Starting phenix.real_space_refine
on Sun May 11 03:45:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8aw5_15691/05_2025/8aw5_15691.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8aw5_15691/05_2025/8aw5_15691.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8aw5_15691/05_2025/8aw5_15691.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8aw5_15691/05_2025/8aw5_15691.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8aw5_15691/05_2025/8aw5_15691.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8aw5_15691/05_2025/8aw5_15691.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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
     Fe      3      7.16       5
     P       9      5.49       5
     S      21      5.16       5
     C    4887      2.51       5
     N     975      2.21       5
     O    1128      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7023
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2142
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 9, 'TRANS': 256}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2142
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 9, 'TRANS': 256}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2142
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 9, 'TRANS': 256}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 199
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 199
          Unusual residues: {'HEM': 1, 'POV': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 199
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 199
          Unusual residues: {'HEM': 1, 'POV': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 199
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 199
          Unusual residues: {'HEM': 1, 'POV': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 4.61, per 1000 atoms: 0.66
  Number of scatterers: 7023
  At special positions: 0
  Unit cell: (88.56, 93.48, 72.57, 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)
     Fe      3     26.01
     S      21     16.00
     P       9     15.00
     O    1128      8.00
     N     975      7.00
     C    4887      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.87
  Conformation dependent library (CDL) restraints added in 887.1 milliseconds
  

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 0 sheets defined
      82.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 33
    Processing helix  chain 'A' and resid 52 through 56
    Processing helix  chain 'A' and resid 74 through 101
      removed outlier: 3.801A  pdb=" N   GLU A  78 " --> pdb=" O   GLN A  74 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   PHE A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LYS A 101 " --> pdb=" O   PHE A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 126
    Processing helix  chain 'A' and resid 133 through 167
      removed outlier: 3.642A  pdb=" N   LEU A 149 " --> pdb=" O   THR A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 200
    Processing helix  chain 'A' and resid 203 through 231
      removed outlier: 4.082A  pdb=" N   GLY A 218 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE A 219 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 256
    Processing helix  chain 'A' and resid 259 through 287
      Proline residue:  A 283  - end of helix
    Processing helix  chain 'B' and resid 11 through 33
    Processing helix  chain 'B' and resid 52 through 56
    Processing helix  chain 'B' and resid 74 through 101
      removed outlier: 3.800A  pdb=" N   GLU B  78 " --> pdb=" O   GLN B  74 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   PHE B 100 " --> pdb=" O   LEU B  96 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LYS B 101 " --> pdb=" O   PHE B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 126
    Processing helix  chain 'B' and resid 133 through 167
      removed outlier: 3.643A  pdb=" N   LEU B 149 " --> pdb=" O   THR B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 200
    Processing helix  chain 'B' and resid 203 through 231
      removed outlier: 4.081A  pdb=" N   GLY B 218 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   PHE B 219 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 256
    Processing helix  chain 'B' and resid 259 through 287
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'C' and resid 11 through 33
    Processing helix  chain 'C' and resid 52 through 56
    Processing helix  chain 'C' and resid 74 through 101
      removed outlier: 3.800A  pdb=" N   GLU C  78 " --> pdb=" O   GLN C  74 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   PHE C 100 " --> pdb=" O   LEU C  96 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LYS C 101 " --> pdb=" O   PHE C  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 126
    Processing helix  chain 'C' and resid 133 through 167
      removed outlier: 3.642A  pdb=" N   LEU C 149 " --> pdb=" O   THR C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 200
    Processing helix  chain 'C' and resid 203 through 231
      removed outlier: 4.081A  pdb=" N   GLY C 218 " --> pdb=" O   ILE C 214 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE C 219 " --> pdb=" O   THR C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 256
    Processing helix  chain 'C' and resid 259 through 287
      Proline residue:  C 283  - end of helix

    523 hydrogen bonds defined for protein.
    1551 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.80

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        1.21 -     1.38: 2444
        1.38 -     1.55: 4708
        1.55 -     1.72: 21
        1.72 -     1.89: 36
        1.89 -     2.06: 12
  Bond restraints: 7221
  Sorted by residual:
  bond pdb=" C21 POV C 404 "
       pdb=" O22 POV C 404 "
    ideal  model  delta    sigma   weight residual
    1.205  1.438 -0.233 2.00e-02 2.50e+03 1.36e+02
  bond pdb=" C21 POV A 402 "
       pdb=" O22 POV A 402 "
    ideal  model  delta    sigma   weight residual
    1.205  1.438 -0.233 2.00e-02 2.50e+03 1.35e+02
  bond pdb=" C21 POV B 402 "
       pdb=" O22 POV B 402 "
    ideal  model  delta    sigma   weight residual
    1.205  1.438 -0.233 2.00e-02 2.50e+03 1.35e+02
  bond pdb=" C21 POV A 404 "
       pdb=" O22 POV A 404 "
    ideal  model  delta    sigma   weight residual
    1.205  1.434 -0.229 2.00e-02 2.50e+03 1.31e+02
  bond pdb=" C21 POV A 403 "
       pdb=" O22 POV A 403 "
    ideal  model  delta    sigma   weight residual
    1.205  1.434 -0.229 2.00e-02 2.50e+03 1.31e+02
  ... (remaining 7216 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.45: 9472
        3.45 -     6.90: 219
        6.90 -    10.35: 29
       10.35 -    13.80: 24
       13.80 -    17.25: 48
  Bond angle restraints: 9792
  Sorted by residual:
  angle pdb=" N   GLU C 204 "
        pdb=" CA  GLU C 204 "
        pdb=" C   GLU C 204 "
      ideal   model   delta    sigma   weight residual
     111.69   99.00   12.69 1.23e+00 6.61e-01 1.07e+02
  angle pdb=" N   GLU A 204 "
        pdb=" CA  GLU A 204 "
        pdb=" C   GLU A 204 "
      ideal   model   delta    sigma   weight residual
     111.69   99.01   12.68 1.23e+00 6.61e-01 1.06e+02
  angle pdb=" N   GLU B 204 "
        pdb=" CA  GLU B 204 "
        pdb=" C   GLU B 204 "
      ideal   model   delta    sigma   weight residual
     112.45   98.98   13.47 1.39e+00 5.18e-01 9.39e+01
  angle pdb=" N   VAL C  32 "
        pdb=" CA  VAL C  32 "
        pdb=" C   VAL C  32 "
      ideal   model   delta    sigma   weight residual
     111.45  103.72    7.73 9.30e-01 1.16e+00 6.92e+01
  angle pdb=" N   VAL B  32 "
        pdb=" CA  VAL B  32 "
        pdb=" C   VAL B  32 "
      ideal   model   delta    sigma   weight residual
     111.45  103.73    7.72 9.30e-01 1.16e+00 6.89e+01
  ... (remaining 9787 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.36: 3951
       28.36 -    56.72: 150
       56.72 -    85.07: 45
       85.07 -   113.43: 18
      113.43 -   141.79: 6
  Dihedral angle restraints: 4170
    sinusoidal: 1827
      harmonic: 2343
  Sorted by residual:
  dihedral pdb=" C3  POV C 404 "
           pdb=" C31 POV C 404 "
           pdb=" O31 POV C 404 "
           pdb=" C32 POV C 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     172.61  -45.60 -141.79     1      3.00e+01 1.11e-03 1.90e+01
  dihedral pdb=" C3  POV A 402 "
           pdb=" C31 POV A 402 "
           pdb=" O31 POV A 402 "
           pdb=" C32 POV A 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     172.61  -45.64 -141.75     1      3.00e+01 1.11e-03 1.90e+01
  dihedral pdb=" C3  POV B 402 "
           pdb=" C31 POV B 402 "
           pdb=" O31 POV B 402 "
           pdb=" C32 POV B 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     172.61  -45.67 -141.72     1      3.00e+01 1.11e-03 1.90e+01
  ... (remaining 4167 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 779
       0.062 -    0.123: 235
       0.123 -    0.185: 65
       0.185 -    0.247: 10
       0.247 -    0.309: 12
  Chirality restraints: 1101
  Sorted by residual:
  chirality pdb=" CA  GLU A 204 "
            pdb=" N   GLU A 204 "
            pdb=" C   GLU A 204 "
            pdb=" CB  GLU A 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" CA  GLU B 204 "
            pdb=" N   GLU B 204 "
            pdb=" C   GLU B 204 "
            pdb=" CB  GLU B 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" CA  GLU C 204 "
            pdb=" N   GLU C 204 "
            pdb=" C   GLU C 204 "
            pdb=" CB  GLU C 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.36e+00
  ... (remaining 1098 not shown)

  Planarity restraints: 1095
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV C 402 "   -0.151 2.00e-02 2.50e+03   2.72e-01 7.38e+02
        pdb=" C29 POV C 402 "    0.352 2.00e-02 2.50e+03
        pdb="C210 POV C 402 "   -0.354 2.00e-02 2.50e+03
        pdb="C211 POV C 402 "    0.152 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV A 403 "   -0.151 2.00e-02 2.50e+03   2.72e-01 7.37e+02
        pdb=" C29 POV A 403 "    0.352 2.00e-02 2.50e+03
        pdb="C210 POV A 403 "   -0.354 2.00e-02 2.50e+03
        pdb="C211 POV A 403 "    0.152 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV B 403 "    0.150 2.00e-02 2.50e+03   2.72e-01 7.37e+02
        pdb=" C29 POV B 403 "   -0.352 2.00e-02 2.50e+03
        pdb="C210 POV B 403 "    0.354 2.00e-02 2.50e+03
        pdb="C211 POV B 403 "   -0.152 2.00e-02 2.50e+03
  ... (remaining 1092 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.92: 2862
        2.92 -     3.42: 7633
        3.42 -     3.91: 12228
        3.91 -     4.41: 13913
        4.41 -     4.90: 22736
  Nonbonded interactions: 59372
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 157 "
            pdb=" OH  TYR A 184 "
     model   vdw
     2.427 3.040
  nonbonded pdb=" OG  SER B 157 "
            pdb=" OH  TYR B 184 "
     model   vdw
     2.427 3.040
  nonbonded pdb=" OG  SER C 157 "
            pdb=" OH  TYR C 184 "
     model   vdw
     2.428 3.040
  nonbonded pdb=" O   GLY B  29 "
            pdb=" OG1 THR B  33 "
     model   vdw
     2.446 3.040
  nonbonded pdb=" O   GLY A  29 "
            pdb=" OG1 THR A  33 "
     model   vdw
     2.446 3.040
  ... (remaining 59367 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  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:             0.790
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.680
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
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      :  0.018   0.351   7224  Z= 0.925
  Angle     :  1.758  17.246   9792  Z= 0.905
  Chirality :  0.070   0.309   1101
  Planarity :  0.036   0.272   1095
  Dihedral  : 18.375 141.787   2676
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  4.58 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  6.06 %
    Favored  : 93.51 %
  Cbeta Deviations :  0.40 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.31), residues: 786
  helix:  1.25 (0.21), residues: 621
  sheet:  None (None), residues: 0
  loop : -3.62 (0.42), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 276 
 HIS   0.002   0.001   HIS C  81 
 PHE   0.014   0.002   PHE A 272 
 TYR   0.010   0.001   TYR B 164 
 ARG   0.002   0.000   ARG A 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12127 (  523)
  hydrogen bonds       : angle       5.69009 ( 1551)
  covalent geometry    : bond        0.01662 ( 7221)
  covalent geometry    : angle       1.75754 ( 9792)
  Misc. bond           : bond        0.35008 (    3)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 178
  time to evaluate  : 0.671 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8819 (mt) cc_final: 0.8500 (mt)
REVERT: A  171 GLU cc_start: 0.8036 (mp0) cc_final: 0.7750 (mp0)
REVERT: B  143 VAL cc_start: 0.8928 (t) cc_final: 0.8700 (t)
REVERT: B  203 LEU cc_start: 0.8183 (tp) cc_final: 0.7942 (tp)
REVERT: B  246 GLN cc_start: 0.9056 (tp40) cc_final: 0.8711 (tp40)
REVERT: C  243 MET cc_start: 0.8768 (mmt) cc_final: 0.8409 (mmt)
  outliers start: 3
  outliers final: 0
  residues processed: 178
  average time/residue: 1.0487
  time to fit residues: 197.3417
Evaluate side-chains
  105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 141 HIS
C  74 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.133487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.096204 restraints weight = 7964.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 1.57
r_work: 0.2788 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2657 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.107   7224  Z= 0.175
  Angle     :  0.672  12.934   9792  Z= 0.318
  Chirality :  0.041   0.197   1101
  Planarity :  0.004   0.045   1095
  Dihedral  : 19.676 133.384   1278
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 14.86 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.30), residues: 786
  helix:  2.45 (0.20), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.82 (0.44), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  44 
 HIS   0.004   0.001   HIS B 213 
 PHE   0.016   0.002   PHE B 272 
 TYR   0.015   0.001   TYR C 199 
 ARG   0.001   0.000   ARG B  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04998 (  523)
  hydrogen bonds       : angle       3.85906 ( 1551)
  covalent geometry    : bond        0.00442 ( 7221)
  covalent geometry    : angle       0.67184 ( 9792)
  Misc. bond           : bond        0.07844 (    3)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.680 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8839 (mt) cc_final: 0.8487 (mt)
REVERT: A   78 GLU cc_start: 0.8015 (tp30) cc_final: 0.7721 (tp30)
REVERT: A  171 GLU cc_start: 0.8425 (mp0) cc_final: 0.7982 (mp0)
REVERT: A  172 ARG cc_start: 0.6735 (tpm170) cc_final: 0.6311 (tpp-160)
REVERT: A  201 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8082 (mmtp)
REVERT: B  171 GLU cc_start: 0.7998 (mp0) cc_final: 0.7765 (mp0)
REVERT: B  172 ARG cc_start: 0.6762 (tpm170) cc_final: 0.6422 (tpp-160)
REVERT: C  243 MET cc_start: 0.9212 (mmt) cc_final: 0.8868 (mmt)
  outliers start: 24
  outliers final: 6
  residues processed: 116
  average time/residue: 1.3924
  time to fit residues: 168.8227
Evaluate side-chains
  95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain C residue  181 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 141 HIS
B 141 HIS
B 246 GLN
C  74 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.131453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.095915 restraints weight = 8086.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 1.48
r_work: 0.2772 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2642 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.117   7224  Z= 0.161
  Angle     :  0.625  13.181   9792  Z= 0.299
  Chirality :  0.039   0.193   1101
  Planarity :  0.004   0.043   1095
  Dihedral  : 18.687 130.952   1278
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 14.14 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.30), residues: 786
  helix:  2.79 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.66 (0.46), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  44 
 HIS   0.004   0.001   HIS B 213 
 PHE   0.016   0.002   PHE B 272 
 TYR   0.014   0.001   TYR C 199 
 ARG   0.002   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04767 (  523)
  hydrogen bonds       : angle       3.76703 ( 1551)
  covalent geometry    : bond        0.00417 ( 7221)
  covalent geometry    : angle       0.62472 ( 9792)
  Misc. bond           : bond        0.10136 (    3)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.742 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8848 (mt) cc_final: 0.8502 (mt)
REVERT: A   78 GLU cc_start: 0.8116 (tp30) cc_final: 0.7724 (tp30)
REVERT: A  171 GLU cc_start: 0.8483 (mp0) cc_final: 0.8174 (mp0)
REVERT: A  172 ARG cc_start: 0.6936 (tpm170) cc_final: 0.6537 (tpp-160)
REVERT: A  201 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8099 (mmtm)
REVERT: A  258 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7136 (t80)
REVERT: B   78 GLU cc_start: 0.7851 (tp30) cc_final: 0.7564 (tp30)
REVERT: B  143 VAL cc_start: 0.9077 (t) cc_final: 0.8821 (t)
REVERT: B  172 ARG cc_start: 0.6895 (tpm170) cc_final: 0.6633 (tpp-160)
REVERT: B  234 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8390 (ptmm)
REVERT: C  243 MET cc_start: 0.9214 (mmt) cc_final: 0.8935 (mmt)
REVERT: C  258 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.6976 (t80)
  outliers start: 30
  outliers final: 12
  residues processed: 117
  average time/residue: 1.3459
  time to fit residues: 164.9899
Evaluate side-chains
  110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 TRP
Chi-restraints excluded: chain A residue   82 ARG
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain B residue   82 ARG
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  234 LYS
Chi-restraints excluded: chain B residue  258 PHE
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  181 ASP
Chi-restraints excluded: chain C residue  258 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 73 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0970
   chunk 28 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
B 141 HIS
B 246 GLN
C  74 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.131790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.095180 restraints weight = 8175.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 1.53
r_work: 0.2773 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2642 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.121   7224  Z= 0.157
  Angle     :  0.621  13.771   9792  Z= 0.294
  Chirality :  0.039   0.212   1101
  Planarity :  0.004   0.044   1095
  Dihedral  : 18.197 133.629   1278
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.58 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.81 (0.30), residues: 786
  helix:  2.85 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.56 (0.46), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 276 
 HIS   0.003   0.001   HIS C 213 
 PHE   0.015   0.002   PHE B 272 
 TYR   0.013   0.001   TYR C 199 
 ARG   0.003   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04638 (  523)
  hydrogen bonds       : angle       3.73055 ( 1551)
  covalent geometry    : bond        0.00408 ( 7221)
  covalent geometry    : angle       0.62119 ( 9792)
  Misc. bond           : bond        0.11195 (    3)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8841 (mt) cc_final: 0.8474 (mt)
REVERT: A   78 GLU cc_start: 0.8198 (tp30) cc_final: 0.7835 (tp30)
REVERT: A  171 GLU cc_start: 0.8576 (mp0) cc_final: 0.8265 (mp0)
REVERT: A  258 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7149 (t80)
REVERT: A  287 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8232 (ptmm)
REVERT: B   78 GLU cc_start: 0.7820 (tp30) cc_final: 0.7511 (tp30)
REVERT: B  143 VAL cc_start: 0.8985 (t) cc_final: 0.8731 (t)
REVERT: B  172 ARG cc_start: 0.6938 (tpm170) cc_final: 0.6614 (tpp-160)
REVERT: B  234 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8341 (ptmm)
REVERT: C   78 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7781 (tp30)
REVERT: C  243 MET cc_start: 0.9207 (mmt) cc_final: 0.8929 (mmt)
REVERT: C  258 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.6928 (t80)
  outliers start: 22
  outliers final: 8
  residues processed: 108
  average time/residue: 1.3893
  time to fit residues: 157.2409
Evaluate side-chains
  105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ARG
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  287 LYS
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  234 LYS
Chi-restraints excluded: chain C residue  181 ASP
Chi-restraints excluded: chain C residue  258 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 75 optimal weight:    0.4980
   chunk 40 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
C  74 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.130594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.094655 restraints weight = 8049.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 1.48
r_work: 0.2776 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.3001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.127   7224  Z= 0.151
  Angle     :  0.615  13.862   9792  Z= 0.292
  Chirality :  0.039   0.211   1101
  Planarity :  0.004   0.044   1095
  Dihedral  : 17.867 131.367   1278
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 14.86 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.84 (0.30), residues: 786
  helix:  2.86 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.50 (0.46), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 276 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.015   0.002   PHE C 272 
 TYR   0.014   0.001   TYR C 199 
 ARG   0.003   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04564 (  523)
  hydrogen bonds       : angle       3.69207 ( 1551)
  covalent geometry    : bond        0.00391 ( 7221)
  covalent geometry    : angle       0.61504 ( 9792)
  Misc. bond           : bond        0.11575 (    3)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 97
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8890 (mt) cc_final: 0.8551 (mt)
REVERT: A   78 GLU cc_start: 0.8194 (tp30) cc_final: 0.7782 (tp30)
REVERT: A  171 GLU cc_start: 0.8584 (mp0) cc_final: 0.8231 (mp0)
REVERT: A  172 ARG cc_start: 0.6639 (tpm170) cc_final: 0.6426 (mmp-170)
REVERT: A  203 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8393 (tm)
REVERT: A  258 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.6951 (t80)
REVERT: B   78 GLU cc_start: 0.7852 (tp30) cc_final: 0.7550 (tp30)
REVERT: B  143 VAL cc_start: 0.9043 (t) cc_final: 0.8796 (t)
REVERT: B  172 ARG cc_start: 0.6966 (tpm170) cc_final: 0.6353 (mmp80)
REVERT: B  234 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8388 (ptmm)
REVERT: C   78 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7648 (tp30)
REVERT: C  243 MET cc_start: 0.9202 (mmt) cc_final: 0.8999 (mmt)
REVERT: C  258 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.6829 (t80)
  outliers start: 29
  outliers final: 13
  residues processed: 115
  average time/residue: 1.3875
  time to fit residues: 166.9898
Evaluate side-chains
  109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ARG
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain B residue   82 ARG
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  174 LYS
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  234 LYS
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  181 ASP
Chi-restraints excluded: chain C residue  258 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0470
   chunk 56 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0570
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 141 HIS
B 141 HIS
C 141 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.132795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.096866 restraints weight = 8197.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 1.50
r_work: 0.2809 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2679 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.098   7224  Z= 0.126
  Angle     :  0.588  13.775   9792  Z= 0.280
  Chirality :  0.038   0.216   1101
  Planarity :  0.004   0.043   1095
  Dihedral  : 17.295 123.591   1278
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.42 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.03 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.97 (0.30), residues: 786
  helix:  2.96 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.50 (0.46), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 276 
 HIS   0.003   0.001   HIS C 213 
 PHE   0.013   0.001   PHE C 272 
 TYR   0.013   0.001   TYR C 199 
 ARG   0.003   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04269 (  523)
  hydrogen bonds       : angle       3.62738 ( 1551)
  covalent geometry    : bond        0.00320 ( 7221)
  covalent geometry    : angle       0.58786 ( 9792)
  Misc. bond           : bond        0.09446 (    3)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8852 (mt) cc_final: 0.8537 (mt)
REVERT: A   78 GLU cc_start: 0.8237 (tp30) cc_final: 0.7808 (tp30)
REVERT: A  171 GLU cc_start: 0.8561 (mp0) cc_final: 0.8231 (mp0)
REVERT: A  258 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.6836 (t80)
REVERT: B   78 GLU cc_start: 0.7851 (tp30) cc_final: 0.7542 (tp30)
REVERT: B  143 VAL cc_start: 0.9007 (t) cc_final: 0.8789 (t)
REVERT: B  172 ARG cc_start: 0.6939 (tpm170) cc_final: 0.6347 (mmp80)
REVERT: C   78 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7562 (tp30)
REVERT: C  243 MET cc_start: 0.9181 (mmt) cc_final: 0.8945 (mmt)
REVERT: C  258 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.6932 (t80)
  outliers start: 17
  outliers final: 7
  residues processed: 110
  average time/residue: 1.3941
  time to fit residues: 160.5384
Evaluate side-chains
  105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 TRP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  258 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 25 optimal weight:    0.1980
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0370
   chunk 40 optimal weight:    0.8980
   chunk 58 optimal weight:    0.2980
   chunk 44 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.3658

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 141 HIS
B 141 HIS
C  74 GLN
C 141 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.133813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.096872 restraints weight = 8108.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 1.55
r_work: 0.2817 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2688 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   7224  Z= 0.123
  Angle     :  0.568   6.342   9792  Z= 0.276
  Chirality :  0.037   0.128   1101
  Planarity :  0.004   0.040   1095
  Dihedral  : 16.947 116.329   1278
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.54 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.88 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.97 (0.30), residues: 786
  helix:  2.97 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.56 (0.46), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 276 
 HIS   0.002   0.001   HIS C 213 
 PHE   0.013   0.001   PHE C 272 
 TYR   0.012   0.001   TYR C 199 
 ARG   0.002   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04186 (  523)
  hydrogen bonds       : angle       3.64072 ( 1551)
  covalent geometry    : bond        0.00311 ( 7221)
  covalent geometry    : angle       0.56835 ( 9792)
  Misc. bond           : bond        0.09141 (    3)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.662 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8864 (mt) cc_final: 0.8538 (mt)
REVERT: A   78 GLU cc_start: 0.8230 (tp30) cc_final: 0.7817 (tp30)
REVERT: A  171 GLU cc_start: 0.8545 (mp0) cc_final: 0.8331 (mp0)
REVERT: A  172 ARG cc_start: 0.7587 (mmp-170) cc_final: 0.7044 (mmp80)
REVERT: A  258 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.6812 (t80)
REVERT: B   78 GLU cc_start: 0.7789 (tp30) cc_final: 0.7487 (tp30)
REVERT: B  143 VAL cc_start: 0.8984 (t) cc_final: 0.8761 (t)
REVERT: B  172 ARG cc_start: 0.6936 (tpm170) cc_final: 0.6364 (mmp80)
REVERT: C   78 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7577 (tp30)
REVERT: C  258 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.6901 (t80)
  outliers start: 21
  outliers final: 8
  residues processed: 110
  average time/residue: 1.3018
  time to fit residues: 150.2742
Evaluate side-chains
  105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  181 ASP
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain C residue  258 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 23 optimal weight:    0.3980
   chunk 59 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0980
   chunk 54 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 141 HIS
B 141 HIS
C 141 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.131868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.095907 restraints weight = 8162.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 1.49
r_work: 0.2790 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2661 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.112   7224  Z= 0.136
  Angle     :  0.601   6.586   9792  Z= 0.292
  Chirality :  0.038   0.132   1101
  Planarity :  0.004   0.041   1095
  Dihedral  : 16.925 113.565   1278
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.67 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.32 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.91 (0.30), residues: 786
  helix:  2.94 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.63 (0.45), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 276 
 HIS   0.002   0.001   HIS C 213 
 PHE   0.014   0.002   PHE B 272 
 TYR   0.014   0.001   TYR C 199 
 ARG   0.002   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04339 (  523)
  hydrogen bonds       : angle       3.68681 ( 1551)
  covalent geometry    : bond        0.00349 ( 7221)
  covalent geometry    : angle       0.60065 ( 9792)
  Misc. bond           : bond        0.10397 (    3)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.862 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8864 (mt) cc_final: 0.8535 (mt)
REVERT: A   78 GLU cc_start: 0.8219 (tp30) cc_final: 0.7789 (tp30)
REVERT: A  171 GLU cc_start: 0.8559 (mp0) cc_final: 0.8275 (mp0)
REVERT: A  247 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9081 (mt)
REVERT: A  258 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.6831 (t80)
REVERT: B   78 GLU cc_start: 0.7775 (tp30) cc_final: 0.7487 (tp30)
REVERT: B  143 VAL cc_start: 0.9016 (t) cc_final: 0.8784 (t)
REVERT: B  172 ARG cc_start: 0.6935 (tpm170) cc_final: 0.6382 (mmp80)
REVERT: C   78 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7398 (tp30)
REVERT: C   82 ARG cc_start: 0.8187 (mtp180) cc_final: 0.7456 (mmm-85)
REVERT: C  258 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.6841 (t80)
  outliers start: 14
  outliers final: 8
  residues processed: 103
  average time/residue: 1.4518
  time to fit residues: 156.3581
Evaluate side-chains
  103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain C residue  181 ASP
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain C residue  258 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 70 optimal weight:    0.1980
   chunk 11 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0170
   chunk 14 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 40 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
A 141 HIS
B 141 HIS
C 141 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.133727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.097168 restraints weight = 8186.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 1.54
r_work: 0.2809 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2681 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105   7224  Z= 0.130
  Angle     :  0.582   6.398   9792  Z= 0.283
  Chirality :  0.038   0.129   1101
  Planarity :  0.004   0.038   1095
  Dihedral  : 16.529 109.446   1278
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.80 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.88 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.94 (0.29), residues: 786
  helix:  2.96 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.61 (0.45), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 276 
 HIS   0.003   0.001   HIS C 213 
 PHE   0.014   0.001   PHE C 272 
 TYR   0.013   0.001   TYR C 199 
 ARG   0.002   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04243 (  523)
  hydrogen bonds       : angle       3.66383 ( 1551)
  covalent geometry    : bond        0.00336 ( 7221)
  covalent geometry    : angle       0.58238 ( 9792)
  Misc. bond           : bond        0.09839 (    3)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.741 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8869 (mt) cc_final: 0.8538 (mt)
REVERT: A   78 GLU cc_start: 0.8251 (tp30) cc_final: 0.7820 (tp30)
REVERT: A  171 GLU cc_start: 0.8560 (mp0) cc_final: 0.8282 (mp0)
REVERT: A  247 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9063 (mt)
REVERT: A  258 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.6795 (t80)
REVERT: B   78 GLU cc_start: 0.7776 (tp30) cc_final: 0.7489 (tp30)
REVERT: B  143 VAL cc_start: 0.9000 (t) cc_final: 0.8785 (t)
REVERT: B  172 ARG cc_start: 0.6924 (tpm170) cc_final: 0.6369 (mmp80)
REVERT: C   78 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7604 (tp30)
REVERT: C  258 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.6883 (t80)
  outliers start: 16
  outliers final: 10
  residues processed: 102
  average time/residue: 1.4783
  time to fit residues: 157.6283
Evaluate side-chains
  106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 TRP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  258 PHE
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain C residue  181 ASP
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain C residue  258 PHE
Chi-restraints excluded: chain C residue  260 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    0.2980
   chunk 72 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 75 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 141 HIS
B 141 HIS
C 141 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.130419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.093247 restraints weight = 8300.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 1.57
r_work: 0.2768 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2637 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.123   7224  Z= 0.159
  Angle     :  0.623   6.498   9792  Z= 0.299
  Chirality :  0.039   0.142   1101
  Planarity :  0.004   0.040   1095
  Dihedral  : 16.903 113.476   1278
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.80 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.03 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.82 (0.29), residues: 786
  helix:  2.86 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.57 (0.46), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  76 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.016   0.002   PHE C 272 
 TYR   0.016   0.001   TYR C 199 
 ARG   0.002   0.000   ARG C 198 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04553 (  523)
  hydrogen bonds       : angle       3.73924 ( 1551)
  covalent geometry    : bond        0.00417 ( 7221)
  covalent geometry    : angle       0.62290 ( 9792)
  Misc. bond           : bond        0.11201 (    3)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.756 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8898 (mt) cc_final: 0.8539 (mt)
REVERT: A   78 GLU cc_start: 0.8238 (tp30) cc_final: 0.7822 (tp30)
REVERT: A  171 GLU cc_start: 0.8600 (mp0) cc_final: 0.8322 (mp0)
REVERT: A  258 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.6905 (t80)
REVERT: B   78 GLU cc_start: 0.7757 (tp30) cc_final: 0.7478 (tp30)
REVERT: B  143 VAL cc_start: 0.9042 (t) cc_final: 0.8806 (t)
REVERT: B  172 ARG cc_start: 0.6948 (tpm170) cc_final: 0.6384 (mmp80)
REVERT: C   78 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7603 (tp30)
REVERT: C  258 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.6767 (t80)
  outliers start: 15
  outliers final: 9
  residues processed: 103
  average time/residue: 1.4030
  time to fit residues: 151.1100
Evaluate side-chains
  104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain C residue  181 ASP
Chi-restraints excluded: chain C residue  203 LEU
Chi-restraints excluded: chain C residue  258 PHE
Chi-restraints excluded: chain C residue  260 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 56 optimal weight:    0.3980
   chunk 40 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0570
   chunk 30 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 141 HIS
B 141 HIS
C 141 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.133526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.096844 restraints weight = 8173.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 1.54
r_work: 0.2816 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2686 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   7224  Z= 0.132
  Angle     :  0.585   6.398   9792  Z= 0.283
  Chirality :  0.038   0.141   1101
  Planarity :  0.004   0.038   1095
  Dihedral  : 16.624 107.299   1278
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.93 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.88 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.91 (0.29), residues: 786
  helix:  2.92 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.56 (0.46), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  76 
 HIS   0.003   0.001   HIS C 213 
 PHE   0.013   0.001   PHE B 272 
 TYR   0.013   0.001   TYR C 199 
 ARG   0.002   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04296 (  523)
  hydrogen bonds       : angle       3.68236 ( 1551)
  covalent geometry    : bond        0.00342 ( 7221)
  covalent geometry    : angle       0.58525 ( 9792)
  Misc. bond           : bond        0.09901 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5498.43 seconds
wall clock time: 95 minutes 18.34 seconds (5718.34 seconds total)