality :  0.041   0.242   1002
  Planarity :  0.004   0.029   1126
  Dihedral  : 25.369 179.225   1475
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 19.03 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.30), residues: 746
  helix:  1.19 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.74 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 321 
 HIS   0.003   0.001   HIS B 172 
 PHE   0.012   0.001   PHE B  21 
 TYR   0.009   0.001   TYR A  17 
 ARG   0.005   0.000   ARG B  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03857 (  405)
  hydrogen bonds       : angle       4.58706 ( 1200)
  covalent geometry    : bond        0.00302 ( 7264)
  covalent geometry    : angle       0.53979 ( 9770)

*********************** 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
  97 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 68
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.6670 (pp-130) cc_final: 0.6225 (ppp)
REVERT: A  309 HIS cc_start: 0.8003 (OUTLIER) cc_final: 0.7459 (m90)
REVERT: A  346 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7547 (mm110)
REVERT: A  393 PHE cc_start: 0.6237 (t80) cc_final: 0.5730 (t80)
REVERT: B   22 ARG cc_start: 0.7421 (ttm-80) cc_final: 0.7170 (ttm-80)
REVERT: B  308 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7211 (ttpt)
  outliers start: 29
  outliers final: 8
  residues processed: 86
  average time/residue: 1.3187
  time to fit residues: 119.8768
Evaluate side-chains
  73 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  346 GLN
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 23 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   chunk 27 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 65 optimal weight:    0.1980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.170698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.141434 restraints weight = 7248.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 1.60
r_work: 0.3493 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.1741

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= 0.119
  Angle     :  0.523   9.523   9770  Z= 0.252
  Chirality :  0.041   0.225   1002
  Planarity :  0.003   0.028   1126
  Dihedral  : 24.546 178.976   1471
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.06 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.30), residues: 746
  helix:  1.44 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.73 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 321 
 HIS   0.003   0.001   HIS B 172 
 PHE   0.009   0.001   PHE B  21 
 TYR   0.008   0.001   TYR A  17 
 ARG   0.004   0.000   ARG B  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03590 (  405)
  hydrogen bonds       : angle       4.42672 ( 1200)
  covalent geometry    : bond        0.00280 ( 7264)
  covalent geometry    : angle       0.52342 ( 9770)

*********************** 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
  85 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.697 
Fit side-chains
REVERT: A  170 PHE cc_start: 0.6614 (OUTLIER) cc_final: 0.6008 (t80)
REVERT: A  309 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.7436 (m90)
REVERT: A  346 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7604 (mm110)
REVERT: B  308 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7239 (ttpt)
  outliers start: 21
  outliers final: 8
  residues processed: 77
  average time/residue: 1.2848
  time to fit residues: 104.4479
Evaluate side-chains
  71 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
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  309 HIS
Chi-restraints excluded: chain A residue  346 GLN
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  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 5 optimal weight:    0.0770
   chunk 20 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 12 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    1.4146

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

Flipped N/Q/H residues before XYZ refinement:
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.157545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.126189 restraints weight = 7312.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 1.71
r_work: 0.3445 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.1604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   7264  Z= 0.196
  Angle     :  0.607   9.627   9770  Z= 0.291
  Chirality :  0.044   0.252   1002
  Planarity :  0.004   0.029   1126
  Dihedral  : 24.886 178.956   1471
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 19.91 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.30), residues: 746
  helix:  1.28 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.76 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 321 
 HIS   0.003   0.001   HIS B 172 
 PHE   0.022   0.001   PHE B  36 
 TYR   0.016   0.001   TYR A 186 
 ARG   0.003   0.001   ARG B  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04239 (  405)
  hydrogen bonds       : angle       4.56786 ( 1200)
  covalent geometry    : bond        0.00485 ( 7264)
  covalent geometry    : angle       0.60744 ( 9770)

*********************** 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: 18
    poor density    : 63
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
REVERT: A  346 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7554 (mm110)
REVERT: A  393 PHE cc_start: 0.6334 (t80) cc_final: 0.5793 (t80)
REVERT: B  308 LYS cc_start: 0.7753 (ttmt) cc_final: 0.7028 (ttpt)
  outliers start: 18
  outliers final: 11
  residues processed: 78
  average time/residue: 1.2647
  time to fit residues: 104.0168
Evaluate side-chains
  72 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
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  275 VAL
Chi-restraints excluded: chain A residue  346 GLN
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0050
   chunk 68 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.170837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.141699 restraints weight = 7247.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 1.61
r_work: 0.3352 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.1892

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= 0.113
  Angle     :  0.536  10.469   9770  Z= 0.255
  Chirality :  0.041   0.228   1002
  Planarity :  0.003   0.028   1126
  Dihedral  : 24.171 178.981   1471
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 20.50 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.30), residues: 746
  helix:  1.58 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.77 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 321 
 HIS   0.002   0.001   HIS B 172 
 PHE   0.008   0.001   PHE B  21 
 TYR   0.013   0.001   TYR A 186 
 ARG   0.003   0.000   ARG B  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03515 (  405)
  hydrogen bonds       : angle       4.34285 ( 1200)
  covalent geometry    : bond        0.00262 ( 7264)
  covalent geometry    : angle       0.53642 ( 9770)

*********************** 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: 16
    poor density    : 58
  time to evaluate  : 0.673 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8204 (mt-10)
REVERT: A  170 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.5860 (t80)
REVERT: A  309 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7406 (m90)
REVERT: A  393 PHE cc_start: 0.6340 (t80) cc_final: 0.5777 (t80)
REVERT: B  130 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7647 (ptp)
REVERT: B  308 LYS cc_start: 0.7689 (ttmt) cc_final: 0.6943 (ttpt)
REVERT: B  399 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.5812 (mp)
  outliers start: 16
  outliers final: 6
  residues processed: 71
  average time/residue: 1.2883
  time to fit residues: 96.4975
Evaluate side-chains
  66 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
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   24 ILE
Chi-restraints excluded: chain B residue   94 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  384 VAL
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0170
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.171122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.142025 restraints weight = 7137.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.59
r_work: 0.3306 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7264  Z= 0.116
  Angle     :  0.538  11.891   9770  Z= 0.255
  Chirality :  0.041   0.216   1002
  Planarity :  0.003   0.027   1126
  Dihedral  : 23.859 179.997   1470
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 20.80 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.30), residues: 746
  helix:  1.67 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.74 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 321 
 HIS   0.002   0.001   HIS B 172 
 PHE   0.026   0.001   PHE B  36 
 TYR   0.013   0.001   TYR A 186 
 ARG   0.005   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03477 (  405)
  hydrogen bonds       : angle       4.28013 ( 1200)
  covalent geometry    : bond        0.00272 ( 7264)
  covalent geometry    : angle       0.53760 ( 9770)

*********************** 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
  71 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.632 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8161 (mt-10)
REVERT: A  162 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7605 (pp)
REVERT: A  170 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.5869 (t80)
REVERT: A  184 ARG cc_start: 0.7563 (tpt170) cc_final: 0.7215 (tmt-80)
REVERT: A  309 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7426 (m90)
REVERT: A  346 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7344 (mm110)
REVERT: A  393 PHE cc_start: 0.6119 (t80) cc_final: 0.5604 (t80)
REVERT: B  308 LYS cc_start: 0.7565 (ttmt) cc_final: 0.6806 (ttpt)
  outliers start: 16
  outliers final: 7
  residues processed: 68
  average time/residue: 1.2215
  time to fit residues: 87.8161
Evaluate side-chains
  65 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
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  205 HIS
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   94 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  384 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.160929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.129834 restraints weight = 7283.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 1.71
r_work: 0.3488 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3346 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7264  Z= 0.131
  Angle     :  0.552  10.705   9770  Z= 0.262
  Chirality :  0.041   0.215   1002
  Planarity :  0.003   0.027   1126
  Dihedral  : 23.660 179.385   1470
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 21.24 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.30), residues: 746
  helix:  1.63 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.77 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 321 
 HIS   0.002   0.001   HIS B 172 
 PHE   0.010   0.001   PHE A  79 
 TYR   0.011   0.001   TYR A 186 
 ARG   0.005   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03642 (  405)
  hydrogen bonds       : angle       4.30635 ( 1200)
  covalent geometry    : bond        0.00314 ( 7264)
  covalent geometry    : angle       0.55151 ( 9770)

*********************** 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: 16
    poor density    : 54
  time to evaluate  : 0.677 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8260 (mt-10)
REVERT: A  162 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7598 (pp)
REVERT: A  170 PHE cc_start: 0.6538 (OUTLIER) cc_final: 0.5932 (t80)
REVERT: A  184 ARG cc_start: 0.7586 (tpt170) cc_final: 0.7288 (tmt-80)
REVERT: A  309 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7466 (m90)
REVERT: A  346 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7405 (mm110)
REVERT: A  393 PHE cc_start: 0.6228 (t80) cc_final: 0.5759 (t80)
REVERT: B  308 LYS cc_start: 0.7724 (ttmt) cc_final: 0.6986 (ttpt)
REVERT: B  399 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.5838 (mp)
  outliers start: 16
  outliers final: 7
  residues processed: 67
  average time/residue: 1.1898
  time to fit residues: 84.4963
Evaluate side-chains
  64 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
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  205 HIS
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain B residue   94 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  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 2 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0050
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.171858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.142086 restraints weight = 7223.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 1.67
r_work: 0.3518 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2179

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= 0.114
  Angle     :  0.543  11.700   9770  Z= 0.255
  Chirality :  0.040   0.196   1002
  Planarity :  0.003   0.027   1126
  Dihedral  : 22.833 178.861   1470
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 21.83 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.30), residues: 746
  helix:  1.75 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.80 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 321 
 HIS   0.002   0.001   HIS B 172 
 PHE   0.031   0.001   PHE B  36 
 TYR   0.012   0.001   TYR A 186 
 ARG   0.004   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03419 (  405)
  hydrogen bonds       : angle       4.22516 ( 1200)
  covalent geometry    : bond        0.00270 ( 7264)
  covalent geometry    : angle       0.54257 ( 9770)

*********************** 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
  68 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.635 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8293 (mt-10)
REVERT: A  162 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7543 (pp)
REVERT: A  170 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.6002 (t80)
REVERT: A  184 ARG cc_start: 0.7574 (tpt170) cc_final: 0.7277 (tmt-80)
REVERT: A  309 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7505 (m90)
REVERT: A  393 PHE cc_start: 0.6210 (t80) cc_final: 0.5742 (t80)
REVERT: A  399 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.5777 (mp)
REVERT: B  308 LYS cc_start: 0.7748 (ttmt) cc_final: 0.7212 (ttpp)
  outliers start: 14
  outliers final: 5
  residues processed: 65
  average time/residue: 1.2846
  time to fit residues: 88.2482
Evaluate side-chains
  63 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
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  205 HIS
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  384 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0770
   chunk 59 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.172151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.142250 restraints weight = 7276.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 1.68
r_work: 0.3519 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.2195

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= 0.114
  Angle     :  0.549  11.634   9770  Z= 0.258
  Chirality :  0.040   0.185   1002
  Planarity :  0.003   0.026   1126
  Dihedral  : 22.178 178.330   1470
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 21.98 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.30), residues: 746
  helix:  1.77 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.79 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 321 
 HIS   0.002   0.001   HIS B 172 
 PHE   0.008   0.001   PHE A  48 
 TYR   0.012   0.001   TYR A 186 
 ARG   0.005   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03465 (  405)
  hydrogen bonds       : angle       4.22818 ( 1200)
  covalent geometry    : bond        0.00270 ( 7264)
  covalent geometry    : angle       0.54851 ( 9770)

********************** 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: 14
    poor density    : 53
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8286 (mt-10)
REVERT: A  162 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7540 (pp)
REVERT: A  170 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.6013 (t80)
REVERT: A  184 ARG cc_start: 0.7549 (tpt170) cc_final: 0.7283 (tmt-80)
REVERT: A  309 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7493 (m90)
REVERT: A  346 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7515 (mm110)
REVERT: A  393 PHE cc_start: 0.6165 (t80) cc_final: 0.5692 (t80)
REVERT: A  399 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.5833 (mp)
REVERT: B  308 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7018 (ttpt)
REVERT: B  399 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.5730 (mp)
  outliers start: 14
  outliers final: 5
  residues processed: 64
  average time/residue: 1.2293
  time to fit residues: 83.3443
Evaluate side-chains
  64 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
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  205 HIS
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  205 HIS
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 58 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0370
   chunk 55 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 17 optimal weight:    0.1980
   overall best weight:    0.8262

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

Flipped N/Q/H residues before XYZ refinement:
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.170378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.140575 restraints weight = 7191.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 1.65
r_work: 0.3504 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7264  Z= 0.134
  Angle     :  0.567  11.206   9770  Z= 0.267
  Chirality :  0.041   0.189   1002
  Planarity :  0.003   0.026   1126
  Dihedral  : 22.300 179.199   1470
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 22.57 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.30), residues: 746
  helix:  1.68 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.80 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 321 
 HIS   0.002   0.001   HIS B 172 
 PHE   0.033   0.001   PHE B  36 
 TYR   0.015   0.001   TYR B 186 
 ARG   0.005   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03670 (  405)
  hydrogen bonds       : angle       4.27398 ( 1200)
  covalent geometry    : bond        0.00324 ( 7264)
  covalent geometry    : angle       0.56653 ( 9770)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4531.44 seconds
wall clock time: 78 minutes 17.31 seconds (4697.31 seconds total)