Starting phenix.real_space_refine
on Sat May 10 22:56:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kqj_62506/05_2025/9kqj_62506.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kqj_62506/05_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_62506/05_2025/9kqj_62506.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kqj_62506/05_2025/9kqj_62506.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kqj_62506/05_2025/9kqj_62506.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kqj_62506/05_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-5687/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: 4.94, per 1000 atoms: 0.70
  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: 2.45
  Conformation dependent library (CDL) restraints added in 655.7 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: 0.53
  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: 1.59

  Time building geometry restraints manager: 2.22 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:             0.710
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.380
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:14.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.940
-------------------------------------------------------------------------------
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  : 0.717 
Fit side-chains
  outliers start: 22
  outliers final: 22
  residues processed: 92
  average time/residue: 1.3417
  time to fit residues: 129.8058
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  : 0.628 
-------------------------------------------------------------------------------
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 = 0.135071 restraints weight = 7185.656|
|-----------------------------------------------------------------------------|
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: 4.49 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
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  : 0.731 
Fit side-chains
REVERT: A   24 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8296 (tp)
REVERT: A  162 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7592 (pp)
REVERT: A  170 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.6067 (t80)
REVERT: A  393 PHE cc_start: 0.6422 (t80) cc_final: 0.5793 (t80)
REVERT: B   22 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.7242 (ttm-80)
REVERT: B  162 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7675 (pp)
REVERT: B  308 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7316 (ttpt)
  outliers start: 26
  outliers final: 8
  residues processed: 84
  average time/residue: 1.2580
  time to fit residues: 111.8513
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  : 0.666 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.3918 r_free = 0.3918 target = 0.168883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.138533 restraints weight = 7228.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.69
r_work: 0.3482 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3340 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7264  Z= 0.138
  Angle     :  0.550   8.706   9770  Z= 0.265
  Chirality :  0.042   0.244   1002
  Planarity :  0.004   0.029   1126
  Dihedral  : 25.509 179.341   1475
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 18.88 %
    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:  0.92 (0.30), residues: 746
  helix:  1.14 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.73 (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   0.010   0.001   TYR A  17 
 ARG   0.006   0.000   ARG B  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (  405)
  hydrogen bonds       : angle       4.63321 ( 1200)
  covalent geometry    : bond        0.00329 ( 7264)
  covalent geometry    : angle       0.55035 ( 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  : 0.618 
Fit side-chains
REVERT: A  170 PHE cc_start: 0.6524 (OUTLIER) cc_final: 0.6206 (t80)
REVERT: A  204 MET cc_start: 0.6668 (pp-130) cc_final: 0.6230 (ppp)
REVERT: A  309 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7443 (m90)
REVERT: A  346 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7558 (mm110)
REVERT: A  393 PHE cc_start: 0.6399 (t80) cc_final: 0.5843 (t80)
REVERT: B   22 ARG cc_start: 0.7400 (ttm-80) cc_final: 0.7154 (ttm-80)
REVERT: B  308 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7210 (ttpt)
  outliers start: 29
  outliers final: 8
  residues processed: 86
  average time/residue: 1.3270
  time to fit residues: 120.2519
Evaluate side-chains
  72 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
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  265 LEU
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:    4.9990
   chunk 18 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 65 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3903 r_free = 0.3903 target = 0.167157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.136524 restraints weight = 7271.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 1.70
r_work: 0.3457 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7264  Z= 0.174
  Angle     :  0.580   8.225   9770  Z= 0.280
  Chirality :  0.043   0.244   1002
  Planarity :  0.004   0.030   1126
  Dihedral  : 25.125 179.037   1471
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 19.17 %
    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:  1.00 (0.30), residues: 746
  helix:  1.21 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.75 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 321 
 HIS   0.003   0.001   HIS B 172 
 PHE   0.013   0.001   PHE B  21 
 TYR   0.010   0.001   TYR A  17 
 ARG   0.004   0.000   ARG B  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04131 (  405)
  hydrogen bonds       : angle       4.61315 ( 1200)
  covalent geometry    : bond        0.00425 ( 7264)
  covalent geometry    : angle       0.57958 ( 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
  91 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 66
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8251 (mt-10)
REVERT: A  204 MET cc_start: 0.6723 (pp-130) cc_final: 0.6517 (ppp)
REVERT: A  346 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7614 (mm110)
REVERT: B  308 LYS cc_start: 0.7848 (ttmt) cc_final: 0.7131 (ttpt)
  outliers start: 25
  outliers final: 12
  residues processed: 83
  average time/residue: 1.2480
  time to fit residues: 109.3720
Evaluate side-chains
  78 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
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  275 VAL
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain B residue   33 THR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.155009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.123420 restraints weight = 7347.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 1.72
r_work: 0.3425 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   7264  Z= 0.237
  Angle     :  0.650   9.010   9770  Z= 0.312
  Chirality :  0.046   0.267   1002
  Planarity :  0.004   0.032   1126
  Dihedral  : 25.447 176.973   1471
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 20.35 %
    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:  0.74 (0.29), residues: 746
  helix:  1.01 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.82 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 321 
 HIS   0.003   0.001   HIS A 246 
 PHE   0.021   0.002   PHE B  36 
 TYR   0.013   0.001   TYR A  17 
 ARG   0.003   0.001   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04636 (  405)
  hydrogen bonds       : angle       4.74948 ( 1200)
  covalent geometry    : bond        0.00587 ( 7264)
  covalent geometry    : angle       0.65020 ( 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
  89 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 64
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8224 (mt-10)
REVERT: A  162 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7674 (pp)
REVERT: A  204 MET cc_start: 0.6805 (pp-130) cc_final: 0.6352 (pp-130)
REVERT: A  278 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7727 (m-80)
REVERT: A  346 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7583 (mm110)
REVERT: A  393 PHE cc_start: 0.6467 (t80) cc_final: 0.5856 (t80)
REVERT: B  162 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7532 (pp)
REVERT: B  204 MET cc_start: 0.6809 (pp-130) cc_final: 0.6396 (pp-130)
REVERT: B  278 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7665 (m-80)
REVERT: B  308 LYS cc_start: 0.7800 (ttmt) cc_final: 0.7125 (ttpt)
  outliers start: 25
  outliers final: 13
  residues processed: 84
  average time/residue: 1.2657
  time to fit residues: 112.1005
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  : 0.694 
-------------------------------------------------------------------------------
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  162 ILE
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  278 PHE
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  384 VAL
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  275 VAL
Chi-restraints excluded: chain B residue  278 PHE
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:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 66 optimal weight:    0.4980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3786 r_free = 0.3786 target = 0.159795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.128611 restraints weight = 7337.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.71
r_work: 0.3481 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3340 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7264  Z= 0.131
  Angle     :  0.547  10.058   9770  Z= 0.263
  Chirality :  0.042   0.237   1002
  Planarity :  0.003   0.031   1126
  Dihedral  : 24.665 178.799   1471
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 21.24 %
    Favored  : 75.52 %
  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:  1.20 (0.30), residues: 746
  helix:  1.38 (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   0.018   0.001   TRP B 321 
 HIS   0.003   0.001   HIS B 172 
 PHE   0.021   0.001   PHE A  36 
 TYR   0.010   0.001   TYR A  17 
 ARG   0.003   0.000   ARG A  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03768 (  405)
  hydrogen bonds       : angle       4.48510 ( 1200)
  covalent geometry    : bond        0.00311 ( 7264)
  covalent geometry    : angle       0.54726 ( 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
  86 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 64
  time to evaluate  : 0.605 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8244 (mt-10)
REVERT: A  170 PHE cc_start: 0.6534 (OUTLIER) cc_final: 0.6066 (t80)
REVERT: A  204 MET cc_start: 0.6654 (pp-130) cc_final: 0.6265 (pp-130)
REVERT: A  309 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.7519 (m90)
REVERT: A  393 PHE cc_start: 0.6473 (t80) cc_final: 0.5890 (t80)
REVERT: B  204 MET cc_start: 0.6715 (pp-130) cc_final: 0.6325 (pp-130)
REVERT: B  308 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7056 (ttpt)
REVERT: B  399 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.5999 (mp)
  outliers start: 22
  outliers final: 11
  residues processed: 81
  average time/residue: 1.2237
  time to fit residues: 104.5166
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  : 0.658 
-------------------------------------------------------------------------------
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  268 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain B residue   33 THR
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  275 VAL
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=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:    0.6980
   chunk 4 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 41 optimal weight:    0.3980
   chunk 21 optimal weight:    0.3980
   chunk 18 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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**
B 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.171338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.142366 restraints weight = 7135.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 1.59
r_work: 0.3429 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7264  Z= 0.109
  Angle     :  0.529  11.942   9770  Z= 0.253
  Chirality :  0.040   0.216   1002
  Planarity :  0.003   0.029   1126
  Dihedral  : 23.991 179.942   1471
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 22.27 %
    Favored  : 75.07 %
  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:  1.62 (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   0.018   0.001   TRP B 321 
 HIS   0.002   0.001   HIS B 172 
 PHE   0.027   0.001   PHE B  36 
 TYR   0.013   0.001   TYR A 186 
 ARG   0.003   0.000   ARG A  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03434 (  405)
  hydrogen bonds       : angle       4.32583 ( 1200)
  covalent geometry    : bond        0.00250 ( 7264)
  covalent geometry    : angle       0.52897 ( 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
  72 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 54
  time to evaluate  : 0.641 
Fit side-chains
REVERT: A  170 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.6059 (t80)
REVERT: A  204 MET cc_start: 0.6657 (pp-130) cc_final: 0.6313 (pp-130)
REVERT: A  309 HIS cc_start: 0.7891 (OUTLIER) cc_final: 0.7506 (m90)
REVERT: A  393 PHE cc_start: 0.6457 (t80) cc_final: 0.5884 (t80)
REVERT: A  399 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6053 (mp)
REVERT: B  130 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7734 (ptp)
REVERT: B  308 LYS cc_start: 0.7866 (ttmt) cc_final: 0.7253 (ttpp)
  outliers start: 18
  outliers final: 8
  residues processed: 67
  average time/residue: 1.1858
  time to fit residues: 84.2259
Evaluate side-chains
  66 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
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  268 THR
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   33 THR
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  268 THR
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:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3810 r_free = 0.3810 target = 0.161747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.130936 restraints weight = 7276.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 1.70
r_work: 0.3494 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7264  Z= 0.129
  Angle     :  0.548  10.902   9770  Z= 0.262
  Chirality :  0.041   0.229   1002
  Planarity :  0.003   0.029   1126
  Dihedral  : 23.721 178.853   1470
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 22.27 %
    Favored  : 74.93 %
  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:  1.47 (0.30), residues: 746
  helix:  1.59 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.72 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 321 
 HIS   0.002   0.001   HIS B 172 
 PHE   0.009   0.001   PHE A  79 
 TYR   0.013   0.001   TYR A 186 
 ARG   0.004   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03640 (  405)
  hydrogen bonds       : angle       4.34158 ( 1200)
  covalent geometry    : bond        0.00308 ( 7264)
  covalent geometry    : angle       0.54836 ( 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
  71 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 52
  time to evaluate  : 0.690 
Fit side-chains
REVERT: A  162 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7540 (pp)
REVERT: A  170 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.5945 (t80)
REVERT: A  184 ARG cc_start: 0.7637 (tpt170) cc_final: 0.7292 (tmt-80)
REVERT: A  204 MET cc_start: 0.6661 (pp-130) cc_final: 0.6309 (pp-130)
REVERT: A  309 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.7501 (m90)
REVERT: A  393 PHE cc_start: 0.6270 (t80) cc_final: 0.5800 (t80)
REVERT: A  399 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.5968 (mp)
REVERT: B  308 LYS cc_start: 0.7821 (ttmt) cc_final: 0.7002 (ttpt)
REVERT: B  399 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.5875 (mp)
  outliers start: 19
  outliers final: 9
  residues processed: 69
  average time/residue: 1.1810
  time to fit residues: 86.4841
Evaluate side-chains
  66 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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   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  268 THR
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:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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 = 0.3882 r_free = 0.3882 target = 0.165831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.135603 restraints weight = 7282.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 1.67
r_work: 0.3471 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.1923

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= 0.160
  Angle     :  0.581  10.495   9770  Z= 0.277
  Chirality :  0.043   0.223   1002
  Planarity :  0.004   0.033   1126
  Dihedral  : 23.742 179.558   1470
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 22.71 %
    Favored  : 74.93 %
  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:  1.33 (0.30), residues: 746
  helix:  1.49 (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   0.031   0.001   PHE B  36 
 TYR   0.017   0.001   TYR A 186 
 ARG   0.005   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  405)
  hydrogen bonds       : angle       4.40903 ( 1200)
  covalent geometry    : bond        0.00392 ( 7264)
  covalent geometry    : angle       0.58073 ( 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
  73 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8116 (mt-10)
REVERT: A  162 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7522 (pp)
REVERT: A  184 ARG cc_start: 0.7704 (tpt170) cc_final: 0.7374 (tmt-80)
REVERT: A  204 MET cc_start: 0.6663 (pp-130) cc_final: 0.6319 (pp-130)
REVERT: A  309 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7452 (m90)
REVERT: A  393 PHE cc_start: 0.6494 (t80) cc_final: 0.5921 (t80)
REVERT: A  399 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.5894 (mp)
REVERT: B  234 MET cc_start: 0.8371 (tpp) cc_final: 0.7969 (mmp)
REVERT: B  308 LYS cc_start: 0.7852 (ttmt) cc_final: 0.7031 (ttpt)
REVERT: B  399 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.5871 (mp)
  outliers start: 16
  outliers final: 10
  residues processed: 71
  average time/residue: 1.1866
  time to fit residues: 89.3899
Evaluate side-chains
  69 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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   24 ILE
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  268 THR
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 63 optimal weight:    0.6980
   chunk 49 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0020
   chunk 59 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0060
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.4004

-------------------------------------------------------------------------------
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 = 0.3927 r_free = 0.3927 target = 0.170709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.140810 restraints weight = 7285.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 1.68
r_work: 0.3527 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7264  Z= 0.100
  Angle     :  0.525  11.581   9770  Z= 0.248
  Chirality :  0.040   0.191   1002
  Planarity :  0.003   0.029   1126
  Dihedral  : 22.376 178.833   1470
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 23.30 %
    Favored  : 74.93 %
  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:  1.76 (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   0.021   0.001   TRP B 321 
 HIS   0.003   0.001   HIS B 172 
 PHE   0.008   0.001   PHE B 313 
 TYR   0.012   0.001   TYR A 186 
 ARG   0.004   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03260 (  405)
  hydrogen bonds       : angle       4.21499 ( 1200)
  covalent geometry    : bond        0.00230 ( 7264)
  covalent geometry    : angle       0.52544 ( 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
  65 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8004 (mt-10)
REVERT: A  170 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.5998 (t80)
REVERT: A  184 ARG cc_start: 0.7653 (tpt170) cc_final: 0.7307 (tmt-80)
REVERT: A  204 MET cc_start: 0.6663 (pp-130) cc_final: 0.6344 (pp-130)
REVERT: A  309 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7456 (m90)
REVERT: A  393 PHE cc_start: 0.6299 (t80) cc_final: 0.5793 (t80)
REVERT: B  308 LYS cc_start: 0.7744 (ttmt) cc_final: 0.7140 (ttpp)
  outliers start: 12
  outliers final: 8
  residues processed: 62
  average time/residue: 1.3642
  time to fit residues: 89.2472
Evaluate side-chains
  61 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
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  268 THR
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   36 PHE
Chi-restraints excluded: chain B residue  162 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0010
   chunk 65 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.6386

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.169750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.139848 restraints weight = 7194.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 1.66
r_work: 0.3518 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.2219

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= 0.116
  Angle     :  0.540  11.384   9770  Z= 0.256
  Chirality :  0.040   0.187   1002
  Planarity :  0.003   0.028   1126
  Dihedral  : 22.296 179.127   1470
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 23.30 %
    Favored  : 75.07 %
  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:  1.64 (0.30), residues: 746
  helix:  1.75 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.76 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 321 
 HIS   0.003   0.001   HIS B  97 
 PHE   0.008   0.001   PHE B  36 
 TYR   0.014   0.001   TYR A 186 
 ARG   0.005   0.000   ARG A 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03388 (  405)
  hydrogen bonds       : angle       4.23488 ( 1200)
  covalent geometry    : bond        0.00273 ( 7264)
  covalent geometry    : angle       0.54047 ( 9770)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4496.50 seconds
wall clock time: 78 minutes 10.27 seconds (4690.27 seconds total)