Starting phenix.real_space_refine
on Thu Jul  2 04:08:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n0x_48797/07_2026/9n0x_48797.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n0x_48797/07_2026/9n0x_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_48797/07_2026/9n0x_48797.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n0x_48797/07_2026/9n0x_48797.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n0x_48797/07_2026/9n0x_48797.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n0x_48797/07_2026/9n0x_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-dev-6108/lib/python3.11/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, 112
          Ad-hoc single atom residues: {' CA': 1}
          Unusual residues: {'RXY': 1}
          Classifications: {'peptide': 2, 'undetermined': 1}
          Link IDs: {'TRANS': 1}
          Chain breaks: 2
          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, 112
          Ad-hoc single atom residues: {' CA': 1}
          Unusual residues: {'RXY': 1}
          Classifications: {'peptide': 2, 'undetermined': 1}
          Link IDs: {'TRANS': 1}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 45
  Time building chain proxies: 1.32, per 1000 atoms: 0.20
  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: 0.43
  Conformation dependent library (CDL) restraints added in 390.3 milliseconds
  

  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: 0.12
  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: 0.74

  Time building geometry restraints manager: 0.58 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:             3.470
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.010
  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:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
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 are 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/Z
  covalent geometry    : bond        0.00812 /  0.40 ( 6816)
  covalent geometry    : angle       0.96130 /  0.40 ( 9274)
  SS BOND              : bond        0.00227 /  0.11 (    2)
  SS BOND              : angle       0.67024 /  0.37 (    4)
  hydrogen bonds       : bond        0.09318 /  6.51 (  404)
  hydrogen bonds       : angle       4.62007 /  3.32 ( 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  : 0.141 
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: 0.6587 (t80)
  outliers start: 2
  outliers final: 2
  residues processed: 55
  average time/residue: 0.0496
  time to fit residues: 4.1785
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  : 0.195 
-------------------------------------------------------------------------------
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...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.215044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.172407 restraints weight = 8522.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.4124 rms_B_bonded: 1.99
r_work: 0.3948 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3821 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.0724

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= 0.130
  Angle     :  0.536   6.281   9278  Z= 0.271
  Chirality :  0.039   0.133    986
  Planarity :  0.005   0.049   1108
  Dihedral  : 23.250 176.384   1059
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.41 %
    Favored  : 82.70 %
  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 are 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 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 363 
 TYR   0.018   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/Z
  covalent geometry    : bond        0.00283 /  0.13 ( 6816)
  covalent geometry    : angle       0.53582 /  0.27 ( 9274)
  SS BOND              : bond        0.00285 /  0.14 (    2)
  SS BOND              : angle       0.82203 /  0.46 (    4)
  hydrogen bonds       : bond        0.04998 /  3.48 (  404)
  hydrogen bonds       : angle       4.15022 /  3.01 ( 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
  73 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.7085 (t80) cc_final: 0.6736 (t80)
REVERT: A  260 CYS cc_start: 0.7894 (m) cc_final: 0.7299 (m)
  outliers start: 13
  outliers final: 12
  residues processed: 67
  average time/residue: 0.0427
  time to fit residues: 4.5594
Evaluate side-chains
  67 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 14 optimal weight:    0.6980
   chunk 73 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 12 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.7380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.214191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 118)---------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.179160 restraints weight = 8492.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.4205 rms_B_bonded: 1.42
r_work: 0.4000 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3894 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.0934

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= 0.127
  Angle     :  0.503   6.217   9278  Z= 0.259
  Chirality :  0.038   0.130    986
  Planarity :  0.004   0.040   1108
  Dihedral  : 20.290 168.737   1056
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.15 %
    Favored  : 80.67 %
  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 are not related in a simple way.
  whole:  1.24 (0.30), residues: 756
  helix:  1.98 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.68 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 363 
 TYR   0.015   0.001   TYR A 366 
 PHE   0.006   0.001   PHE A 303 
 TRP   0.013   0.001   TRP B 204 
 HIS   0.004   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.13 ( 6816)
  covalent geometry    : angle       0.50312 /  0.26 ( 9274)
  SS BOND              : bond        0.00122 /  0.06 (    2)
  SS BOND              : angle       0.61767 /  0.38 (    4)
  hydrogen bonds       : bond        0.05031 /  3.51 (  404)
  hydrogen bonds       : angle       4.17075 /  3.02 ( 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
  70 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A  223 MET cc_start: 0.6757 (mmm) cc_final: 0.6475 (mmm)
REVERT: A  224 PHE cc_start: 0.6995 (t80) cc_final: 0.6708 (t80)
REVERT: A  260 CYS cc_start: 0.7694 (m) cc_final: 0.7036 (m)
  outliers start: 15
  outliers final: 13
  residues processed: 65
  average time/residue: 0.0397
  time to fit residues: 4.0871
Evaluate side-chains
  66 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
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  218 MET
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  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:    0.9990
   chunk 22 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 71 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.6180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.215079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 110)---------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.174629 restraints weight = 8540.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.4164 rms_B_bonded: 2.01
r_work: 0.3983 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3869 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.1147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6818  Z= 0.115
  Angle     :  0.483   6.034   9278  Z= 0.247
  Chirality :  0.038   0.128    986
  Planarity :  0.004   0.035   1108
  Dihedral  : 19.371 167.813   1056
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.72 %
    Favored  : 80.09 %
  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 are not related in a simple way.
  whole:  1.40 (0.31), residues: 756
  helix:  2.09 (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   0.004   0.000   ARG A 363 
 TYR   0.014   0.001   TYR B 366 
 PHE   0.009   0.001   PHE B 354 
 TRP   0.013   0.001   TRP A 204 
 HIS   0.004   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 6816)
  covalent geometry    : angle       0.48246 /  0.25 ( 9274)
  SS BOND              : bond        0.00095 /  0.05 (    2)
  SS BOND              : angle       0.61712 /  0.35 (    4)
  hydrogen bonds       : bond        0.04724 /  3.29 (  404)
  hydrogen bonds       : angle       4.12208 /  2.99 ( 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
  79 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 57
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.6961 (t80) cc_final: 0.6673 (t80)
REVERT: A  260 CYS cc_start: 0.7707 (m) cc_final: 0.7045 (m)
REVERT: A  324 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.7896 (t80)
REVERT: B  224 PHE cc_start: 0.7004 (t80) cc_final: 0.6689 (t80)
REVERT: B  324 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7881 (t80)
  outliers start: 22
  outliers final: 14
  residues processed: 74
  average time/residue: 0.0577
  time to fit residues: 6.2895
Evaluate side-chains
  72 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
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  248 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  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:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0980
   chunk 57 optimal weight:    3.9990
   chunk 74 optimal weight:   20.0000
   chunk 18 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 69 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4558 r_free = 0.4558 target = 0.215461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.179159 restraints weight = 8588.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.4205 rms_B_bonded: 1.58
r_work: 0.3993 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3884 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1235

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= 0.112
  Angle     :  0.484   7.810   9278  Z= 0.245
  Chirality :  0.037   0.125    986
  Planarity :  0.004   0.035   1108
  Dihedral  : 19.211 167.174   1056
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.01 %
    Favored  : 80.23 %
  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 are not related in a simple way.
  whole:  1.50 (0.30), residues: 756
  helix:  2.15 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.58 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 119 
 TYR   0.014   0.001   TYR A 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/Z
  covalent geometry    : bond        0.00241 /  0.11 ( 6816)
  covalent geometry    : angle       0.48413 /  0.25 ( 9274)
  SS BOND              : bond        0.00152 /  0.08 (    2)
  SS BOND              : angle       0.55955 /  0.33 (    4)
  hydrogen bonds       : bond        0.04639 /  3.24 (  404)
  hydrogen bonds       : angle       4.08944 /  2.97 ( 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
  75 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 56
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.6969 (t80) cc_final: 0.6685 (t80)
REVERT: A  260 CYS cc_start: 0.7713 (m) cc_final: 0.7056 (m)
REVERT: A  324 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7855 (t80)
REVERT: B  224 PHE cc_start: 0.7030 (t80) cc_final: 0.6716 (t80)
REVERT: B  260 CYS cc_start: 0.7861 (m) cc_final: 0.7018 (m)
REVERT: B  324 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.7849 (t80)
  outliers start: 19
  outliers final: 14
  residues processed: 70
  average time/residue: 0.0419
  time to fit residues: 4.6335
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  : 0.268 
-------------------------------------------------------------------------------
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  188 ASN
Chi-restraints excluded: chain A residue  218 MET
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  163 VAL
Chi-restraints excluded: chain B residue  218 MET
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 43 optimal weight:    0.4980
   chunk 55 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 58 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0970
   chunk 14 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 74 optimal weight:   20.0000
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.4978

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4564 r_free = 0.4564 target = 0.215892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 94)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.181920 restraints weight = 8569.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.4232 rms_B_bonded: 1.42
r_work: 0.4014 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3911 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6818  Z= 0.106
  Angle     :  0.469   7.026   9278  Z= 0.239
  Chirality :  0.037   0.126    986
  Planarity :  0.004   0.035   1108
  Dihedral  : 18.922 166.573   1056
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.44 %
    Favored  : 79.65 %
  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 are not related in a simple way.
  whole:  1.58 (0.30), residues: 756
  helix:  2.22 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.55 (0.37), 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 B 354 
 TRP   0.012   0.001   TRP B 204 
 HIS   0.004   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00225 /  0.11 ( 6816)
  covalent geometry    : angle       0.46879 /  0.24 ( 9274)
  SS BOND              : bond        0.00034 /  0.02 (    2)
  SS BOND              : angle       0.45649 /  0.25 (    4)
  hydrogen bonds       : bond        0.04498 /  3.14 (  404)
  hydrogen bonds       : angle       4.04239 /  2.94 ( 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
  76 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 56
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.6871 (t80) cc_final: 0.6606 (t80)
REVERT: A  260 CYS cc_start: 0.7615 (m) cc_final: 0.6950 (m)
REVERT: A  324 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7856 (t80)
REVERT: B  224 PHE cc_start: 0.6977 (t80) cc_final: 0.6649 (t80)
REVERT: B  260 CYS cc_start: 0.7716 (m) cc_final: 0.6852 (m)
REVERT: B  324 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7854 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 72
  average time/residue: 0.0431
  time to fit residues: 4.8909
Evaluate side-chains
  75 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
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  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  146 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  218 MET
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:    9.9990
   chunk 60 optimal weight:   20.0000
   chunk 66 optimal weight:    0.0030
   chunk 62 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.7192

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.220149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.178397 restraints weight = 8750.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.4171 rms_B_bonded: 1.68
r_work: 0.3957 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3849 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1453

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= 0.122
  Angle     :  0.495   8.763   9278  Z= 0.249
  Chirality :  0.038   0.127    986
  Planarity :  0.004   0.033   1108
  Dihedral  : 18.794 165.416   1056
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.01 %
    Favored  : 79.51 %
  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 are not related in a simple way.
  whole:  1.54 (0.30), residues: 756
  helix:  2.16 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.51 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 363 
 TYR   0.013   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/Z
  covalent geometry    : bond        0.00268 /  0.12 ( 6816)
  covalent geometry    : angle       0.49470 /  0.25 ( 9274)
  SS BOND              : bond        0.00159 /  0.08 (    2)
  SS BOND              : angle       0.42940 /  0.26 (    4)
  hydrogen bonds       : bond        0.04847 /  3.40 (  404)
  hydrogen bonds       : angle       4.08260 /  2.97 ( 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
  79 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 55
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.7030 (t80) cc_final: 0.6743 (t80)
REVERT: A  260 CYS cc_start: 0.7772 (m) cc_final: 0.7126 (m)
REVERT: A  324 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7884 (t80)
REVERT: B  260 CYS cc_start: 0.7856 (m) cc_final: 0.7019 (m)
REVERT: B  324 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7878 (t80)
  outliers start: 24
  outliers final: 16
  residues processed: 74
  average time/residue: 0.0391
  time to fit residues: 4.5885
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  : 0.168 
-------------------------------------------------------------------------------
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  218 MET
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 A residue  369 MET
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  218 MET
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:    0.7980
   chunk 75 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 74 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4548 r_free = 0.4548 target = 0.219621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.179125 restraints weight = 8900.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.4180 rms_B_bonded: 1.85
r_work: 0.3929 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.1542

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= 0.129
  Angle     :  0.503   8.030   9278  Z= 0.253
  Chirality :  0.038   0.130    986
  Planarity :  0.004   0.033   1108
  Dihedral  : 18.712 164.691   1056
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.31 %
    Favored  : 78.49 %
  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 are not related in a simple way.
  whole:  1.46 (0.30), residues: 756
  helix:  2.12 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.59 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 363 
 TYR   0.013   0.001   TYR B 366 
 PHE   0.008   0.001   PHE A 354 
 TRP   0.013   0.001   TRP B 204 
 HIS   0.004   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 ( 6816)
  covalent geometry    : angle       0.50335 /  0.25 ( 9274)
  SS BOND              : bond        0.00065 /  0.03 (    2)
  SS BOND              : angle       0.27816 /  0.13 (    4)
  hydrogen bonds       : bond        0.04952 /  3.47 (  404)
  hydrogen bonds       : angle       4.13174 /  3.01 ( 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
  78 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  223 MET cc_start: 0.6721 (mmm) cc_final: 0.6414 (mmm)
REVERT: A  224 PHE cc_start: 0.7029 (t80) cc_final: 0.6743 (t80)
REVERT: A  260 CYS cc_start: 0.7545 (m) cc_final: 0.6867 (m)
REVERT: A  324 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7838 (t80)
REVERT: B  260 CYS cc_start: 0.7634 (m) cc_final: 0.6727 (m)
REVERT: B  324 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.7918 (t80)
  outliers start: 22
  outliers final: 18
  residues processed: 72
  average time/residue: 0.0435
  time to fit residues: 4.9836
Evaluate side-chains
  76 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 56
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
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  264 THR
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  369 MET
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  218 MET
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 21 optimal weight:    9.9990
   chunk 62 optimal weight:    0.5980
   chunk 3 optimal weight:    0.1980
   chunk 60 optimal weight:   10.0000
   chunk 24 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4555 r_free = 0.4555 target = 0.214882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.180729 restraints weight = 8595.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.4224 rms_B_bonded: 1.43
r_work: 0.4003 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3897 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1594

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     :  0.484   8.224   9278  Z= 0.244
  Chirality :  0.038   0.125    986
  Planarity :  0.004   0.033   1108
  Dihedral  : 18.449 164.717   1056
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.60 %
    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 are not related in a simple way.
  whole:  1.58 (0.30), residues: 756
  helix:  2.22 (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 B 366 
 PHE   0.008   0.001   PHE B 354 
 TRP   0.012   0.001   TRP B 204 
 HIS   0.003   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 ( 6816)
  covalent geometry    : angle       0.48403 /  0.24 ( 9274)
  SS BOND              : bond        0.00143 /  0.07 (    2)
  SS BOND              : angle       0.58584 /  0.34 (    4)
  hydrogen bonds       : bond        0.04650 /  3.25 (  404)
  hydrogen bonds       : angle       4.08909 /  2.98 ( 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
  75 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 54
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.7008 (t80) cc_final: 0.6734 (t80)
REVERT: A  238 PHE cc_start: 0.4794 (OUTLIER) cc_final: 0.4492 (m-80)
REVERT: A  260 CYS cc_start: 0.7627 (m) cc_final: 0.6989 (m)
REVERT: A  324 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7859 (t80)
REVERT: B  224 PHE cc_start: 0.7024 (t80) cc_final: 0.6711 (t80)
REVERT: B  260 CYS cc_start: 0.7738 (m) cc_final: 0.6891 (m)
REVERT: B  324 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.7845 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 70
  average time/residue: 0.0358
  time to fit residues: 3.9677
Evaluate side-chains
  73 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
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  218 MET
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 A residue  369 MET
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  218 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 45 optimal weight:    0.3980
   chunk 34 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0000
   chunk 56 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 51 optimal weight:    7.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    0.5184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4561 r_free = 0.4561 target = 0.215520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 97)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.174822 restraints weight = 8513.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.4143 rms_B_bonded: 1.91
r_work: 0.3974 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3857 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6818  Z= 0.109
  Angle     :  0.479   7.790   9278  Z= 0.240
  Chirality :  0.037   0.124    986
  Planarity :  0.004   0.034   1108
  Dihedral  : 18.142 164.916   1056
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.90 %
    Favored  : 78.05 %
  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 are not related in a simple way.
  whole:  1.66 (0.30), residues: 756
  helix:  2.28 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.52 (0.37), 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 B 354 
 TRP   0.012   0.001   TRP A 204 
 HIS   0.003   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.11 ( 6816)
  covalent geometry    : angle       0.47884 /  0.24 ( 9274)
  SS BOND              : bond        0.00017 /  0.01 (    2)
  SS BOND              : angle       0.36582 /  0.18 (    4)
  hydrogen bonds       : bond        0.04481 /  3.13 (  404)
  hydrogen bonds       : angle       4.05430 /  2.96 ( 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
  76 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  223 MET cc_start: 0.6719 (mmm) cc_final: 0.6454 (mmm)
REVERT: A  224 PHE cc_start: 0.6929 (t80) cc_final: 0.6679 (t80)
REVERT: A  238 PHE cc_start: 0.4799 (OUTLIER) cc_final: 0.4484 (m-80)
REVERT: A  260 CYS cc_start: 0.7810 (m) cc_final: 0.7174 (m)
REVERT: A  324 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7874 (t80)
REVERT: B  223 MET cc_start: 0.6818 (mmm) cc_final: 0.6538 (mmm)
REVERT: B  224 PHE cc_start: 0.6946 (t80) cc_final: 0.6659 (t80)
REVERT: B  260 CYS cc_start: 0.7834 (m) cc_final: 0.6983 (m)
REVERT: B  324 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.7876 (t80)
  outliers start: 21
  outliers final: 18
  residues processed: 72
  average time/residue: 0.0488
  time to fit residues: 5.5594
Evaluate side-chains
  75 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 54
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
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  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 A residue  369 MET
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  218 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0060
   chunk 51 optimal weight:    8.9990
   chunk 75 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0060
   chunk 38 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.4212

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4569 r_free = 0.4569 target = 0.216484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 95)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.181249 restraints weight = 8572.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.4230 rms_B_bonded: 1.68
r_work: 0.4008 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3895 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6818  Z= 0.102
  Angle     :  0.471   8.126   9278  Z= 0.235
  Chirality :  0.037   0.124    986
  Planarity :  0.004   0.034   1108
  Dihedral  : 17.768 165.299   1056
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 19.04 %
    Favored  : 77.91 %
  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 are not related in a simple way.
  whole:  1.78 (0.30), residues: 756
  helix:  2.37 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.48 (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 B 354 
 TRP   0.012   0.001   TRP B 204 
 HIS   0.003   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00215 /  0.10 ( 6816)
  covalent geometry    : angle       0.47061 /  0.23 ( 9274)
  SS BOND              : bond        0.00229 /  0.12 (    2)
  SS BOND              : angle       0.72760 /  0.42 (    4)
  hydrogen bonds       : bond        0.04295 /  3.00 (  404)
  hydrogen bonds       : angle       4.00492 /  2.92 ( 1212)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1592.95 seconds
wall clock time: 27 minutes 54.66 seconds (1674.66 seconds total)