Starting phenix.real_space_refine
on Sat May 10 20:06:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qhp_18415/05_2025/8qhp_18415.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qhp_18415/05_2025/8qhp_18415.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qhp_18415/05_2025/8qhp_18415.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qhp_18415/05_2025/8qhp_18415.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qhp_18415/05_2025/8qhp_18415.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qhp_18415/05_2025/8qhp_18415.cif"
  }
  resolution = 2.8
  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=  -0.000 sd=   0.010
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: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      22      5.16       5
     C    4392      2.51       5
     N    1128      2.21       5
     O    1244      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 6788
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 410, 3393
          Classifications: {'peptide': 410}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 393}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 410, 3393
          Classifications: {'peptide': 410}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 393}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    236  SG  CYS A  28      36.433  38.017  33.062  1.00137.77           S
  ATOM   1644  SG  CYS A 208      33.883  39.740  30.430  1.00155.64           S
  ATOM   3629  SG  CYS B  28      36.336  40.874  90.477  1.00138.97           S
  ATOM   5037  SG  CYS B 208      37.721  38.524  92.922  1.00158.95           S

  Time building chain proxies: 4.77, per 1000 atoms: 0.70
  Number of scatterers: 6788
  At special positions: 0
  Unit cell: (67.518, 71.148, 124.872, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      22     16.00
     O    1244      8.00
     N    1128      7.00
     C    4392      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: 1.74
  Conformation dependent library (CDL) restraints added in 925.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 208 "
        pdb="ZN    ZN A 501 " - pdb=" NE2 HIS A 233 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A  28 "
      pdb="  ZN B 501 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B  28 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B 208 "
        pdb="ZN    ZN B 501 " - pdb=" ND1 HIS B 233 "


  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1520

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 8 sheets defined
      55.7% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 57
    Processing helix  chain 'A' and resid 71 through 82
    Processing helix  chain 'A' and resid 86 through 103
    Processing helix  chain 'A' and resid 113 through 116
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 145 through 148
    Processing helix  chain 'A' and resid 158 through 163
      removed outlier: 3.540A  pdb=" N   LEU A 162 " --> pdb=" O   LYS A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 217
      removed outlier: 3.974A  pdb=" N   SER A 209 " --> pdb=" O   HIS A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 3.679A  pdb=" N   PHE A 231 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 232 through 246
    Processing helix  chain 'A' and resid 275 through 281
    Processing helix  chain 'A' and resid 284 through 294
    Processing helix  chain 'A' and resid 304 through 329
    Processing helix  chain 'A' and resid 339 through 362
    Processing helix  chain 'A' and resid 365 through 387
    Processing helix  chain 'A' and resid 391 through 410
      removed outlier: 3.502A  pdb=" N   LEU A 395 " --> pdb=" O   LYS A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 418
      removed outlier: 3.715A  pdb=" N   GLU A 418 " --> pdb=" O   ASP A 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 57
    Processing helix  chain 'B' and resid 71 through 82
    Processing helix  chain 'B' and resid 84 through 103
    Processing helix  chain 'B' and resid 117 through 131
    Processing helix  chain 'B' and resid 158 through 163
      removed outlier: 3.572A  pdb=" N   LEU B 162 " --> pdb=" O   LYS B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 216
      removed outlier: 3.927A  pdb=" N   SER B 209 " --> pdb=" O   HIS B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 230
      No H-bonds generated for 'chain 'B' and resid 228 through 230'
    Processing helix  chain 'B' and resid 232 through 246
    Processing helix  chain 'B' and resid 275 through 283
    Processing helix  chain 'B' and resid 284 through 294
    Processing helix  chain 'B' and resid 304 through 332
      removed outlier: 3.710A  pdb=" N   ARG B 330 " --> pdb=" O   ARG B 326 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   ASN B 331 " --> pdb=" O   VAL B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 362
    Processing helix  chain 'B' and resid 365 through 387
    Processing helix  chain 'B' and resid 391 through 410
    Processing helix  chain 'B' and resid 412 through 418
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 65
      removed outlier: 9.433A  pdb=" N   PHE A 220 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LYS A  24 " --> pdb=" O   PHE A 220 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ASP A 221 " --> pdb=" O   TYR A 252 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   LEU A 254 " --> pdb=" O   ASP A 221 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   HIS A 223 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   THR A 256 " --> pdb=" O   HIS A 223 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   GLY A 225 " --> pdb=" O   THR A 256 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 136
      removed outlier: 6.453A  pdb=" N   ILE A 141 " --> pdb=" O   LEU A 182 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE A 180 " --> pdb=" O   PHE A 143 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 265
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 65
      removed outlier: 11.532A  pdb=" N   GLU B  22 " --> pdb=" O   PHE B 220 " (cutoff:3.500A)
      removed outlier: 8.164A  pdb=" N   ILE B 222 " --> pdb=" O   GLU B  22 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   LYS B  24 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   GLY B 224 " --> pdb=" O   LYS B  24 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   TYR B  26 " --> pdb=" O   GLY B 224 " (cutoff:3.500A)
      removed outlier: 8.652A  pdb=" N   GLY B 226 " --> pdb=" O   TYR B  26 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ASP B 221 " --> pdb=" O   TYR B 252 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   LEU B 254 " --> pdb=" O   ASP B 221 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   HIS B 223 " --> pdb=" O   LEU B 254 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   THR B 256 " --> pdb=" O   HIS B 223 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   GLY B 225 " --> pdb=" O   THR B 256 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 136
      removed outlier: 6.385A  pdb=" N   ILE B 141 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   PHE B 180 " --> pdb=" O   PHE B 143 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 264 through 265

    363 hydrogen bonds defined for protein.
    1071 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: 2.02

  Time building geometry restraints manager: 1.99 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2164
        1.34 -     1.46: 1623
        1.46 -     1.58: 3137
        1.58 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 6962
  Sorted by residual:
  bond pdb=" N   VAL B  32 "
       pdb=" CA  VAL B  32 "
    ideal  model  delta    sigma   weight residual
    1.474  1.458  0.017 1.57e-02 4.06e+03 1.15e+00
  bond pdb=" CA  VAL A  32 "
       pdb=" C   VAL A  32 "
    ideal  model  delta    sigma   weight residual
    1.526  1.535 -0.008 9.00e-03 1.23e+04 8.57e-01
  bond pdb=" CG  ARG A  51 "
       pdb=" CD  ARG A  51 "
    ideal  model  delta    sigma   weight residual
    1.520  1.498  0.022 3.00e-02 1.11e+03 5.18e-01
  bond pdb=" CG1 ILE B  93 "
       pdb=" CD1 ILE B  93 "
    ideal  model  delta    sigma   weight residual
    1.513  1.487  0.026 3.90e-02 6.57e+02 4.51e-01
  bond pdb=" C   ASP A  84 "
       pdb=" N   PRO A  85 "
    ideal  model  delta    sigma   weight residual
    1.336  1.342 -0.007 1.08e-02 8.57e+03 3.82e-01
  ... (remaining 6957 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.85: 9020
        0.85 -     1.70: 300
        1.70 -     2.56: 23
        2.56 -     3.41: 26
        3.41 -     4.26: 1
  Bond angle restraints: 9370
  Sorted by residual:
  angle pdb=" N   VAL B  32 "
        pdb=" CA  VAL B  32 "
        pdb=" C   VAL B  32 "
      ideal   model   delta    sigma   weight residual
     106.21  110.47   -4.26 1.07e+00 8.73e-01 1.58e+01
  angle pdb=" C   VAL B  32 "
        pdb=" CA  VAL B  32 "
        pdb=" CB  VAL B  32 "
      ideal   model   delta    sigma   weight residual
     113.22  110.73    2.49 1.12e+00 7.97e-01 4.93e+00
  angle pdb=" CA  VAL B  32 "
        pdb=" C   VAL B  32 "
        pdb=" O   VAL B  32 "
      ideal   model   delta    sigma   weight residual
     122.63  120.99    1.64 8.70e-01 1.32e+00 3.56e+00
  angle pdb=" CA  TYR A  44 "
        pdb=" CB  TYR A  44 "
        pdb=" CG  TYR A  44 "
      ideal   model   delta    sigma   weight residual
     113.90  111.19    2.71 1.80e+00 3.09e-01 2.27e+00
  angle pdb=" CA  TYR B  44 "
        pdb=" CB  TYR B  44 "
        pdb=" CG  TYR B  44 "
      ideal   model   delta    sigma   weight residual
     113.90  111.31    2.59 1.80e+00 3.09e-01 2.07e+00
  ... (remaining 9365 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.35: 3658
       12.35 -    24.70: 347
       24.70 -    37.05: 86
       37.05 -    49.40: 34
       49.40 -    61.75: 19
  Dihedral angle restraints: 4144
    sinusoidal: 1762
      harmonic: 2382
  Sorted by residual:
  dihedral pdb=" CA  LYS B  57 "
           pdb=" CB  LYS B  57 "
           pdb=" CG  LYS B  57 "
           pdb=" CD  LYS B  57 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.56   59.56     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  LYS A 295 "
           pdb=" CB  LYS A 295 "
           pdb=" CG  LYS A 295 "
           pdb=" CD  LYS A 295 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.96   58.96     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" CA  ARG A  51 "
           pdb=" CB  ARG A  51 "
           pdb=" CG  ARG A  51 "
           pdb=" CD  ARG A  51 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.05  -56.95     3      1.50e+01 4.44e-03 9.42e+00
  ... (remaining 4141 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 570
       0.027 -    0.054: 237
       0.054 -    0.082: 109
       0.082 -    0.109: 33
       0.109 -    0.136: 7
  Chirality restraints: 956
  Sorted by residual:
  chirality pdb=" CA  ILE B 141 "
            pdb=" N   ILE B 141 "
            pdb=" C   ILE B 141 "
            pdb=" CB  ILE B 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CA  ILE A 141 "
            pdb=" N   ILE A 141 "
            pdb=" C   ILE A 141 "
            pdb=" CB  ILE A 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.65e-01
  chirality pdb=" CA  PHE A  92 "
            pdb=" N   PHE A  92 "
            pdb=" C   PHE A  92 "
            pdb=" CB  PHE A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.52e-01
  ... (remaining 953 not shown)

  Planarity restraints: 1202
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 195 "   -0.020 5.00e-02 4.00e+02   3.03e-02 1.46e+00
        pdb=" N   PRO A 196 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 196 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 196 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 201 "    0.018 5.00e-02 4.00e+02   2.75e-02 1.21e+00
        pdb=" N   PRO A 202 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO A 202 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 202 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 148 "    0.018 5.00e-02 4.00e+02   2.70e-02 1.16e+00
        pdb=" N   PRO B 149 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO B 149 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 149 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1199 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 235
        2.72 -     3.27: 6703
        3.27 -     3.81: 11579
        3.81 -     4.36: 14304
        4.36 -     4.90: 24475
  Nonbonded interactions: 57296
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 237 "
            pdb="ZN    ZN B 501 "
     model   vdw
     2.176 2.230
  nonbonded pdb=" OG  SER B 195 "
            pdb=" O   GLY B 198 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OE1 GLU B 286 "
            pdb=" OH  TYR B 319 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" OG  SER A 335 "
            pdb=" O   ASP B 109 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OD1 ASP A 139 "
            pdb=" OH  TYR A 142 "
     model   vdw
     2.219 3.040
  ... (remaining 57291 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.840
  Find NCS groups from input model:        0.250
  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:             0.010
  Load rotamer database and sin/cos tables:12.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6968  Z= 0.105
  Angle     :  0.384   4.260   9370  Z= 0.218
  Chirality :  0.038   0.136    956
  Planarity :  0.003   0.030   1202
  Dihedral  : 11.643  61.754   2624
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.77 (0.29), residues: 812
  helix:  1.87 (0.25), residues: 424
  sheet:  0.25 (0.53), residues: 84
  loop :  0.61 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 249 
 HIS   0.001   0.000   HIS A  40 
 PHE   0.007   0.001   PHE B 356 
 TYR   0.010   0.001   TYR A  44 
 ARG   0.002   0.000   ARG A  51 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12780 (  363)
  hydrogen bonds       : angle       5.33363 ( 1071)
  metal coordination   : bond        0.00185 (    6)
  covalent geometry    : bond        0.00221 ( 6962)
  covalent geometry    : angle       0.38369 ( 9370)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.932 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.8638 (tttt) cc_final: 0.8371 (tppt)
REVERT: A  185 LYS cc_start: 0.9067 (mttt) cc_final: 0.8815 (mtmm)
REVERT: A  199 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8222 (mt-10)
REVERT: B   76 LYS cc_start: 0.8952 (tppp) cc_final: 0.8701 (ttmm)
REVERT: B   90 GLU cc_start: 0.8410 (tt0) cc_final: 0.7956 (tm-30)
REVERT: B  207 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7598 (pt0)
REVERT: B  382 LYS cc_start: 0.8817 (tttt) cc_final: 0.8560 (tppp)
REVERT: B  386 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8662 (mt-10)
REVERT: B  414 ASP cc_start: 0.8827 (m-30) cc_final: 0.8347 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 1.4074
  time to fit residues: 160.5321
Evaluate side-chains
  78 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
B  11 GLN
B  66 ASN
B 233 HIS
B 309 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.110309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.073377 restraints weight = 9835.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 2.86
r_work: 0.2640 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.024   1.921   6968  Z= 0.804
  Angle     :  0.513  11.467   9370  Z= 0.268
  Chirality :  0.042   0.159    956
  Planarity :  0.004   0.035   1202
  Dihedral  :  3.974  16.051    902
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  8.80 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.89 (0.29), residues: 812
  helix:  1.84 (0.24), residues: 442
  sheet:  0.08 (0.50), residues: 92
  loop :  0.92 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 249 
 HIS   0.003   0.001   HIS B 255 
 PHE   0.013   0.002   PHE A  92 
 TYR   0.018   0.001   TYR B  44 
 ARG   0.004   0.001   ARG A  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04722 (  363)
  hydrogen bonds       : angle       4.46849 ( 1071)
  metal coordination   : bond        0.78419 (    6)
  covalent geometry    : bond        0.00564 ( 6962)
  covalent geometry    : angle       0.51329 ( 9370)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8492 (tmm)
REVERT: A   86 LYS cc_start: 0.8485 (tttt) cc_final: 0.8161 (tppt)
REVERT: A  123 GLU cc_start: 0.9056 (tt0) cc_final: 0.8367 (tp30)
REVERT: A  185 LYS cc_start: 0.9005 (mttt) cc_final: 0.8676 (mtmm)
REVERT: A  199 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8015 (mt-10)
REVERT: B   90 GLU cc_start: 0.8468 (tt0) cc_final: 0.7954 (tm-30)
  outliers start: 14
  outliers final: 3
  residues processed: 91
  average time/residue: 1.4462
  time to fit residues: 137.6513
Evaluate side-chains
  75 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  380 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0670
   chunk 56 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
B  11 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.113969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.076346 restraints weight = 9365.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 2.97
r_work: 0.2720 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6968  Z= 0.118
  Angle     :  0.444  12.385   9370  Z= 0.230
  Chirality :  0.039   0.145    956
  Planarity :  0.003   0.034   1202
  Dihedral  :  3.781  14.718    902
  Min Nonbonded Distance : 1.553

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 11.59 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.20 (0.30), residues: 812
  helix:  2.14 (0.25), residues: 442
  sheet: -0.05 (0.49), residues: 92
  loop :  1.06 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 204 
 HIS   0.021   0.001   HIS B 233 
 PHE   0.030   0.001   PHE A 273 
 TYR   0.013   0.001   TYR B 111 
 ARG   0.008   0.000   ARG A  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03713 (  363)
  hydrogen bonds       : angle       4.07882 ( 1071)
  metal coordination   : bond        0.02997 (    6)
  covalent geometry    : bond        0.00259 ( 6962)
  covalent geometry    : angle       0.44435 ( 9370)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8511 (tmm)
REVERT: A   86 LYS cc_start: 0.8455 (tttt) cc_final: 0.8164 (tppt)
REVERT: A  123 GLU cc_start: 0.9047 (tt0) cc_final: 0.8357 (tp30)
REVERT: A  185 LYS cc_start: 0.9046 (mttt) cc_final: 0.8732 (mtmm)
REVERT: A  199 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7979 (mt-10)
REVERT: A  260 MET cc_start: 0.7962 (mmt) cc_final: 0.7241 (mmm)
REVERT: A  266 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7698 (tpp)
REVERT: B   71 ASP cc_start: 0.8537 (t0) cc_final: 0.8190 (t0)
REVERT: B   90 GLU cc_start: 0.8447 (tt0) cc_final: 0.7905 (tm-30)
  outliers start: 11
  outliers final: 4
  residues processed: 90
  average time/residue: 1.2914
  time to fit residues: 122.5861
Evaluate side-chains
  75 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 64 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0670
   chunk 24 optimal weight:    4.9990
   overall best weight:    1.1122

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
A 294 GLN
B 309 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.112868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.075324 restraints weight = 9400.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.2858 rms_B_bonded: 2.96
r_work: 0.2681 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6968  Z= 0.156
  Angle     :  0.463  11.948   9370  Z= 0.237
  Chirality :  0.039   0.138    956
  Planarity :  0.003   0.034   1202
  Dihedral  :  3.766  15.120    902
  Min Nonbonded Distance : 1.690

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.85 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.29 (0.30), residues: 812
  helix:  2.22 (0.25), residues: 442
  sheet: -0.02 (0.51), residues: 92
  loop :  1.11 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 249 
 HIS   0.012   0.001   HIS B 233 
 PHE   0.011   0.001   PHE A  92 
 TYR   0.012   0.001   TYR B  44 
 ARG   0.005   0.000   ARG A  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03948 (  363)
  hydrogen bonds       : angle       4.05808 ( 1071)
  metal coordination   : bond        0.02507 (    6)
  covalent geometry    : bond        0.00359 ( 6962)
  covalent geometry    : angle       0.46306 ( 9370)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8298 (mt-10)
REVERT: A   63 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8504 (ttm)
REVERT: A   86 LYS cc_start: 0.8426 (tttt) cc_final: 0.8138 (tppt)
REVERT: A  123 GLU cc_start: 0.9056 (tt0) cc_final: 0.8371 (tp30)
REVERT: A  185 LYS cc_start: 0.9027 (mttt) cc_final: 0.8690 (mtmm)
REVERT: A  199 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7968 (mt-10)
REVERT: A  211 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5060 (mmt)
REVERT: A  260 MET cc_start: 0.7882 (mmt) cc_final: 0.7155 (mmm)
REVERT: A  266 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7802 (tpp)
REVERT: B   63 MET cc_start: 0.9386 (ttp) cc_final: 0.8695 (ttm)
REVERT: B   71 ASP cc_start: 0.8579 (t0) cc_final: 0.8274 (t0)
REVERT: B   90 GLU cc_start: 0.8463 (tt0) cc_final: 0.7906 (tm-30)
REVERT: B  144 GLU cc_start: 0.7949 (tt0) cc_final: 0.7591 (tp30)
  outliers start: 10
  outliers final: 5
  residues processed: 79
  average time/residue: 1.3234
  time to fit residues: 110.1072
Evaluate side-chains
  76 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 77 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0060
   chunk 51 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
A 294 GLN
B  11 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.114013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.076593 restraints weight = 9190.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 2.81
r_work: 0.2725 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6968  Z= 0.114
  Angle     :  0.430  11.868   9370  Z= 0.221
  Chirality :  0.039   0.135    956
  Planarity :  0.003   0.029   1202
  Dihedral  :  3.678  14.416    902
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 12.29 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.47 (0.30), residues: 812
  helix:  2.39 (0.25), residues: 438
  sheet: -0.07 (0.51), residues: 92
  loop :  1.21 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 197 
 HIS   0.002   0.000   HIS B 255 
 PHE   0.031   0.001   PHE A 273 
 TYR   0.011   0.001   TYR B 111 
 ARG   0.004   0.000   ARG A  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03586 (  363)
  hydrogen bonds       : angle       3.93409 ( 1071)
  metal coordination   : bond        0.00174 (    6)
  covalent geometry    : bond        0.00261 ( 6962)
  covalent geometry    : angle       0.43019 ( 9370)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.834 
Fit side-chains
REVERT: A   63 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8476 (tmm)
REVERT: A   86 LYS cc_start: 0.8420 (tttt) cc_final: 0.8133 (tppt)
REVERT: A  123 GLU cc_start: 0.9064 (tt0) cc_final: 0.8355 (tp30)
REVERT: A  185 LYS cc_start: 0.9012 (mttt) cc_final: 0.8654 (mtmm)
REVERT: A  199 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7914 (mt-10)
REVERT: A  211 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.5179 (mmt)
REVERT: A  260 MET cc_start: 0.7905 (mmt) cc_final: 0.7206 (mmm)
REVERT: B   63 MET cc_start: 0.9381 (ttp) cc_final: 0.8737 (ttm)
REVERT: B   71 ASP cc_start: 0.8596 (t0) cc_final: 0.8270 (t70)
REVERT: B   90 GLU cc_start: 0.8446 (tt0) cc_final: 0.7895 (tm-30)
REVERT: B  144 GLU cc_start: 0.7922 (tt0) cc_final: 0.7547 (tp30)
REVERT: B  382 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8504 (tppp)
  outliers start: 11
  outliers final: 4
  residues processed: 83
  average time/residue: 1.3153
  time to fit residues: 114.7810
Evaluate side-chains
  78 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue  382 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 58 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
B  11 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.112301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.074811 restraints weight = 9387.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.2847 rms_B_bonded: 2.81
r_work: 0.2669 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6968  Z= 0.163
  Angle     :  0.459  11.617   9370  Z= 0.237
  Chirality :  0.040   0.151    956
  Planarity :  0.003   0.028   1202
  Dihedral  :  3.726  15.476    902
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.57 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.43 (0.30), residues: 812
  helix:  2.37 (0.25), residues: 438
  sheet: -0.05 (0.52), residues: 92
  loop :  1.16 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 197 
 HIS   0.002   0.000   HIS A 255 
 PHE   0.010   0.001   PHE B  47 
 TYR   0.012   0.001   TYR B  44 
 ARG   0.009   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03967 (  363)
  hydrogen bonds       : angle       4.00895 ( 1071)
  metal coordination   : bond        0.00260 (    6)
  covalent geometry    : bond        0.00384 ( 6962)
  covalent geometry    : angle       0.45866 ( 9370)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A   63 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8456 (ttm)
REVERT: A   86 LYS cc_start: 0.8383 (tttt) cc_final: 0.8035 (tppt)
REVERT: A  123 GLU cc_start: 0.9047 (tt0) cc_final: 0.8312 (tp30)
REVERT: A  185 LYS cc_start: 0.9011 (mttt) cc_final: 0.8653 (mtmm)
REVERT: A  199 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7920 (mt-10)
REVERT: A  211 MET cc_start: 0.6226 (OUTLIER) cc_final: 0.5211 (mmt)
REVERT: A  260 MET cc_start: 0.7832 (mmt) cc_final: 0.7144 (mmm)
REVERT: A  266 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7759 (tpp)
REVERT: B   90 GLU cc_start: 0.8471 (tt0) cc_final: 0.7892 (tm-30)
REVERT: B  218 GLU cc_start: 0.8912 (tp30) cc_final: 0.8369 (tp30)
REVERT: B  382 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8264 (tttp)
REVERT: B  386 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8777 (pt0)
  outliers start: 15
  outliers final: 5
  residues processed: 82
  average time/residue: 1.5307
  time to fit residues: 131.4115
Evaluate side-chains
  79 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue   28 CYS
Chi-restraints excluded: chain B residue  382 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0670
   chunk 29 optimal weight:    0.9980
   chunk 8 optimal weight:    7.9990
   overall best weight:    0.9322

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
B  11 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.112960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.075516 restraints weight = 9054.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 2.77
r_work: 0.2670 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6968  Z= 0.137
  Angle     :  0.447  11.111   9370  Z= 0.232
  Chirality :  0.039   0.143    956
  Planarity :  0.003   0.031   1202
  Dihedral  :  3.680  14.793    902
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.55 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.44 (0.30), residues: 812
  helix:  2.41 (0.25), residues: 438
  sheet: -0.15 (0.52), residues: 92
  loop :  1.14 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 197 
 HIS   0.001   0.000   HIS B 255 
 PHE   0.031   0.001   PHE A 273 
 TYR   0.011   0.001   TYR A  44 
 ARG   0.005   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03713 (  363)
  hydrogen bonds       : angle       3.94568 ( 1071)
  metal coordination   : bond        0.00322 (    6)
  covalent geometry    : bond        0.00321 ( 6962)
  covalent geometry    : angle       0.44682 ( 9370)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.854 
Fit side-chains
REVERT: A   63 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8319 (ttm)
REVERT: A   86 LYS cc_start: 0.8349 (tttt) cc_final: 0.8055 (tppt)
REVERT: A  113 ARG cc_start: 0.7799 (mmm-85) cc_final: 0.7469 (mtp85)
REVERT: A  123 GLU cc_start: 0.9053 (tt0) cc_final: 0.8311 (tp30)
REVERT: A  185 LYS cc_start: 0.8996 (mttt) cc_final: 0.8707 (mttp)
REVERT: A  199 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7956 (mt-10)
REVERT: A  211 MET cc_start: 0.6195 (OUTLIER) cc_final: 0.5161 (mmt)
REVERT: A  218 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8065 (mm-30)
REVERT: A  260 MET cc_start: 0.7829 (mmt) cc_final: 0.7171 (mmm)
REVERT: A  266 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7695 (tpp)
REVERT: B   63 MET cc_start: 0.9163 (tmm) cc_final: 0.8947 (ttp)
REVERT: B   71 ASP cc_start: 0.8523 (t0) cc_final: 0.8165 (t0)
REVERT: B   90 GLU cc_start: 0.8464 (tt0) cc_final: 0.7870 (tm-30)
REVERT: B  144 GLU cc_start: 0.7973 (tt0) cc_final: 0.7635 (tp30)
REVERT: B  218 GLU cc_start: 0.8943 (tp30) cc_final: 0.8295 (tp30)
REVERT: B  382 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8376 (tttp)
REVERT: B  386 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8617 (mt-10)
  outliers start: 15
  outliers final: 6
  residues processed: 87
  average time/residue: 1.4098
  time to fit residues: 128.6115
Evaluate side-chains
  85 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue   28 CYS
Chi-restraints excluded: chain B residue  382 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 18 optimal weight:    0.1980
   chunk 68 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 14 optimal weight:    5.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
B  11 GLN
** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.114043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.076698 restraints weight = 9152.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 2.77
r_work: 0.2672 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6968  Z= 0.121
  Angle     :  0.446  10.913   9370  Z= 0.229
  Chirality :  0.039   0.129    956
  Planarity :  0.003   0.028   1202
  Dihedral  :  3.615  14.540    902
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.83 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.46 (0.30), residues: 812
  helix:  2.45 (0.25), residues: 438
  sheet: -0.20 (0.52), residues: 92
  loop :  1.12 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 197 
 HIS   0.001   0.000   HIS B 255 
 PHE   0.010   0.001   PHE B  67 
 TYR   0.010   0.001   TYR B 111 
 ARG   0.006   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03571 (  363)
  hydrogen bonds       : angle       3.88104 ( 1071)
  metal coordination   : bond        0.00351 (    6)
  covalent geometry    : bond        0.00280 ( 6962)
  covalent geometry    : angle       0.44642 ( 9370)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.865 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.8356 (tttt) cc_final: 0.8033 (tppt)
REVERT: A  113 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7407 (mtp85)
REVERT: A  123 GLU cc_start: 0.9043 (tt0) cc_final: 0.8304 (tp30)
REVERT: A  143 PHE cc_start: 0.7584 (t80) cc_final: 0.7184 (t80)
REVERT: A  185 LYS cc_start: 0.8987 (mttt) cc_final: 0.8717 (mttp)
REVERT: A  199 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7952 (mt-10)
REVERT: A  211 MET cc_start: 0.6275 (OUTLIER) cc_final: 0.5244 (mmt)
REVERT: A  218 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8088 (mm-30)
REVERT: A  260 MET cc_start: 0.7833 (mmt) cc_final: 0.7164 (mmm)
REVERT: A  266 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7711 (tpp)
REVERT: B   63 MET cc_start: 0.9176 (tmm) cc_final: 0.8889 (ttp)
REVERT: B   71 ASP cc_start: 0.8557 (t0) cc_final: 0.8188 (t0)
REVERT: B   90 GLU cc_start: 0.8464 (tt0) cc_final: 0.7881 (tm-30)
REVERT: B  144 GLU cc_start: 0.7966 (tt0) cc_final: 0.7631 (tp30)
REVERT: B  218 GLU cc_start: 0.8948 (tp30) cc_final: 0.8428 (tp30)
REVERT: B  382 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8373 (tttp)
REVERT: B  386 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8637 (mt-10)
  outliers start: 12
  outliers final: 6
  residues processed: 85
  average time/residue: 1.4098
  time to fit residues: 125.8672
Evaluate side-chains
  83 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue   28 CYS
Chi-restraints excluded: chain B residue  382 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
B  11 GLN
** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.111835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.074325 restraints weight = 9288.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 2.80
r_work: 0.2662 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6968  Z= 0.173
  Angle     :  0.466  10.955   9370  Z= 0.243
  Chirality :  0.039   0.125    956
  Planarity :  0.003   0.027   1202
  Dihedral  :  3.687  15.387    902
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.83 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.42 (0.30), residues: 812
  helix:  2.42 (0.25), residues: 438
  sheet: -0.16 (0.53), residues: 92
  loop :  1.08 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 197 
 HIS   0.001   0.000   HIS A  37 
 PHE   0.031   0.002   PHE A 273 
 TYR   0.013   0.001   TYR B  44 
 ARG   0.006   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03931 (  363)
  hydrogen bonds       : angle       3.97793 ( 1071)
  metal coordination   : bond        0.00414 (    6)
  covalent geometry    : bond        0.00407 ( 6962)
  covalent geometry    : angle       0.46611 ( 9370)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.778 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.8379 (tttt) cc_final: 0.8042 (tppt)
REVERT: A  113 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.7419 (mtp85)
REVERT: A  123 GLU cc_start: 0.9056 (tt0) cc_final: 0.8314 (tp30)
REVERT: A  185 LYS cc_start: 0.9001 (mttt) cc_final: 0.8724 (mttp)
REVERT: A  199 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7922 (mt-10)
REVERT: A  211 MET cc_start: 0.6263 (OUTLIER) cc_final: 0.5238 (mmt)
REVERT: A  218 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8085 (mm-30)
REVERT: A  266 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7766 (tpp)
REVERT: B   63 MET cc_start: 0.9163 (tmm) cc_final: 0.8918 (ttp)
REVERT: B   71 ASP cc_start: 0.8566 (t0) cc_final: 0.8223 (t0)
REVERT: B   90 GLU cc_start: 0.8471 (tt0) cc_final: 0.7869 (tm-30)
REVERT: B  144 GLU cc_start: 0.8003 (tt0) cc_final: 0.7667 (tp30)
REVERT: B  218 GLU cc_start: 0.8928 (tp30) cc_final: 0.8475 (mm-30)
REVERT: B  266 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.7504 (tpp)
REVERT: B  382 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8375 (tttp)
REVERT: B  386 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8572 (mt-10)
  outliers start: 13
  outliers final: 7
  residues processed: 82
  average time/residue: 1.3512
  time to fit residues: 116.2110
Evaluate side-chains
  84 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue   28 CYS
Chi-restraints excluded: chain B residue  266 MET
Chi-restraints excluded: chain B residue  382 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 44 optimal weight:    0.3980
   chunk 30 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
B  11 GLN
** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.111336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.073950 restraints weight = 9297.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 2.78
r_work: 0.2671 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6968  Z= 0.186
  Angle     :  0.479  10.789   9370  Z= 0.249
  Chirality :  0.040   0.126    956
  Planarity :  0.003   0.027   1202
  Dihedral  :  3.721  15.695    902
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.97 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.38 (0.30), residues: 812
  helix:  2.41 (0.25), residues: 438
  sheet: -0.21 (0.52), residues: 92
  loop :  1.04 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 197 
 HIS   0.002   0.000   HIS A 296 
 PHE   0.011   0.001   PHE B  67 
 TYR   0.013   0.001   TYR B  44 
 ARG   0.006   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03954 (  363)
  hydrogen bonds       : angle       4.01208 ( 1071)
  metal coordination   : bond        0.00434 (    6)
  covalent geometry    : bond        0.00439 ( 6962)
  covalent geometry    : angle       0.47940 ( 9370)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.860 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.8401 (tttt) cc_final: 0.8050 (tppt)
REVERT: A  123 GLU cc_start: 0.9053 (tt0) cc_final: 0.8318 (tp30)
REVERT: A  185 LYS cc_start: 0.9018 (mttt) cc_final: 0.8743 (mttp)
REVERT: A  199 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7932 (mt-10)
REVERT: A  211 MET cc_start: 0.6381 (OUTLIER) cc_final: 0.6011 (mtt)
REVERT: A  218 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8141 (mm-30)
REVERT: A  266 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7781 (tpp)
REVERT: B   63 MET cc_start: 0.9186 (tmm) cc_final: 0.8938 (ttp)
REVERT: B   71 ASP cc_start: 0.8597 (t0) cc_final: 0.8232 (t0)
REVERT: B   90 GLU cc_start: 0.8495 (tt0) cc_final: 0.7891 (tm-30)
REVERT: B  144 GLU cc_start: 0.8018 (tt0) cc_final: 0.7690 (tp30)
REVERT: B  218 GLU cc_start: 0.8925 (tp30) cc_final: 0.8489 (mm-30)
REVERT: B  266 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.7602 (tpp)
REVERT: B  382 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8398 (tttp)
REVERT: B  386 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8543 (mt-10)
  outliers start: 13
  outliers final: 8
  residues processed: 77
  average time/residue: 1.4277
  time to fit residues: 115.3627
Evaluate side-chains
  81 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue   28 CYS
Chi-restraints excluded: chain B residue  131 LYS
Chi-restraints excluded: chain B residue  266 MET
Chi-restraints excluded: chain B residue  382 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 63 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
A 240 GLN
A 294 GLN
B  11 GLN
** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.112806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.075418 restraints weight = 9220.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 2.79
r_work: 0.2698 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6968  Z= 0.133
  Angle     :  0.460  10.437   9370  Z= 0.240
  Chirality :  0.039   0.127    956
  Planarity :  0.003   0.028   1202
  Dihedral  :  3.658  15.239    902
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.39 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.42 (0.30), residues: 812
  helix:  2.46 (0.25), residues: 438
  sheet: -0.28 (0.52), residues: 92
  loop :  1.06 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 197 
 HIS   0.002   0.000   HIS A 255 
 PHE   0.032   0.001   PHE A 273 
 TYR   0.010   0.001   TYR A  44 
 ARG   0.007   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03669 (  363)
  hydrogen bonds       : angle       3.91512 ( 1071)
  metal coordination   : bond        0.00391 (    6)
  covalent geometry    : bond        0.00310 ( 6962)
  covalent geometry    : angle       0.45961 ( 9370)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4331.85 seconds
wall clock time: 75 minutes 45.85 seconds (4545.85 seconds total)