Starting phenix.real_space_refine
on Wed Sep 17 07:11:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n0x_48797/09_2025/9n0x_48797.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n0x_48797/09_2025/9n0x_48797.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n0x_48797/09_2025/9n0x_48797.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n0x_48797/09_2025/9n0x_48797.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n0x_48797/09_2025/9n0x_48797.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n0x_48797/09_2025/9n0x_48797.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.021
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       6      5.49       5
     S      40      5.16       5
     C    4432      2.51       5
     N    1008      2.21       5
     O    1100      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6588
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3181
          Classifications: {'peptide': 380}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 358}
    Chain: "B"
      Number of atoms: 3181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3181
          Classifications: {'peptide': 380}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 358}
    Chain: "A"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 113
          Unusual residues: {' CA': 1, 'RXY': 1}
          Classifications: {'peptide': 2, 'undetermined': 2}
          Link IDs: {'TRANS': 1, None: 2}
            Not linked:
              pdbres="P5S A 502 "
              pdbres=" CA A 503 "
            Not linked:
              pdbres=" CA A 503 "
              pdbres="RXY A 504 "
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 45
    Chain: "B"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 113
          Unusual residues: {' CA': 1, 'RXY': 1}
          Classifications: {'peptide': 2, 'undetermined': 2}
          Link IDs: {'TRANS': 1, None: 2}
            Not linked:
              pdbres="P5S B 502 "
              pdbres=" CA B 503 "
            Not linked:
              pdbres=" CA B 503 "
              pdbres="RXY B 504 "
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 45
  Time building chain proxies: 1.69, per 1000 atoms: 0.26
  Number of scatterers: 6588
  At special positions: 0
  Unit cell: (107.748, 118.818, 69.372, 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       6     15.00
     O    1100      8.00
     N    1008      7.00
     C    4432      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 174 " - pdb=" SG  CYS A 241 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 174 " - pdb=" SG  CYS B 241 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 360.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1448

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      73.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 82
    Processing helix  chain 'A' and resid 88 through 112
      removed outlier: 3.851A  pdb=" N   LYS A  94 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 144
      removed outlier: 3.950A  pdb=" N   TRP A 125 " --> pdb=" O   HIS A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 158
    Processing helix  chain 'A' and resid 186 through 193
      removed outlier: 4.047A  pdb=" N   ASP A 191 " --> pdb=" O   HIS A 187 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LYS A 192 " --> pdb=" O   ASN A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 212
      removed outlier: 3.663A  pdb=" N   LEU A 202 " --> pdb=" O   PRO A 198 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE A 211 " --> pdb=" O   LYS A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 231
      removed outlier: 3.509A  pdb=" N   CYS A 217 " --> pdb=" O   ASP A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
    Processing helix  chain 'A' and resid 249 through 256
    Processing helix  chain 'A' and resid 256 through 269
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 311 through 338
      removed outlier: 3.609A  pdb=" N   GLU A 328 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 371
      removed outlier: 3.613A  pdb=" N   LEU A 348 " --> pdb=" O   HIS A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 400
      removed outlier: 3.558A  pdb=" N   ASP A 400 " --> pdb=" O   VAL A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 405
      removed outlier: 3.605A  pdb=" N   LEU A 404 " --> pdb=" O   ASP A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 437
      removed outlier: 3.874A  pdb=" N   CYS A 415 " --> pdb=" O   TYR A 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 82
    Processing helix  chain 'B' and resid 88 through 112
      removed outlier: 3.916A  pdb=" N   LYS B  94 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 144
      removed outlier: 3.953A  pdb=" N   TRP B 125 " --> pdb=" O   HIS B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 158
    Processing helix  chain 'B' and resid 186 through 193
      removed outlier: 4.013A  pdb=" N   ASP B 191 " --> pdb=" O   HIS B 187 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LYS B 192 " --> pdb=" O   ASN B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 212
      removed outlier: 3.548A  pdb=" N   PHE B 201 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU B 202 " --> pdb=" O   PRO B 198 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE B 211 " --> pdb=" O   LYS B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 231
      removed outlier: 3.513A  pdb=" N   CYS B 217 " --> pdb=" O   ASP B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 247
    Processing helix  chain 'B' and resid 249 through 256
    Processing helix  chain 'B' and resid 256 through 269
    Processing helix  chain 'B' and resid 283 through 294
    Processing helix  chain 'B' and resid 311 through 338
      removed outlier: 3.607A  pdb=" N   GLU B 328 " --> pdb=" O   PHE B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 370
      removed outlier: 3.632A  pdb=" N   LEU B 348 " --> pdb=" O   HIS B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 400
      removed outlier: 3.560A  pdb=" N   ASP B 400 " --> pdb=" O   VAL B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 405
      removed outlier: 3.618A  pdb=" N   LEU B 404 " --> pdb=" O   ASP B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 437
      removed outlier: 3.875A  pdb=" N   CYS B 415 " --> pdb=" O   TYR B 411 " (cutoff:3.500A)

    404 hydrogen bonds defined for protein.
    1212 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.82

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 950
        1.30 -     1.43: 2022
        1.43 -     1.56: 3766
        1.56 -     1.69: 18
        1.69 -     1.81: 60
  Bond restraints: 6816
  Sorted by residual:
  bond pdb=" CBJ RXY A 504 "
       pdb=" CBK RXY A 504 "
    ideal  model  delta    sigma   weight residual
    1.533  1.317  0.216 2.00e-02 2.50e+03 1.16e+02
  bond pdb=" CBJ RXY B 504 "
       pdb=" CBK RXY B 504 "
    ideal  model  delta    sigma   weight residual
    1.533  1.318  0.215 2.00e-02 2.50e+03 1.16e+02
  bond pdb=" CBG RXY B 504 "
       pdb=" CBH RXY B 504 "
    ideal  model  delta    sigma   weight residual
    1.525  1.318  0.207 2.00e-02 2.50e+03 1.07e+02
  bond pdb=" CBG RXY A 504 "
       pdb=" CBH RXY A 504 "
    ideal  model  delta    sigma   weight residual
    1.525  1.318  0.207 2.00e-02 2.50e+03 1.07e+02
  bond pdb=" CAK RXY A 504 "
       pdb=" CAL RXY A 504 "
    ideal  model  delta    sigma   weight residual
    1.333  1.529 -0.196 2.00e-02 2.50e+03 9.59e+01
  ... (remaining 6811 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.82: 9088
        2.82 -     5.64: 130
        5.64 -     8.47: 34
        8.47 -    11.29: 14
       11.29 -    14.11: 8
  Bond angle restraints: 9274
  Sorted by residual:
  angle pdb=" CAK RXY B 504 "
        pdb=" CAL RXY B 504 "
        pdb=" CAM RXY B 504 "
      ideal   model   delta    sigma   weight residual
     126.11  112.00   14.11 3.00e+00 1.11e-01 2.21e+01
  angle pdb=" CAK RXY A 504 "
        pdb=" CAL RXY A 504 "
        pdb=" CAM RXY A 504 "
      ideal   model   delta    sigma   weight residual
     126.11  112.03   14.08 3.00e+00 1.11e-01 2.20e+01
  angle pdb=" OAB RXY A 504 "
        pdb=" PAZ RXY A 504 "
        pdb=" OBX RXY A 504 "
      ideal   model   delta    sigma   weight residual
     123.18  109.25   13.93 3.00e+00 1.11e-01 2.16e+01
  angle pdb=" OAB RXY B 504 "
        pdb=" PAZ RXY B 504 "
        pdb=" OBX RXY B 504 "
      ideal   model   delta    sigma   weight residual
     123.18  109.29   13.89 3.00e+00 1.11e-01 2.14e+01
  angle pdb=" CAJ RXY A 504 "
        pdb=" CAK RXY A 504 "
        pdb=" CAL RXY A 504 "
      ideal   model   delta    sigma   weight residual
     125.80  112.37   13.43 3.00e+00 1.11e-01 2.00e+01
  ... (remaining 9269 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.80: 3752
       35.80 -    71.60: 180
       71.60 -   107.40: 24
      107.40 -   143.20: 7
      143.20 -   179.00: 11
  Dihedral angle restraints: 3974
    sinusoidal: 1732
      harmonic: 2242
  Sorted by residual:
  dihedral pdb=" C38 P5S A 502 "
           pdb=" C39 P5S A 502 "
           pdb=" C40 P5S A 502 "
           pdb=" C41 P5S A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
      64.51 -114.49  179.00     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C38 P5S B 502 "
           pdb=" C39 P5S B 502 "
           pdb=" C40 P5S B 502 "
           pdb=" C41 P5S B 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
      64.51 -114.47  178.98     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CBF RXY B 504 "
           pdb=" CBG RXY B 504 "
           pdb=" CBH RXY B 504 "
           pdb=" CBI RXY B 504 "
      ideal   model   delta sinusoidal    sigma   weight residual
     178.53   -0.14  178.67     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 3971 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 841
       0.056 -    0.112: 132
       0.112 -    0.167: 9
       0.167 -    0.223: 2
       0.223 -    0.279: 2
  Chirality restraints: 986
  Sorted by residual:
  chirality pdb=" CAW RXY B 504 "
            pdb=" CAV RXY B 504 "
            pdb=" CAX RXY B 504 "
            pdb=" OBW RXY B 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.21    2.49   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CAW RXY A 504 "
            pdb=" CAV RXY A 504 "
            pdb=" CAX RXY A 504 "
            pdb=" OBW RXY A 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.21    2.49   -0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  P5S B 501 "
            pdb=" N   P5S B 501 "
            pdb=" C   P5S B 501 "
            pdb=" CB  P5S B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.59   -0.19 2.00e-01 2.50e+01 9.09e-01
  ... (remaining 983 not shown)

  Planarity restraints: 1108
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAJ RXY B 504 "   -0.142 2.00e-02 2.50e+03   2.39e-01 5.73e+02
        pdb=" CAK RXY B 504 "    0.308 2.00e-02 2.50e+03
        pdb=" CAL RXY B 504 "   -0.307 2.00e-02 2.50e+03
        pdb=" CAM RXY B 504 "    0.140 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAJ RXY A 504 "    0.141 2.00e-02 2.50e+03   2.37e-01 5.62e+02
        pdb=" CAK RXY A 504 "   -0.305 2.00e-02 2.50e+03
        pdb=" CAL RXY A 504 "    0.304 2.00e-02 2.50e+03
        pdb=" CAM RXY A 504 "   -0.140 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 296 "    0.048 5.00e-02 4.00e+02   7.13e-02 8.13e+00
        pdb=" N   PRO B 297 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B 297 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 297 "    0.040 5.00e-02 4.00e+02
  ... (remaining 1105 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 781
        2.75 -     3.29: 6415
        3.29 -     3.82: 11099
        3.82 -     4.36: 11856
        4.36 -     4.90: 21679
  Nonbonded interactions: 51830
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 293 "
            pdb=" OG1 THR B 296 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   PHE A 293 "
            pdb=" OG1 THR A 296 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OG1 THR A 331 "
            pdb=" NH1 ARG A 350 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" OG1 THR B 331 "
            pdb=" NH1 ARG B 350 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" O   LEU A 268 "
            pdb=" OH  TYR A 273 "
     model   vdw
     2.284 3.040
  ... (remaining 51825 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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:             3.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.410
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
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      :  0.008   0.216   6818  Z= 0.405
  Angle     :  0.961  14.112   9278  Z= 0.399
  Chirality :  0.041   0.279    986
  Planarity :  0.011   0.239   1108
  Dihedral  : 23.177 178.998   2520
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 15.84 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.30), residues: 756
  helix:  2.05 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.00 (0.35), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 119 
 TYR   0.019   0.001   TYR B 366 
 PHE   0.008   0.001   PHE A 303 
 TRP   0.015   0.001   TRP B 204 
 HIS   0.004   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00812 ( 6816)
  covalent geometry    : angle       0.96130 ( 9274)
  SS BOND              : bond        0.00227 (    2)
  SS BOND              : angle       0.67024 (    4)
  hydrogen bonds       : bond        0.09318 (  404)
  hydrogen bonds       : angle       4.62007 ( 1212)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.6820 (t80) cc_final: 0.6572 (t80)
REVERT: B  224 PHE cc_start: 0.6909 (t80) cc_final: 0.6588 (t80)
  outliers start: 2
  outliers final: 2
  residues processed: 55
  average time/residue: 0.0526
  time to fit residues: 4.3765
Evaluate side-chains
  56 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain B residue  188 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:   30.0000
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4557 r_free = 0.4557 target = 0.214916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 96)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.174442 restraints weight = 8552.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.4150 rms_B_bonded: 1.95
r_work: 0.3978 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3854 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.0639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6818  Z= 0.132
  Angle     :  0.532   6.284   9278  Z= 0.269
  Chirality :  0.039   0.137    986
  Planarity :  0.005   0.049   1108
  Dihedral  : 23.586 174.888   1059
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.97 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.30), residues: 756
  helix:  1.97 (0.23), residues: 502
  sheet:  None (None), residues: 0
  loop : -1.83 (0.35), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 350 
 TYR   0.017   0.001   TYR A 366 
 PHE   0.008   0.001   PHE A 303 
 TRP   0.015   0.001   TRP A 204 
 HIS   0.004   0.001   HIS B 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6816)
  covalent geometry    : angle       0.53159 ( 9274)
  SS BOND              : bond        0.00252 (    2)
  SS BOND              : angle       0.65370 (    4)
  hydrogen bonds       : bond        0.05023 (  404)
  hydrogen bonds       : angle       4.14580 ( 1212)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.7029 (t80) cc_final: 0.6685 (t80)
REVERT: A  260 CYS cc_start: 0.7883 (m) cc_final: 0.7268 (m)
REVERT: B  223 MET cc_start: 0.6913 (mmm) cc_final: 0.6633 (mmm)
  outliers start: 13
  outliers final: 12
  residues processed: 66
  average time/residue: 0.0533
  time to fit residues: 5.5472
Evaluate side-chains
  64 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  188 ASN
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  260 CYS
Chi-restraints excluded: chain B residue  264 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4544 r_free = 0.4544 target = 0.213541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.178662 restraints weight = 8517.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.4200 rms_B_bonded: 1.46
r_work: 0.3985 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3878 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.0912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6818  Z= 0.133
  Angle     :  0.513   6.270   9278  Z= 0.264
  Chirality :  0.039   0.132    986
  Planarity :  0.004   0.041   1108
  Dihedral  : 20.636 168.586   1056
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.99 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.30), residues: 756
  helix:  1.95 (0.23), residues: 502
  sheet:  None (None), residues: 0
  loop : -1.76 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 363 
 TYR   0.016   0.001   TYR A 366 
 PHE   0.007   0.001   PHE B 354 
 TRP   0.014   0.001   TRP A 204 
 HIS   0.005   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6816)
  covalent geometry    : angle       0.51311 ( 9274)
  SS BOND              : bond        0.00124 (    2)
  SS BOND              : angle       0.57520 (    4)
  hydrogen bonds       : bond        0.05173 (  404)
  hydrogen bonds       : angle       4.19222 ( 1212)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.7031 (t80) cc_final: 0.6726 (t80)
REVERT: A  260 CYS cc_start: 0.7701 (m) cc_final: 0.7033 (m)
  outliers start: 18
  outliers final: 16
  residues processed: 66
  average time/residue: 0.0498
  time to fit residues: 5.2174
Evaluate side-chains
  69 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  188 ASN
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  260 CYS
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 24 optimal weight:    0.2980
   chunk 27 optimal weight:    0.9980
   chunk 22 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4548 r_free = 0.4548 target = 0.214022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 101)---------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.178822 restraints weight = 8547.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.4206 rms_B_bonded: 1.48
r_work: 0.3996 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3890 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6818  Z= 0.123
  Angle     :  0.492   6.080   9278  Z= 0.252
  Chirality :  0.038   0.128    986
  Planarity :  0.004   0.036   1108
  Dihedral  : 19.283 166.889   1056
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.15 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.30), residues: 756
  helix:  2.02 (0.23), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.65 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 363 
 TYR   0.015   0.001   TYR B 366 
 PHE   0.009   0.001   PHE B 354 
 TRP   0.014   0.001   TRP A 204 
 HIS   0.004   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6816)
  covalent geometry    : angle       0.49150 ( 9274)
  SS BOND              : bond        0.00116 (    2)
  SS BOND              : angle       0.55483 (    4)
  hydrogen bonds       : bond        0.04907 (  404)
  hydrogen bonds       : angle       4.17052 ( 1212)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 56
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.6988 (t80) cc_final: 0.6696 (t80)
REVERT: A  260 CYS cc_start: 0.7588 (m) cc_final: 0.6946 (m)
REVERT: A  324 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.7876 (t80)
REVERT: B  223 MET cc_start: 0.6782 (mmm) cc_final: 0.6476 (mmm)
REVERT: B  231 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7289 (mp)
REVERT: B  324 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7879 (t80)
  outliers start: 21
  outliers final: 13
  residues processed: 71
  average time/residue: 0.0643
  time to fit residues: 6.6175
Evaluate side-chains
  71 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  324 PHE
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 74 optimal weight:   30.0000
   chunk 18 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.4541 r_free = 0.4541 target = 0.213210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 105)---------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.178925 restraints weight = 8598.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.4211 rms_B_bonded: 1.46
r_work: 0.3983 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3885 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6818  Z= 0.132
  Angle     :  0.509   8.303   9278  Z= 0.258
  Chirality :  0.039   0.131    986
  Planarity :  0.004   0.034   1108
  Dihedral  : 19.250 165.547   1056
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 16.42 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.30), residues: 756
  helix:  1.99 (0.23), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.61 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 119 
 TYR   0.014   0.001   TYR A 366 
 PHE   0.008   0.001   PHE A 354 
 TRP   0.013   0.001   TRP A 204 
 HIS   0.004   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6816)
  covalent geometry    : angle       0.50892 ( 9274)
  SS BOND              : bond        0.00129 (    2)
  SS BOND              : angle       0.47345 (    4)
  hydrogen bonds       : bond        0.05069 (  404)
  hydrogen bonds       : angle       4.18889 ( 1212)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 56
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.7049 (t80) cc_final: 0.6754 (t80)
REVERT: A  260 CYS cc_start: 0.7611 (m) cc_final: 0.6968 (m)
REVERT: A  324 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.7881 (t80)
REVERT: B  231 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7489 (mp)
REVERT: B  324 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.7887 (t80)
  outliers start: 26
  outliers final: 18
  residues processed: 76
  average time/residue: 0.0515
  time to fit residues: 6.1354
Evaluate side-chains
  74 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 53
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  188 ASN
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  324 PHE
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0370
   chunk 14 optimal weight:    4.9990
   chunk 70 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 74 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.6458

-------------------------------------------------------------------------------
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 = 0.4551 r_free = 0.4551 target = 0.214322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.179877 restraints weight = 8574.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.4213 rms_B_bonded: 1.45
r_work: 0.3999 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3887 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6818  Z= 0.115
  Angle     :  0.481   6.976   9278  Z= 0.246
  Chirality :  0.038   0.127    986
  Planarity :  0.004   0.034   1108
  Dihedral  : 18.927 164.695   1056
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.73 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.30), residues: 756
  helix:  2.11 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.60 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 363 
 TYR   0.014   0.001   TYR B 366 
 PHE   0.007   0.001   PHE B 354 
 TRP   0.012   0.001   TRP B 204 
 HIS   0.004   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 6816)
  covalent geometry    : angle       0.48141 ( 9274)
  SS BOND              : bond        0.00067 (    2)
  SS BOND              : angle       0.47244 (    4)
  hydrogen bonds       : bond        0.04739 (  404)
  hydrogen bonds       : angle       4.13657 ( 1212)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 55
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.7018 (t80) cc_final: 0.6760 (t80)
REVERT: A  238 PHE cc_start: 0.4752 (OUTLIER) cc_final: 0.4487 (m-80)
REVERT: A  260 CYS cc_start: 0.7666 (m) cc_final: 0.7032 (m)
REVERT: A  324 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7846 (t80)
REVERT: B  224 PHE cc_start: 0.7005 (t80) cc_final: 0.6677 (t80)
REVERT: B  231 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7310 (mp)
REVERT: B  260 CYS cc_start: 0.7789 (m) cc_final: 0.6944 (m)
REVERT: B  324 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7853 (t80)
  outliers start: 24
  outliers final: 19
  residues processed: 73
  average time/residue: 0.0509
  time to fit residues: 5.8600
Evaluate side-chains
  77 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 54
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  188 ASN
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  324 PHE
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 22 optimal weight:   20.0000
   chunk 60 optimal weight:   20.0000
   chunk 66 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 11 optimal weight:   20.0000
   chunk 34 optimal weight:    0.0570
   chunk 46 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
** B 233 HIS ** 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 = 0.4556 r_free = 0.4556 target = 0.214627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 100)---------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.174155 restraints weight = 8440.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.4150 rms_B_bonded: 2.04
r_work: 0.3978 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3861 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6818  Z= 0.113
  Angle     :  0.482   7.171   9278  Z= 0.244
  Chirality :  0.038   0.125    986
  Planarity :  0.004   0.034   1108
  Dihedral  : 18.748 164.026   1056
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 17.15 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.30), residues: 756
  helix:  2.15 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.55 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 363 
 TYR   0.014   0.001   TYR A 366 
 PHE   0.008   0.001   PHE A 354 
 TRP   0.012   0.001   TRP B 204 
 HIS   0.004   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 6816)
  covalent geometry    : angle       0.48154 ( 9274)
  SS BOND              : bond        0.00187 (    2)
  SS BOND              : angle       0.52441 (    4)
  hydrogen bonds       : bond        0.04648 (  404)
  hydrogen bonds       : angle       4.09604 ( 1212)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 53
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.6984 (t80) cc_final: 0.6722 (t80)
REVERT: A  238 PHE cc_start: 0.4749 (OUTLIER) cc_final: 0.4491 (m-80)
REVERT: A  260 CYS cc_start: 0.7785 (m) cc_final: 0.7140 (m)
REVERT: A  324 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7852 (t80)
REVERT: B  224 PHE cc_start: 0.6980 (t80) cc_final: 0.6671 (t80)
REVERT: B  231 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7324 (mp)
REVERT: B  260 CYS cc_start: 0.7866 (m) cc_final: 0.7016 (m)
REVERT: B  324 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7865 (t80)
  outliers start: 29
  outliers final: 18
  residues processed: 76
  average time/residue: 0.0529
  time to fit residues: 6.3698
Evaluate side-chains
  78 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  188 ASN
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  324 PHE
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 60 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   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 233 HIS ** 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 = 0.4546 r_free = 0.4546 target = 0.213815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 120)---------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.172844 restraints weight = 8570.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.4147 rms_B_bonded: 2.14
r_work: 0.3962 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3848 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6818  Z= 0.125
  Angle     :  0.500   8.426   9278  Z= 0.252
  Chirality :  0.038   0.130    986
  Planarity :  0.004   0.033   1108
  Dihedral  : 18.680 163.073   1056
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 17.88 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.30), residues: 756
  helix:  2.11 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.58 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 363 
 TYR   0.013   0.001   TYR B 366 
 PHE   0.007   0.001   PHE A 354 
 TRP   0.012   0.001   TRP B 204 
 HIS   0.004   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6816)
  covalent geometry    : angle       0.50012 ( 9274)
  SS BOND              : bond        0.00051 (    2)
  SS BOND              : angle       0.27031 (    4)
  hydrogen bonds       : bond        0.04885 (  404)
  hydrogen bonds       : angle       4.13318 ( 1212)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 55
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A  223 MET cc_start: 0.6831 (mmm) cc_final: 0.6545 (mmm)
REVERT: A  224 PHE cc_start: 0.7029 (t80) cc_final: 0.6762 (t80)
REVERT: A  238 PHE cc_start: 0.4741 (OUTLIER) cc_final: 0.4501 (m-80)
REVERT: A  260 CYS cc_start: 0.7795 (m) cc_final: 0.7171 (m)
REVERT: A  324 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7886 (t80)
REVERT: B  224 PHE cc_start: 0.7019 (t80) cc_final: 0.6684 (t80)
REVERT: B  231 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7326 (mp)
REVERT: B  233 HIS cc_start: 0.7581 (OUTLIER) cc_final: 0.6666 (p-80)
REVERT: B  260 CYS cc_start: 0.7820 (m) cc_final: 0.6965 (m)
REVERT: B  324 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.7889 (t80)
  outliers start: 27
  outliers final: 18
  residues processed: 75
  average time/residue: 0.0518
  time to fit residues: 6.0958
Evaluate side-chains
  78 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  188 ASN
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  233 HIS
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  324 PHE
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 72 optimal weight:    0.4980
   chunk 45 optimal weight:    0.5980
   chunk 21 optimal weight:    9.9990
   chunk 62 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   chunk 60 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B 233 HIS ** 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 = 0.4553 r_free = 0.4553 target = 0.214681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.180404 restraints weight = 8597.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.4222 rms_B_bonded: 1.46
r_work: 0.4004 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3900 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6818  Z= 0.111
  Angle     :  0.481   7.758   9278  Z= 0.243
  Chirality :  0.037   0.125    986
  Planarity :  0.004   0.034   1108
  Dihedral  : 18.511 162.933   1056
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 18.31 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.30), residues: 756
  helix:  2.20 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.54 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 363 
 TYR   0.014   0.001   TYR B 366 
 PHE   0.008   0.001   PHE A 354 
 TRP   0.012   0.001   TRP B 204 
 HIS   0.003   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 6816)
  covalent geometry    : angle       0.48116 ( 9274)
  SS BOND              : bond        0.00112 (    2)
  SS BOND              : angle       0.50845 (    4)
  hydrogen bonds       : bond        0.04623 (  404)
  hydrogen bonds       : angle       4.10172 ( 1212)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.6925 (t80) cc_final: 0.6657 (t80)
REVERT: A  238 PHE cc_start: 0.4752 (OUTLIER) cc_final: 0.4537 (m-80)
REVERT: A  260 CYS cc_start: 0.7634 (m) cc_final: 0.7012 (m)
REVERT: A  324 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.7832 (t80)
REVERT: B  224 PHE cc_start: 0.6929 (t80) cc_final: 0.6622 (t80)
REVERT: B  231 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7420 (mp)
REVERT: B  260 CYS cc_start: 0.7715 (m) cc_final: 0.6867 (m)
REVERT: B  324 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7851 (t80)
  outliers start: 23
  outliers final: 19
  residues processed: 73
  average time/residue: 0.0498
  time to fit residues: 5.7236
Evaluate side-chains
  77 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 54
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  188 ASN
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  324 PHE
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 39 optimal weight:    0.1980
   chunk 45 optimal weight:    0.5980
   chunk 34 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0870
   chunk 56 optimal weight:    0.3980
   chunk 14 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
** B 233 HIS ** 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 = 0.4574 r_free = 0.4574 target = 0.222349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.181189 restraints weight = 8825.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.4206 rms_B_bonded: 1.69
r_work: 0.3996 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3884 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6818  Z= 0.101
  Angle     :  0.471   8.580   9278  Z= 0.236
  Chirality :  0.037   0.125    986
  Planarity :  0.004   0.037   1108
  Dihedral  : 18.095 163.080   1056
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 19.19 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.30), residues: 756
  helix:  2.32 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.53 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 363 
 TYR   0.014   0.001   TYR B 366 
 PHE   0.008   0.001   PHE A 354 
 TRP   0.011   0.001   TRP B 204 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 6816)
  covalent geometry    : angle       0.47101 ( 9274)
  SS BOND              : bond        0.00009 (    2)
  SS BOND              : angle       0.41202 (    4)
  hydrogen bonds       : bond        0.04226 (  404)
  hydrogen bonds       : angle       4.01788 ( 1212)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 54
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  223 MET cc_start: 0.6719 (mmm) cc_final: 0.6452 (mmm)
REVERT: A  224 PHE cc_start: 0.6834 (t80) cc_final: 0.6604 (t80)
REVERT: A  260 CYS cc_start: 0.7782 (m) cc_final: 0.7153 (m)
REVERT: A  324 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.7840 (t80)
REVERT: B  223 MET cc_start: 0.6743 (mmm) cc_final: 0.6454 (mmm)
REVERT: B  224 PHE cc_start: 0.6783 (t80) cc_final: 0.6460 (t80)
REVERT: B  231 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7373 (mp)
REVERT: B  260 CYS cc_start: 0.7789 (OUTLIER) cc_final: 0.6931 (m)
REVERT: B  324 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7853 (t80)
  outliers start: 18
  outliers final: 13
  residues processed: 67
  average time/residue: 0.0533
  time to fit residues: 5.6640
Evaluate side-chains
  70 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  260 CYS
Chi-restraints excluded: chain B residue  324 PHE
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0470
   chunk 33 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0570
   chunk 51 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0010
   chunk 38 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.3202

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

Flipped N/Q/H residues before XYZ refinement:
** B 233 HIS ** 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 = 0.4579 r_free = 0.4579 target = 0.217371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.182942 restraints weight = 8574.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.4250 rms_B_bonded: 1.42
r_work: 0.4052 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3947 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6818  Z= 0.097
  Angle     :  0.465   7.975   9278  Z= 0.232
  Chirality :  0.037   0.124    986
  Planarity :  0.004   0.037   1108
  Dihedral  : 17.806 163.172   1056
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 19.77 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.30), residues: 756
  helix:  2.41 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.45 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 363 
 TYR   0.014   0.001   TYR B 366 
 PHE   0.007   0.001   PHE A 354 
 TRP   0.011   0.001   TRP A 204 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 6816)
  covalent geometry    : angle       0.46477 ( 9274)
  SS BOND              : bond        0.00160 (    2)
  SS BOND              : angle       0.70106 (    4)
  hydrogen bonds       : bond        0.04142 (  404)
  hydrogen bonds       : angle       3.96412 ( 1212)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1886.64 seconds
wall clock time: 32 minutes 56.86 seconds (1976.86 seconds total)