Starting phenix.real_space_refine
on Fri Jul 25 10:05:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8aw5_15691/07_2025/8aw5_15691.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8aw5_15691/07_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_15691/07_2025/8aw5_15691.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8aw5_15691/07_2025/8aw5_15691.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8aw5_15691/07_2025/8aw5_15691.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8aw5_15691/07_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 4.81, per 1000 atoms: 0.68
  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: 2.01
  Conformation dependent library (CDL) restraints added in 979.0 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: 0.56
  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: 1.91

  Time building geometry restraints manager: 2.32 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:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.400
  Find NCS groups from input model:        0.130
  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:12.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.560
-------------------------------------------------------------------------------
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  : 0.669 
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: 1.0666
  time to fit residues: 200.5727
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  : 0.682 
-------------------------------------------------------------------------------
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 = 49)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.096219 restraints weight = 7964.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 1.57
r_work: 0.2793 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2661 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
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  : 0.719 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8839 (mt) cc_final: 0.8488 (mt)
REVERT: A   78 GLU cc_start: 0.8014 (tp30) cc_final: 0.7720 (tp30)
REVERT: A  171 GLU cc_start: 0.8424 (mp0) cc_final: 0.7981 (mp0)
REVERT: A  172 ARG cc_start: 0.6735 (tpm170) cc_final: 0.6312 (tpp-160)
REVERT: A  201 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8080 (mmtp)
REVERT: B  171 GLU cc_start: 0.8001 (mp0) cc_final: 0.7766 (mp0)
REVERT: B  172 ARG cc_start: 0.6761 (tpm170) cc_final: 0.6422 (tpp-160)
REVERT: C  243 MET cc_start: 0.9213 (mmt) cc_final: 0.8869 (mmt)
  outliers start: 24
  outliers final: 6
  residues processed: 116
  average time/residue: 1.4270
  time to fit residues: 173.2601
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  : 0.718 
-------------------------------------------------------------------------------
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:    0.9980
   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:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3512 r_free = 0.3512 target = 0.132399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.095261 restraints weight = 8083.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 1.55
r_work: 0.2774 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2644 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.114   7224  Z= 0.158
  Angle     :  0.622  13.179   9792  Z= 0.297
  Chirality :  0.039   0.194   1101
  Planarity :  0.004   0.043   1095
  Dihedral  : 18.626 130.058   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 :  4.18 %
    Allowed  : 14.14 %
    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:  2.72 (0.30), residues: 786
  helix:  2.80 (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   0.003   0.001   HIS C 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        0.04740 (  523)
  hydrogen bonds       : angle       3.76286 ( 1551)
  covalent geometry    : bond        0.00410 ( 7221)
  covalent geometry    : angle       0.62151 ( 9792)
  Misc. bond           : bond        0.09824 (    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
  131 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 102
  time to evaluate  : 0.712 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8849 (mt) cc_final: 0.8503 (mt)
REVERT: A   78 GLU cc_start: 0.8113 (tp30) cc_final: 0.7720 (tp30)
REVERT: A  171 GLU cc_start: 0.8481 (mp0) cc_final: 0.8179 (mp0)
REVERT: A  172 ARG cc_start: 0.6935 (tpm170) cc_final: 0.6533 (tpp-160)
REVERT: A  201 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8098 (mmtm)
REVERT: A  258 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.7128 (t80)
REVERT: B   78 GLU cc_start: 0.7843 (tp30) cc_final: 0.7557 (tp30)
REVERT: B  143 VAL cc_start: 0.9075 (t) cc_final: 0.8818 (t)
REVERT: B  172 ARG cc_start: 0.6894 (tpm170) cc_final: 0.6635 (tpp-160)
REVERT: B  234 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8389 (ptmm)
REVERT: C  243 MET cc_start: 0.9213 (mmt) cc_final: 0.8938 (mmt)
REVERT: C  258 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.6974 (t80)
  outliers start: 29
  outliers final: 11
  residues processed: 117
  average time/residue: 1.3824
  time to fit residues: 169.2785
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  : 0.732 
-------------------------------------------------------------------------------
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  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:    0.2980
   chunk 28 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0870
   chunk 53 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.4558

-------------------------------------------------------------------------------
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 = 0.3529 r_free = 0.3529 target = 0.133928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.096029 restraints weight = 8186.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 1.59
r_work: 0.2800 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2671 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.2872

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= 0.133
  Angle     :  0.579   6.812   9792  Z= 0.280
  Chirality :  0.038   0.132   1101
  Planarity :  0.004   0.039   1095
  Dihedral  : 17.836 125.956   1278
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 15.87 %
    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:  2.95 (0.30), residues: 786
  helix:  2.95 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.53 (0.47), 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 213 
 PHE   0.013   0.001   PHE C 272 
 TYR   0.012   0.001   TYR C 164 
 ARG   0.003   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04371 (  523)
  hydrogen bonds       : angle       3.69252 ( 1551)
  covalent geometry    : bond        0.00340 ( 7221)
  covalent geometry    : angle       0.57907 ( 9792)
  Misc. bond           : bond        0.09738 (    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: 20
    poor density    : 99
  time to evaluate  : 0.769 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8859 (mt) cc_final: 0.8519 (mt)
REVERT: A   78 GLU cc_start: 0.8201 (tp30) cc_final: 0.7787 (tp30)
REVERT: A  171 GLU cc_start: 0.8567 (mp0) cc_final: 0.8257 (mp0)
REVERT: A  258 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7048 (t80)
REVERT: B   78 GLU cc_start: 0.7852 (tp30) cc_final: 0.7542 (tp30)
REVERT: B  143 VAL cc_start: 0.9038 (t) cc_final: 0.8812 (t)
REVERT: B  172 ARG cc_start: 0.6848 (tpm170) cc_final: 0.6224 (mmp80)
REVERT: C   78 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7696 (tp30)
REVERT: C  243 MET cc_start: 0.9201 (mmt) cc_final: 0.8949 (mmt)
REVERT: C  258 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.6970 (t80)
  outliers start: 20
  outliers final: 7
  residues processed: 108
  average time/residue: 1.4257
  time to fit residues: 161.3697
Evaluate side-chains
  102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
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 B residue   82 ARG
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  181 ASP
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:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0370
   chunk 16 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.5458

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.130706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.094578 restraints weight = 8058.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 1.49
r_work: 0.2785 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2654 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.121   7224  Z= 0.142
  Angle     :  0.589   6.589   9792  Z= 0.285
  Chirality :  0.038   0.133   1101
  Planarity :  0.004   0.040   1095
  Dihedral  : 17.573 123.818   1278
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 15.01 %
    Favored  : 81.39 %
  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:  2.93 (0.30), residues: 786
  helix:  2.94 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.54 (0.46), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 276 
 HIS   0.003   0.001   HIS B 213 
 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        0.04460 (  523)
  hydrogen bonds       : angle       3.69306 ( 1551)
  covalent geometry    : bond        0.00367 ( 7221)
  covalent geometry    : angle       0.58866 ( 9792)
  Misc. bond           : bond        0.10916 (    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
  121 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.681 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8869 (mt) cc_final: 0.8524 (mt)
REVERT: A   78 GLU cc_start: 0.8202 (tp30) cc_final: 0.7848 (tp30)
REVERT: A  171 GLU cc_start: 0.8504 (mp0) cc_final: 0.8222 (mp0)
REVERT: A  258 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7025 (t80)
REVERT: B   78 GLU cc_start: 0.7829 (tp30) cc_final: 0.7520 (tp30)
REVERT: B  143 VAL cc_start: 0.9015 (t) cc_final: 0.8794 (t)
REVERT: B  172 ARG cc_start: 0.6818 (tpm170) cc_final: 0.6211 (mmp80)
REVERT: B  234 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8402 (ptmm)
REVERT: C   78 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7414 (tp30)
REVERT: C   82 ARG cc_start: 0.7947 (mtp180) cc_final: 0.7272 (mmm-85)
REVERT: C  243 MET cc_start: 0.9167 (mmt) cc_final: 0.8899 (mmt)
REVERT: C  258 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.6842 (t80)
  outliers start: 25
  outliers final: 11
  residues processed: 112
  average time/residue: 1.3554
  time to fit residues: 159.2229
Evaluate side-chains
  104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
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  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  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  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:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0030
   chunk 56 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.5190

-------------------------------------------------------------------------------
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 = 0.3504 r_free = 0.3504 target = 0.131729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.094278 restraints weight = 8209.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 1.56
r_work: 0.2786 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2657 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.108   7224  Z= 0.139
  Angle     :  0.584   6.456   9792  Z= 0.283
  Chirality :  0.038   0.132   1101
  Planarity :  0.004   0.041   1095
  Dihedral  : 17.322 122.772   1278
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  2.54 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 16.02 %
    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:  2.92 (0.30), residues: 786
  helix:  2.93 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.55 (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   0.014   0.002   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        0.04371 (  523)
  hydrogen bonds       : angle       3.68068 ( 1551)
  covalent geometry    : bond        0.00357 ( 7221)
  covalent geometry    : angle       0.58407 ( 9792)
  Misc. bond           : bond        0.10475 (    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
  117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8856 (mt) cc_final: 0.8528 (mt)
REVERT: A   78 GLU cc_start: 0.8229 (tp30) cc_final: 0.7817 (tp30)
REVERT: A  171 GLU cc_start: 0.8559 (mp0) cc_final: 0.8275 (mp0)
REVERT: A  258 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.6898 (t80)
REVERT: B   78 GLU cc_start: 0.7796 (tp30) cc_final: 0.7501 (tp30)
REVERT: B  143 VAL cc_start: 0.9039 (t) cc_final: 0.8813 (t)
REVERT: B  172 ARG cc_start: 0.6937 (tpm170) cc_final: 0.6337 (mmp80)
REVERT: B  201 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8166 (mmtm)
REVERT: B  234 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8461 (ptmm)
REVERT: C   78 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7577 (tp30)
REVERT: C  243 MET cc_start: 0.9156 (mmt) cc_final: 0.8954 (mmt)
REVERT: C  258 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.6816 (t80)
  outliers start: 19
  outliers final: 8
  residues processed: 108
  average time/residue: 1.4145
  time to fit residues: 159.8346
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  : 0.682 
-------------------------------------------------------------------------------
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   82 ARG
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  201 LYS
Chi-restraints excluded: chain B residue  234 LYS
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain C residue  181 ASP
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:    0.5980
   chunk 25 optimal weight:    0.2980
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 10 optimal weight:    0.2980
   chunk 40 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0870
   chunk 44 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.3758

-------------------------------------------------------------------------------
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 = 0.3533 r_free = 0.3533 target = 0.134218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.097741 restraints weight = 8105.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 1.53
r_work: 0.2810 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.107   7224  Z= 0.124
  Angle     :  0.571   6.448   9792  Z= 0.278
  Chirality :  0.037   0.127   1101
  Planarity :  0.004   0.040   1095
  Dihedral  : 16.880 114.299   1278
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.54 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.45 %
    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:  2.98 (0.30), residues: 786
  helix:  2.99 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.60 (0.45), 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   0.012   0.001   TYR C 199 
 ARG   0.002   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04163 (  523)
  hydrogen bonds       : angle       3.64908 ( 1551)
  covalent geometry    : bond        0.00315 ( 7221)
  covalent geometry    : angle       0.57093 ( 9792)
  Misc. bond           : bond        0.09796 (    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
  119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8862 (mt) cc_final: 0.8535 (mt)
REVERT: A   78 GLU cc_start: 0.8226 (tp30) cc_final: 0.7809 (tp30)
REVERT: A  171 GLU cc_start: 0.8521 (mp0) cc_final: 0.8255 (mp0)
REVERT: A  258 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.6775 (t80)
REVERT: B   78 GLU cc_start: 0.7813 (tp30) cc_final: 0.7527 (tp30)
REVERT: B  143 VAL cc_start: 0.8986 (t) cc_final: 0.8766 (t)
REVERT: B  172 ARG cc_start: 0.6936 (tpm170) cc_final: 0.6377 (mmp80)
REVERT: B  201 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8158 (mmtm)
REVERT: B  260 LEU cc_start: 0.8978 (mt) cc_final: 0.8691 (mp)
REVERT: C   78 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7547 (tp30)
REVERT: C  243 MET cc_start: 0.9152 (mmt) cc_final: 0.8920 (mmt)
REVERT: C  258 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.6892 (t80)
  outliers start: 20
  outliers final: 4
  residues processed: 107
  average time/residue: 1.8556
  time to fit residues: 207.3845
Evaluate side-chains
  102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
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 B residue  181 ASP
Chi-restraints excluded: chain B residue  201 LYS
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:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 59 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 68 optimal weight:    0.5980
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3491 r_free = 0.3491 target = 0.130711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.093696 restraints weight = 8191.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 1.56
r_work: 0.2766 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2637 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.3162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.120   7224  Z= 0.157
  Angle     :  0.618   6.537   9792  Z= 0.299
  Chirality :  0.039   0.136   1101
  Planarity :  0.004   0.040   1095
  Dihedral  : 17.000 117.327   1278
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.93 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.74 %
    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:  2.83 (0.29), residues: 786
  helix:  2.88 (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 266 
 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        0.04530 (  523)
  hydrogen bonds       : angle       3.72703 ( 1551)
  covalent geometry    : bond        0.00408 ( 7221)
  covalent geometry    : angle       0.61810 ( 9792)
  Misc. bond           : bond        0.11123 (    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
  112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.657 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8901 (mt) cc_final: 0.8543 (mt)
REVERT: A   78 GLU cc_start: 0.8244 (tp30) cc_final: 0.7824 (tp30)
REVERT: A  171 GLU cc_start: 0.8577 (mp0) cc_final: 0.8302 (mp0)
REVERT: A  247 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9158 (mt)
REVERT: A  258 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.6917 (t80)
REVERT: B   78 GLU cc_start: 0.7773 (tp30) cc_final: 0.7479 (tp30)
REVERT: B  143 VAL cc_start: 0.9043 (t) cc_final: 0.8800 (t)
REVERT: B  172 ARG cc_start: 0.6960 (tpm170) cc_final: 0.6387 (mmp80)
REVERT: B  201 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8128 (mmmm)
REVERT: C   78 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7575 (tp30)
REVERT: C  243 MET cc_start: 0.9147 (mmt) cc_final: 0.8892 (mmt)
REVERT: C  258 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.6757 (t80)
  outliers start: 16
  outliers final: 8
  residues processed: 105
  average time/residue: 1.4902
  time to fit residues: 163.3903
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  : 0.704 
-------------------------------------------------------------------------------
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  247 ILE
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  201 LYS
Chi-restraints excluded: chain B residue  228 MET
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:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0980
   chunk 11 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0020
   chunk 14 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 40 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.4188

-------------------------------------------------------------------------------
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 = 0.3520 r_free = 0.3520 target = 0.133195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.096424 restraints weight = 8202.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 1.56
r_work: 0.2795 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106   7224  Z= 0.128
  Angle     :  0.576   6.420   9792  Z= 0.280
  Chirality :  0.037   0.127   1101
  Planarity :  0.004   0.037   1095
  Dihedral  : 16.610 112.270   1278
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.67 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.74 %
    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:  2.92 (0.29), residues: 786
  helix:  2.95 (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   0.002   0.001   HIS C 213 
 PHE   0.013   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        0.04234 (  523)
  hydrogen bonds       : angle       3.66180 ( 1551)
  covalent geometry    : bond        0.00330 ( 7221)
  covalent geometry    : angle       0.57648 ( 9792)
  Misc. bond           : bond        0.09597 (    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
  113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8871 (mt) cc_final: 0.8542 (mt)
REVERT: A   78 GLU cc_start: 0.8249 (tp30) cc_final: 0.7817 (tp30)
REVERT: A  171 GLU cc_start: 0.8514 (mp0) cc_final: 0.8254 (mp0)
REVERT: A  201 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8351 (mmtp)
REVERT: A  247 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9068 (mt)
REVERT: A  258 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.6773 (t80)
REVERT: B   78 GLU cc_start: 0.7801 (tp30) cc_final: 0.7505 (tp30)
REVERT: B  143 VAL cc_start: 0.8985 (t) cc_final: 0.8762 (t)
REVERT: B  172 ARG cc_start: 0.6934 (tpm170) cc_final: 0.6374 (mmp80)
REVERT: B  201 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8118 (mmmm)
REVERT: C   78 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7582 (tp30)
REVERT: C  243 MET cc_start: 0.9128 (mmt) cc_final: 0.8899 (mmt)
REVERT: C  258 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.6866 (t80)
  outliers start: 16
  outliers final: 7
  residues processed: 104
  average time/residue: 1.5170
  time to fit residues: 164.4950
Evaluate side-chains
  108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 TRP
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  201 LYS
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  201 LYS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    0.4980
   chunk 72 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 75 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   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 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 = 0.3485 r_free = 0.3485 target = 0.130457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.092999 restraints weight = 8299.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 1.59
r_work: 0.2774 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2646 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.119   7224  Z= 0.152
  Angle     :  0.606   6.455   9792  Z= 0.293
  Chirality :  0.038   0.134   1101
  Planarity :  0.004   0.039   1095
  Dihedral  : 16.830 113.712   1278
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  3.18 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.17 %
    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:  2.84 (0.29), residues: 786
  helix:  2.87 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.55 (0.45), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  76 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.015   0.002   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        0.04475 (  523)
  hydrogen bonds       : angle       3.71313 ( 1551)
  covalent geometry    : bond        0.00396 ( 7221)
  covalent geometry    : angle       0.60631 ( 9792)
  Misc. bond           : bond        0.11343 (    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
  110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.669 
Fit side-chains
REVERT: A   14 LEU cc_start: 0.8871 (mt) cc_final: 0.8523 (mt)
REVERT: A   78 GLU cc_start: 0.8243 (tp30) cc_final: 0.7823 (tp30)
REVERT: A  171 GLU cc_start: 0.8569 (mp0) cc_final: 0.8301 (mp0)
REVERT: A  201 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8352 (mmtp)
REVERT: A  247 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9151 (mt)
REVERT: A  258 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.6882 (t80)
REVERT: B   78 GLU cc_start: 0.7778 (tp30) cc_final: 0.7484 (tp30)
REVERT: B  143 VAL cc_start: 0.9044 (t) cc_final: 0.8803 (t)
REVERT: B  172 ARG cc_start: 0.6939 (tpm170) cc_final: 0.6387 (mmp80)
REVERT: B  201 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8110 (mmmm)
REVERT: C   78 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7585 (tp30)
REVERT: C  243 MET cc_start: 0.9163 (mmt) cc_final: 0.8952 (mmt)
REVERT: C  258 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.6716 (t80)
  outliers start: 15
  outliers final: 8
  residues processed: 107
  average time/residue: 1.5210
  time to fit residues: 169.7460
Evaluate side-chains
  107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  201 LYS
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  149 LEU
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  201 LYS
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=1.00
-------------------------------------------------------------------------------
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:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 49 optimal weight:    0.4980
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3500 r_free = 0.3500 target = 0.131704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.095107 restraints weight = 8193.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 1.55
r_work: 0.2773 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2645 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.3292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.115   7224  Z= 0.152
  Angle     :  0.603   6.463   9792  Z= 0.290
  Chirality :  0.038   0.134   1101
  Planarity :  0.004   0.039   1095
  Dihedral  : 16.921 109.733   1278
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.80 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.59 %
    Favored  : 81.10 %
  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:  2.80 (0.29), residues: 786
  helix:  2.85 (0.19), residues: 627
  sheet:  None (None), residues: 0
  loop : -2.60 (0.45), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  76 
 HIS   0.003   0.001   HIS C 213 
 PHE   0.016   0.002   PHE B 272 
 TYR   0.012   0.001   TYR C 164 
 ARG   0.002   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04485 (  523)
  hydrogen bonds       : angle       3.71840 ( 1551)
  covalent geometry    : bond        0.00398 ( 7221)
  covalent geometry    : angle       0.60316 ( 9792)
  Misc. bond           : bond        0.10795 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5848.36 seconds
wall clock time: 101 minutes 16.73 seconds (6076.73 seconds total)