Starting phenix.real_space_refine
on Fri May  9 20:05:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mel_48217/05_2025/9mel_48217.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mel_48217/05_2025/9mel_48217.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mel_48217/05_2025/9mel_48217.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mel_48217/05_2025/9mel_48217.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mel_48217/05_2025/9mel_48217.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mel_48217/05_2025/9mel_48217.cif"
  }
  resolution = 3.17
  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=  -0.001 sd=   0.049
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
     K       3      8.98       5
     S      14      5.16       5
     C    2410      2.51       5
     N     562      2.21       5
     O     596      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3589
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1759
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 238, 1754
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 9, 'TRANS': 228}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 53
      Conformer: "B"
        Number of residues, atoms: 238, 1754
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 9, 'TRANS': 228}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 53
          bond proxies already assigned to first conformer: 1788
    Chain: "B"
      Number of atoms: 1759
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 238, 1754
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 9, 'TRANS': 228}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 53
      Conformer: "B"
        Number of residues, atoms: 238, 1754
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 9, 'TRANS': 228}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 53
          bond proxies already assigned to first conformer: 1788
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {'  K': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 68
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 34
          Unusual residues: {'1II': 1}
          Classifications: {'undetermined': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 34
          Unusual residues: {'1II': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C07A1II B 401 " occ=0.50
      ... (66 atoms not shown)
      pdb=" O03B1II B 401 " occ=0.50
  Time building chain proxies: 5.47, per 1000 atoms: 1.52
  Number of scatterers: 3589
  At special positions: 0
  Unit cell: (71.775, 61.625, 88.45, 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)
     K       3     19.00
     S      14     16.00
     F       4      9.00
     O     596      8.00
     N     562      7.00
     C    2410      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS B  53 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 874.8 milliseconds
  

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  892

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      77.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 51
      Proline residue:  A  31  - end of helix
    Processing helix  chain 'A' and resid 55 through 69
    Processing helix  chain 'A' and resid 72 through 78
      removed outlier: 4.171A  pdb=" N   VAL A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 105
    Processing helix  chain 'A' and resid 116 through 150
      Proline residue:  A 132  - end of helix
    Processing helix  chain 'A' and resid 167 through 195
      removed outlier: 3.604A  pdb=" N   TRP A 171 " --> pdb=" O   ARG A 167 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   LEU A 186 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   VAL A 187 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
      Proline residue:  A 188  - end of helix
    Processing helix  chain 'A' and resid 200 through 213
    Processing helix  chain 'A' and resid 230 through 263
    Processing helix  chain 'A' and resid 266 through 271
    Processing helix  chain 'B' and resid 8 through 51
      Proline residue:  B  31  - end of helix
    Processing helix  chain 'B' and resid 55 through 69
    Processing helix  chain 'B' and resid 72 through 78
      removed outlier: 4.171A  pdb=" N   VAL B  76 " --> pdb=" O   LEU B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 105
    Processing helix  chain 'B' and resid 116 through 150
      Proline residue:  B 132  - end of helix
    Processing helix  chain 'B' and resid 200 through 213
    Processing helix  chain 'B' and resid 230 through 263
    Processing helix  chain 'B' and resid 266 through 271

    280 hydrogen bonds defined for protein.
    838 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.95

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1066
        1.34 -     1.46: 840
        1.46 -     1.58: 1750
        1.58 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 3676
  Sorted by residual:
  bond pdb=" C31B1II B 401 "
       pdb=" C33B1II B 401 "
    ideal  model  delta    sigma   weight residual
    1.378  1.350  0.028 2.00e-02 2.50e+03 1.99e+00
  bond pdb=" C31A1II B 401 "
       pdb=" C33A1II B 401 "
    ideal  model  delta    sigma   weight residual
    1.378  1.351  0.027 2.00e-02 2.50e+03 1.88e+00
  bond pdb=" C07A1II B 401 "
       pdb=" C09A1II B 401 "
    ideal  model  delta    sigma   weight residual
    1.546  1.521  0.025 2.00e-02 2.50e+03 1.58e+00
  bond pdb=" C07B1II B 401 "
       pdb=" C09B1II B 401 "
    ideal  model  delta    sigma   weight residual
    1.546  1.521  0.025 2.00e-02 2.50e+03 1.50e+00
  bond pdb=" C30A1II B 401 "
       pdb=" C34A1II B 401 "
    ideal  model  delta    sigma   weight residual
    1.383  1.360  0.023 2.00e-02 2.50e+03 1.31e+00
  ... (remaining 3671 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 4891
        1.73 -     3.46: 110
        3.46 -     5.19: 33
        5.19 -     6.92: 7
        6.92 -     8.64: 5
  Bond angle restraints: 5046
  Sorted by residual:
  angle pdb=" C20B1II B 401 "
        pdb=" C17B1II B 401 "
        pdb=" C21B1II B 401 "
      ideal   model   delta    sigma   weight residual
     110.45  119.09   -8.64 3.00e+00 1.11e-01 8.30e+00
  angle pdb=" C20A1II B 401 "
        pdb=" C17A1II B 401 "
        pdb=" C21A1II B 401 "
      ideal   model   delta    sigma   weight residual
     110.45  118.50   -8.05 3.00e+00 1.11e-01 7.20e+00
  angle pdb=" C   LEU B 265 "
        pdb=" N   THR B 266 "
        pdb=" CA  THR B 266 "
      ideal   model   delta    sigma   weight residual
     121.54  126.54   -5.00 1.91e+00 2.74e-01 6.85e+00
  angle pdb=" C   LEU A 265 "
        pdb=" N   THR A 266 "
        pdb=" CA  THR A 266 "
      ideal   model   delta    sigma   weight residual
     121.54  126.52   -4.98 1.91e+00 2.74e-01 6.78e+00
  angle pdb=" C   THR B 105 "
        pdb=" N   THR B 106 "
        pdb=" CA  THR B 106 "
      ideal   model   delta    sigma   weight residual
     122.08  125.67   -3.59 1.47e+00 4.63e-01 5.96e+00
  ... (remaining 5041 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.02: 2015
       31.02 -    62.04: 87
       62.04 -    93.06: 11
       93.06 -   124.08: 4
      124.08 -   155.10: 6
  Dihedral angle restraints: 2123
    sinusoidal: 739
      harmonic: 1384
  Sorted by residual:
  dihedral pdb=" C15A1II B 401 "
           pdb=" C12A1II B 401 "
           pdb=" C13A1II B 401 "
           pdb=" N04A1II B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     187.89   32.79  155.10     1      3.00e+01 1.11e-03 2.03e+01
  dihedral pdb=" C11B1II B 401 "
           pdb=" C12B1II B 401 "
           pdb=" N04B1II B 401 "
           pdb=" C13B1II B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -58.54   88.01 -146.55     1      3.00e+01 1.11e-03 1.96e+01
  dihedral pdb=" C11A1II B 401 "
           pdb=" C12A1II B 401 "
           pdb=" N04A1II B 401 "
           pdb=" C13A1II B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -58.54   82.41 -140.95     1      3.00e+01 1.11e-03 1.90e+01
  ... (remaining 2120 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.109: 626
       0.109 -    0.218: 8
       0.218 -    0.327: 0
       0.327 -    0.436: 0
       0.436 -    0.545: 2
  Chirality restraints: 636
  Sorted by residual:
  chirality pdb=" C07B1II B 401 "
            pdb=" C08B1II B 401 "
            pdb=" C09B1II B 401 "
            pdb=" N05B1II B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -1.77   -0.55 2.00e-01 2.50e+01 7.44e+00
  chirality pdb=" C07A1II B 401 "
            pdb=" C08A1II B 401 "
            pdb=" C09A1II B 401 "
            pdb=" N05A1II B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -1.82   -0.49 2.00e-01 2.50e+01 6.03e+00
  chirality pdb=" CA  THR A 214 "
            pdb=" N   THR A 214 "
            pdb=" C   THR A 214 "
            pdb=" CB  THR A 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.76e-01
  ... (remaining 633 not shown)

  Planarity restraints: 600
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 266 "   -0.010 2.00e-02 2.50e+03   2.05e-02 4.19e+00
        pdb=" C   THR A 266 "    0.035 2.00e-02 2.50e+03
        pdb=" O   THR A 266 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLU A 267 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 266 "    0.010 2.00e-02 2.50e+03   2.04e-02 4.18e+00
        pdb=" C   THR B 266 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   THR B 266 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLU B 267 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 181 "   -0.005 2.00e-02 2.50e+03   1.02e-02 1.03e+00
        pdb=" C   VAL B 181 "    0.018 2.00e-02 2.50e+03
        pdb=" O   VAL B 181 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   THR B 182 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 597 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.79: 857
        2.79 -     3.38: 4311
        3.38 -     3.97: 6823
        3.97 -     4.55: 9414
        4.55 -     5.14: 13336
  Nonbonded interactions: 34741
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 108 "
            pdb=" K     K A 401 "
     model   vdw
     2.206 2.850
  nonbonded pdb=" O   GLY B 108 "
            pdb=" K     K A 401 "
     model   vdw
     2.218 2.850
  nonbonded pdb=" O   GLY B 216 "
            pdb=" K     K A 401 "
     model   vdw
     2.362 2.850
  nonbonded pdb=" O   GLY A 216 "
            pdb=" K     K A 401 "
     model   vdw
     2.378 2.850
  nonbonded pdb=" O   SER B 213 "
            pdb=" OG1 THR B 214 "
     model   vdw
     2.566 3.040
  ... (remaining 34736 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 7 through 134 or resid 136 through 271))
  selection = (chain 'B' and (resid 7 through 134 or resid 136 through 271))
}

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=0.47 max=1.00 mean=0.99
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:             2.310
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.670
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
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      :  0.004   0.030   3677  Z= 0.192
  Angle     :  0.733   8.644   5048  Z= 0.337
  Chirality :  0.047   0.545    636
  Planarity :  0.003   0.024    600
  Dihedral  : 20.720 155.097   1228
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 17.82 %
    Favored  : 80.46 %
  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:  3.40 (0.40), residues: 466
  helix:  2.98 (0.25), residues: 374
  sheet:  None (None), residues: 0
  loop : -1.07 (0.80), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 171 
 HIS   0.003   0.001   HIS A  32 
 PHE   0.013   0.002   PHE A 122 
 TYR   0.010   0.002   TYR B 206 
 ARG   0.001   0.000   ARG A 144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10239 (  280)
  hydrogen bonds       : angle       4.74274 (  838)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       0.02827 (    2)
  covalent geometry    : bond        0.00446 ( 3676)
  covalent geometry    : angle       0.73350 ( 5046)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8165 (tp) cc_final: 0.7552 (mt)
REVERT: A   64 GLU cc_start: 0.8263 (tp30) cc_final: 0.7613 (mt-10)
REVERT: A  144 ARG cc_start: 0.6391 (mtt180) cc_final: 0.5868 (mmm160)
REVERT: A  237 LEU cc_start: 0.8110 (mm) cc_final: 0.7705 (mm)
REVERT: A  257 ARG cc_start: 0.7644 (ttp80) cc_final: 0.6559 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8154 (tp) cc_final: 0.7540 (mt)
REVERT: B   64 GLU cc_start: 0.8261 (tp30) cc_final: 0.7607 (mt-10)
REVERT: B  144 ARG cc_start: 0.6345 (mtt180) cc_final: 0.5842 (mmm160)
REVERT: B  237 LEU cc_start: 0.8103 (mm) cc_final: 0.7697 (mm)
REVERT: B  257 ARG cc_start: 0.7643 (ttp80) cc_final: 0.6558 (tpp-160)
  outliers start: 6
  outliers final: 6
  residues processed: 54
  average time/residue: 0.2918
  time to fit residues: 17.8932
Evaluate side-chains
  56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  236 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 38 optimal weight:    0.1980
   chunk 34 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0470
   overall best weight:    0.4078

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.176753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.133878 restraints weight = 8002.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 3.15
r_work: 0.3144 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.0526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3677  Z= 0.137
  Angle     :  0.623   9.838   5048  Z= 0.286
  Chirality :  0.037   0.191    636
  Planarity :  0.003   0.024    600
  Dihedral  : 19.629 131.240    570
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 18.39 %
    Favored  : 79.89 %
  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:  3.83 (0.41), residues: 466
  helix:  3.21 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.70 (0.86), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A  32 
 PHE   0.012   0.002   PHE A 122 
 TYR   0.010   0.002   TYR B 206 
 ARG   0.001   0.000   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03034 (  280)
  hydrogen bonds       : angle       3.66091 (  838)
  SS BOND              : bond        0.00115 (    1)
  SS BOND              : angle       0.20910 (    2)
  covalent geometry    : bond        0.00327 ( 3676)
  covalent geometry    : angle       0.62328 ( 5046)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8159 (tp) cc_final: 0.7543 (mt)
REVERT: A  144 ARG cc_start: 0.6354 (mtt180) cc_final: 0.5915 (mmm160)
REVERT: A  237 LEU cc_start: 0.8133 (mm) cc_final: 0.7736 (mm)
REVERT: A  257 ARG cc_start: 0.7619 (ttp80) cc_final: 0.6549 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8137 (tp) cc_final: 0.7515 (mt)
REVERT: B  144 ARG cc_start: 0.6343 (mtt180) cc_final: 0.5925 (mmm160)
REVERT: B  237 LEU cc_start: 0.8112 (mm) cc_final: 0.7718 (mm)
REVERT: B  257 ARG cc_start: 0.7616 (ttp80) cc_final: 0.6552 (tpp-160)
  outliers start: 6
  outliers final: 2
  residues processed: 54
  average time/residue: 0.2878
  time to fit residues: 17.5557
Evaluate side-chains
  49 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain B residue  123 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.178395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.134200 restraints weight = 11248.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 4.25
r_work: 0.3079 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.0705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3677  Z= 0.161
  Angle     :  0.633  10.554   5048  Z= 0.292
  Chirality :  0.037   0.175    636
  Planarity :  0.003   0.025    600
  Dihedral  : 19.639 136.099    562
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.67 %
    Favored  : 81.03 %
  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:  3.84 (0.41), residues: 466
  helix:  3.21 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.63 (0.87), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 171 
 HIS   0.002   0.001   HIS B  32 
 PHE   0.014   0.002   PHE A 122 
 TYR   0.012   0.002   TYR B 234 
 ARG   0.001   0.000   ARG B  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03110 (  280)
  hydrogen bonds       : angle       3.49384 (  838)
  SS BOND              : bond        0.00111 (    1)
  SS BOND              : angle       0.19316 (    2)
  covalent geometry    : bond        0.00395 ( 3676)
  covalent geometry    : angle       0.63318 ( 5046)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8154 (tp) cc_final: 0.7533 (mt)
REVERT: A  144 ARG cc_start: 0.6362 (mtt180) cc_final: 0.5872 (mmm160)
REVERT: A  237 LEU cc_start: 0.8115 (mm) cc_final: 0.7699 (mm)
REVERT: A  257 ARG cc_start: 0.7628 (ttp80) cc_final: 0.6501 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8147 (tp) cc_final: 0.7520 (mt)
REVERT: B  144 ARG cc_start: 0.6352 (mtt180) cc_final: 0.5883 (mmm160)
REVERT: B  237 LEU cc_start: 0.8109 (mm) cc_final: 0.7699 (mm)
REVERT: B  257 ARG cc_start: 0.7637 (ttp80) cc_final: 0.6510 (tpp-160)
  outliers start: 8
  outliers final: 5
  residues processed: 59
  average time/residue: 0.2746
  time to fit residues: 18.4407
Evaluate side-chains
  56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue  123 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.178692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.134070 restraints weight = 9865.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 3.84
r_work: 0.3091 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3068
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3068
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.0834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3677  Z= 0.162
  Angle     :  0.643  10.643   5048  Z= 0.294
  Chirality :  0.037   0.151    636
  Planarity :  0.003   0.025    600
  Dihedral  : 19.318 133.338    562
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 18.10 %
    Favored  : 80.17 %
  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:  3.79 (0.41), residues: 466
  helix:  3.18 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.67 (0.86), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 171 
 HIS   0.003   0.001   HIS B  32 
 PHE   0.014   0.002   PHE A 122 
 TYR   0.013   0.002   TYR B 234 
 ARG   0.001   0.000   ARG B 144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03034 (  280)
  hydrogen bonds       : angle       3.40659 (  838)
  SS BOND              : bond        0.00102 (    1)
  SS BOND              : angle       0.16422 (    2)
  covalent geometry    : bond        0.00398 ( 3676)
  covalent geometry    : angle       0.64273 ( 5046)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8173 (tp) cc_final: 0.7543 (mt)
REVERT: A  144 ARG cc_start: 0.6411 (mtt180) cc_final: 0.5948 (mmm160)
REVERT: A  237 LEU cc_start: 0.8163 (mm) cc_final: 0.7757 (mm)
REVERT: A  257 ARG cc_start: 0.7634 (ttp80) cc_final: 0.6499 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8164 (tp) cc_final: 0.7543 (mt)
REVERT: B  144 ARG cc_start: 0.6386 (mtt180) cc_final: 0.5938 (mmm160)
REVERT: B  237 LEU cc_start: 0.8150 (mm) cc_final: 0.7747 (mm)
REVERT: B  257 ARG cc_start: 0.7671 (ttp80) cc_final: 0.6543 (tpp-160)
  outliers start: 6
  outliers final: 6
  residues processed: 57
  average time/residue: 0.2906
  time to fit residues: 18.8757
Evaluate side-chains
  58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue  123 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 44 optimal weight:    0.1980
   chunk 24 optimal weight:    0.3980
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0980
   chunk 1 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.4180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.180509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.136406 restraints weight = 9726.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 3.72
r_work: 0.3120 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3100
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3100
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.0955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3677  Z= 0.133
  Angle     :  0.625  10.432   5048  Z= 0.282
  Chirality :  0.036   0.127    636
  Planarity :  0.003   0.025    600
  Dihedral  : 18.595 127.370    562
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.95 %
    Favored  : 80.75 %
  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:  3.96 (0.41), residues: 466
  helix:  3.31 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.67 (0.86), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A  32 
 PHE   0.012   0.001   PHE A 122 
 TYR   0.009   0.001   TYR B 234 
 ARG   0.001   0.000   ARG B 144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02839 (  280)
  hydrogen bonds       : angle       3.29344 (  838)
  SS BOND              : bond        0.00097 (    1)
  SS BOND              : angle       0.19535 (    2)
  covalent geometry    : bond        0.00319 ( 3676)
  covalent geometry    : angle       0.62529 ( 5046)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8128 (tp) cc_final: 0.7520 (mt)
REVERT: A  144 ARG cc_start: 0.6403 (mtt180) cc_final: 0.5943 (mmm160)
REVERT: A  237 LEU cc_start: 0.8137 (mm) cc_final: 0.7728 (mm)
REVERT: A  257 ARG cc_start: 0.7606 (ttp80) cc_final: 0.6488 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8129 (tp) cc_final: 0.7513 (mt)
REVERT: B  144 ARG cc_start: 0.6395 (mtt180) cc_final: 0.5942 (mmm160)
REVERT: B  237 LEU cc_start: 0.8128 (mm) cc_final: 0.7722 (mm)
REVERT: B  257 ARG cc_start: 0.7635 (ttp80) cc_final: 0.6522 (tpp-160)
  outliers start: 8
  outliers final: 6
  residues processed: 55
  average time/residue: 0.2905
  time to fit residues: 18.1203
Evaluate side-chains
  57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  129 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0570
   chunk 15 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0010
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.4104

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.180071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.136606 restraints weight = 7525.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 3.04
r_work: 0.3148 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3677  Z= 0.132
  Angle     :  0.628  10.578   5048  Z= 0.283
  Chirality :  0.035   0.125    636
  Planarity :  0.003   0.025    600
  Dihedral  : 18.330 126.064    562
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.95 %
    Favored  : 80.46 %
  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:  3.95 (0.41), residues: 466
  helix:  3.31 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.73 (0.85), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 171 
 HIS   0.002   0.001   HIS B  32 
 PHE   0.012   0.001   PHE A 122 
 TYR   0.010   0.001   TYR B 234 
 ARG   0.001   0.000   ARG B 144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02824 (  280)
  hydrogen bonds       : angle       3.21897 (  838)
  SS BOND              : bond        0.00084 (    1)
  SS BOND              : angle       0.23011 (    2)
  covalent geometry    : bond        0.00319 ( 3676)
  covalent geometry    : angle       0.62825 ( 5046)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8148 (tp) cc_final: 0.7534 (mt)
REVERT: A  144 ARG cc_start: 0.6437 (mtt180) cc_final: 0.5983 (mmm160)
REVERT: A  237 LEU cc_start: 0.8136 (mm) cc_final: 0.7733 (mm)
REVERT: A  257 ARG cc_start: 0.7657 (ttp80) cc_final: 0.6542 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8138 (tp) cc_final: 0.7523 (mt)
REVERT: B  144 ARG cc_start: 0.6435 (mtt180) cc_final: 0.6019 (mmm160)
REVERT: B  237 LEU cc_start: 0.8131 (mm) cc_final: 0.7730 (mm)
REVERT: B  257 ARG cc_start: 0.7652 (ttp80) cc_final: 0.6541 (tpp-160)
  outliers start: 9
  outliers final: 8
  residues processed: 57
  average time/residue: 0.2822
  time to fit residues: 18.3756
Evaluate side-chains
  59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  183 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0670
   chunk 44 optimal weight:    0.6980
   chunk 32 optimal weight:    0.1980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.5518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.179978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.133856 restraints weight = 11904.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 4.33
r_work: 0.3073 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3048
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3048
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.1025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3677  Z= 0.155
  Angle     :  0.645  11.175   5048  Z= 0.293
  Chirality :  0.036   0.129    636
  Planarity :  0.003   0.025    600
  Dihedral  : 18.423 128.029    562
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.24 %
    Favored  : 80.17 %
  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:  3.85 (0.40), residues: 466
  helix:  3.23 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.70 (0.86), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 171 
 HIS   0.002   0.001   HIS B  32 
 PHE   0.013   0.002   PHE B 122 
 TYR   0.012   0.002   TYR B 234 
 ARG   0.001   0.000   ARG B 144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02938 (  280)
  hydrogen bonds       : angle       3.26599 (  838)
  SS BOND              : bond        0.00089 (    1)
  SS BOND              : angle       0.17427 (    2)
  covalent geometry    : bond        0.00380 ( 3676)
  covalent geometry    : angle       0.64534 ( 5046)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8136 (tp) cc_final: 0.7517 (mt)
REVERT: A  144 ARG cc_start: 0.6409 (mtt180) cc_final: 0.5896 (mmm160)
REVERT: A  237 LEU cc_start: 0.8126 (mm) cc_final: 0.7721 (mm)
REVERT: A  257 ARG cc_start: 0.7574 (ttp80) cc_final: 0.6442 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8134 (tp) cc_final: 0.7513 (mt)
REVERT: B  144 ARG cc_start: 0.6368 (mtt180) cc_final: 0.5892 (mmm160)
REVERT: B  237 LEU cc_start: 0.8115 (mm) cc_final: 0.7713 (mm)
REVERT: B  257 ARG cc_start: 0.7590 (ttp80) cc_final: 0.6492 (tpp-160)
  outliers start: 9
  outliers final: 9
  residues processed: 56
  average time/residue: 0.2802
  time to fit residues: 17.8796
Evaluate side-chains
  60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  183 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0010
   chunk 40 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.6186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.177616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.133710 restraints weight = 7990.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 3.21
r_work: 0.3116 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3099
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3099
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3677  Z= 0.165
  Angle     :  0.660  11.454   5048  Z= 0.299
  Chirality :  0.037   0.133    636
  Planarity :  0.003   0.025    600
  Dihedral  : 18.266 128.591    562
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.53 %
    Favored  : 79.60 %
  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:  3.79 (0.40), residues: 466
  helix:  3.18 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.70 (0.86), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 171 
 HIS   0.003   0.001   HIS B  32 
 PHE   0.014   0.002   PHE A 122 
 TYR   0.014   0.002   TYR B 234 
 ARG   0.001   0.000   ARG B 144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03000 (  280)
  hydrogen bonds       : angle       3.31248 (  838)
  SS BOND              : bond        0.00095 (    1)
  SS BOND              : angle       0.16531 (    2)
  covalent geometry    : bond        0.00407 ( 3676)
  covalent geometry    : angle       0.66003 ( 5046)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8184 (tp) cc_final: 0.7557 (mt)
REVERT: A  144 ARG cc_start: 0.6463 (mtt180) cc_final: 0.5986 (mmm160)
REVERT: A  237 LEU cc_start: 0.8140 (mm) cc_final: 0.7730 (mm)
REVERT: A  257 ARG cc_start: 0.7568 (ttp80) cc_final: 0.6512 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8179 (tp) cc_final: 0.7553 (mt)
REVERT: B  144 ARG cc_start: 0.6410 (mtt180) cc_final: 0.5959 (mmm160)
REVERT: B  237 LEU cc_start: 0.8140 (mm) cc_final: 0.7735 (mm)
REVERT: B  257 ARG cc_start: 0.7569 (ttp80) cc_final: 0.6518 (tpp-160)
  outliers start: 10
  outliers final: 10
  residues processed: 57
  average time/residue: 0.2794
  time to fit residues: 18.1699
Evaluate side-chains
  62 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  270 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.178951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.136064 restraints weight = 12857.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 4.24
r_work: 0.3057 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3677  Z= 0.177
  Angle     :  0.664  11.669   5048  Z= 0.303
  Chirality :  0.038   0.241    636
  Planarity :  0.003   0.025    600
  Dihedral  : 17.939 130.457    562
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.82 %
    Favored  : 79.31 %
  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:  3.74 (0.41), residues: 466
  helix:  3.14 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.68 (0.86), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 171 
 HIS   0.003   0.001   HIS B  32 
 PHE   0.014   0.002   PHE B 122 
 TYR   0.016   0.002   TYR B 234 
 ARG   0.001   0.000   ARG B  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03056 (  280)
  hydrogen bonds       : angle       3.35539 (  838)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.13402 (    2)
  covalent geometry    : bond        0.00440 ( 3676)
  covalent geometry    : angle       0.66387 ( 5046)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8264 (tp) cc_final: 0.7623 (mt)
REVERT: A  144 ARG cc_start: 0.6576 (mtt180) cc_final: 0.6088 (mmm160)
REVERT: A  237 LEU cc_start: 0.8244 (mm) cc_final: 0.7837 (mm)
REVERT: A  257 ARG cc_start: 0.7686 (ttp80) cc_final: 0.6555 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8261 (tp) cc_final: 0.7623 (mt)
REVERT: B  144 ARG cc_start: 0.6542 (mtt180) cc_final: 0.6073 (mmm160)
REVERT: B  237 LEU cc_start: 0.8260 (mm) cc_final: 0.7858 (mm)
REVERT: B  257 ARG cc_start: 0.7693 (ttp80) cc_final: 0.6592 (tpp-160)
  outliers start: 10
  outliers final: 10
  residues processed: 58
  average time/residue: 0.2752
  time to fit residues: 18.2745
Evaluate side-chains
  60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  270 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0870
   chunk 1 optimal weight:    0.3980
   chunk 24 optimal weight:    0.4980
   chunk 31 optimal weight:    0.2980
   chunk 44 optimal weight:    0.0980
   chunk 15 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0870
   chunk 17 optimal weight:    0.1980
   overall best weight:    0.1536

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.183881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.140845 restraints weight = 9599.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 3.70
r_work: 0.3158 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3137
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3137
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3677  Z= 0.107
  Angle     :  0.611  10.288   5048  Z= 0.273
  Chirality :  0.034   0.120    636
  Planarity :  0.003   0.027    600
  Dihedral  : 14.986 112.735    562
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.39 %
    Favored  : 79.31 %
  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:  3.95 (0.41), residues: 466
  helix:  3.21 (0.25), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.70 (0.90), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 171 
 HIS   0.002   0.001   HIS B 263 
 PHE   0.009   0.001   PHE A 122 
 TYR   0.009   0.001   TYR B 206 
 ARG   0.001   0.000   ARG B  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02601 (  280)
  hydrogen bonds       : angle       3.12310 (  838)
  SS BOND              : bond        0.00066 (    1)
  SS BOND              : angle       0.32487 (    2)
  covalent geometry    : bond        0.00241 ( 3676)
  covalent geometry    : angle       0.61061 ( 5046)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8204 (tp) cc_final: 0.7611 (mt)
REVERT: A  144 ARG cc_start: 0.6489 (mtt180) cc_final: 0.6045 (mmm160)
REVERT: A  237 LEU cc_start: 0.8162 (mm) cc_final: 0.7787 (mm)
REVERT: A  257 ARG cc_start: 0.7688 (ttp80) cc_final: 0.6612 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8189 (tp) cc_final: 0.7598 (mt)
REVERT: B  144 ARG cc_start: 0.6488 (mtt180) cc_final: 0.6101 (mmm160)
REVERT: B  237 LEU cc_start: 0.8171 (mm) cc_final: 0.7807 (mm)
REVERT: B  257 ARG cc_start: 0.7696 (ttp80) cc_final: 0.6631 (tpp-160)
  outliers start: 8
  outliers final: 8
  residues processed: 54
  average time/residue: 0.2920
  time to fit residues: 18.0664
Evaluate side-chains
  59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  270 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 41 optimal weight:    0.0170
   chunk 1 optimal weight:    0.6980
   chunk 9 optimal weight:    0.2980
   chunk 29 optimal weight:    0.0970
   chunk 42 optimal weight:    0.0570
   chunk 40 optimal weight:    0.2980
   chunk 34 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 44 optimal weight:    0.1980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.1334

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.184518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.142495 restraints weight = 9647.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 3.52
r_work: 0.3189 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3170
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3677  Z= 0.108
  Angle     :  0.595  10.080   5048  Z= 0.269
  Chirality :  0.034   0.123    636
  Planarity :  0.003   0.027    600
  Dihedral  : 12.420 101.821    562
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 18.39 %
    Favored  : 79.60 %
  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:  4.14 (0.41), residues: 466
  helix:  3.34 (0.25), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.64 (0.90), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 171 
 HIS   0.002   0.001   HIS B 263 
 PHE   0.008   0.001   PHE A 122 
 TYR   0.009   0.001   TYR A 109 
 ARG   0.002   0.000   ARG A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02521 (  280)
  hydrogen bonds       : angle       3.01366 (  838)
  SS BOND              : bond        0.00034 (    1)
  SS BOND              : angle       0.32890 (    2)
  covalent geometry    : bond        0.00245 ( 3676)
  covalent geometry    : angle       0.59553 ( 5046)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2668.78 seconds
wall clock time: 46 minutes 39.82 seconds (2799.82 seconds total)