Starting phenix.real_space_refine
on Wed Sep 17 09:32:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y2n_38858/09_2025/8y2n_38858.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y2n_38858/09_2025/8y2n_38858.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y2n_38858/09_2025/8y2n_38858.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y2n_38858/09_2025/8y2n_38858.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y2n_38858/09_2025/8y2n_38858.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y2n_38858/09_2025/8y2n_38858.map"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.087
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      38      5.16       5
     C    5198      2.51       5
     N    1204      2.21       5
     O    1272      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7714
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2674
          Classifications: {'peptide': 315}
          Link IDs: {'PTRANS': 8, 'TRANS': 306}
    Chain: "B"
      Number of atoms: 1089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 1089
          Classifications: {'peptide': 133}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 124}
    Chain: "A"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 36
          Unusual residues: {'6PL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 86
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'6PL:plan-1': 2, '6PL:plan-2': 2}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 58
          Unusual residues: {'6PL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'6PL:plan-1': 1, '6PL:plan-2': 1}
          Unresolved non-hydrogen planarities: 6
  Restraints were copied for chains:
    C, D
  Time building chain proxies: 2.25, per 1000 atoms: 0.29
  Number of scatterers: 7714
  At special positions: 0
  Unit cell: (121.136, 97.552, 99.696, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P       2     15.00
     O    1272      8.00
     N    1204      7.00
     C    5198      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  53 " - pdb=" SG  CYS B  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 102 " - pdb=" SG  CYS B 142 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  53 " - pdb=" SG  CYS D  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 102 " - pdb=" SG  CYS D 142 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 433.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1712

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 2 sheets defined
      67.1% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 71 through 82
    Processing helix  chain 'A' and resid 84 through 101
    Processing helix  chain 'A' and resid 109 through 115
    Processing helix  chain 'A' and resid 129 through 160
      removed outlier: 3.970A  pdb=" N   LEU A 133 " --> pdb=" O   GLY A 129 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLU A 148 " --> pdb=" O   THR A 144 " (cutoff:3.500A)
      Proline residue:  A 157  - end of helix
    Processing helix  chain 'A' and resid 167 through 196
      Proline residue:  A 188  - end of helix
    Processing helix  chain 'A' and resid 203 through 207
    Processing helix  chain 'A' and resid 217 through 240
    Processing helix  chain 'A' and resid 248 through 269
      removed outlier: 3.627A  pdb=" N   PHE A 269 " --> pdb=" O   SER A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 297
    Processing helix  chain 'A' and resid 301 through 335
      removed outlier: 4.509A  pdb=" N   PHE A 305 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   THR A 335 " --> pdb=" O   THR A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 384
      removed outlier: 4.363A  pdb=" N   ILE A 356 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   LEU A 364 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 47
    Processing helix  chain 'B' and resid 48 through 53
    Processing helix  chain 'B' and resid 76 through 92
      removed outlier: 3.841A  pdb=" N   TYR B  92 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 142
      removed outlier: 3.633A  pdb=" N   VAL B 138 " --> pdb=" O   ASP B 134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 82
    Processing helix  chain 'C' and resid 84 through 101
    Processing helix  chain 'C' and resid 109 through 115
    Processing helix  chain 'C' and resid 129 through 160
      removed outlier: 3.970A  pdb=" N   LEU C 133 " --> pdb=" O   GLY C 129 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLU C 148 " --> pdb=" O   THR C 144 " (cutoff:3.500A)
      Proline residue:  C 157  - end of helix
    Processing helix  chain 'C' and resid 167 through 196
      Proline residue:  C 188  - end of helix
    Processing helix  chain 'C' and resid 203 through 207
    Processing helix  chain 'C' and resid 217 through 240
    Processing helix  chain 'C' and resid 248 through 269
      removed outlier: 3.628A  pdb=" N   PHE C 269 " --> pdb=" O   SER C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 275 through 297
    Processing helix  chain 'C' and resid 301 through 335
      removed outlier: 4.508A  pdb=" N   PHE C 305 " --> pdb=" O   GLY C 301 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   THR C 335 " --> pdb=" O   THR C 331 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 352 through 384
      removed outlier: 4.363A  pdb=" N   ILE C 356 " --> pdb=" O   ILE C 352 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   LEU C 364 " --> pdb=" O   LEU C 360 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 47
    Processing helix  chain 'D' and resid 48 through 53
    Processing helix  chain 'D' and resid 76 through 92
      removed outlier: 3.840A  pdb=" N   TYR D  92 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 134 through 142
      removed outlier: 3.633A  pdb=" N   VAL D 138 " --> pdb=" O   ASP D 134 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 54 through 59
      removed outlier: 3.555A  pdb=" N   THR B  54 " --> pdb=" O   ARG B  70 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ALA B  69 " --> pdb=" O   TYR B 125 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   TYR B 125 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER B 100 " --> pdb=" O   GLY B 130 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 54 through 59
      removed outlier: 3.557A  pdb=" N   THR D  54 " --> pdb=" O   ARG D  70 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   ALA D  69 " --> pdb=" O   TYR D 125 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   TYR D 125 " --> pdb=" O   ALA D  69 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER D 100 " --> pdb=" O   GLY D 130 " (cutoff:3.500A)

    485 hydrogen bonds defined for protein.
    1431 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: 1.00

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1098
        1.28 -     1.41: 2413
        1.41 -     1.54: 4274
        1.54 -     1.67: 117
        1.67 -     1.80: 58
  Bond restraints: 7960
  Sorted by residual:
  bond pdb=" CA  PHE C 202 "
       pdb=" C   PHE C 202 "
    ideal  model  delta    sigma   weight residual
    1.531  1.444  0.088 1.08e-02 8.57e+03 6.57e+01
  bond pdb=" CA  PHE A 202 "
       pdb=" C   PHE A 202 "
    ideal  model  delta    sigma   weight residual
    1.531  1.444  0.087 1.08e-02 8.57e+03 6.48e+01
  bond pdb=" CA  ASN A 203 "
       pdb=" C   ASN A 203 "
    ideal  model  delta    sigma   weight residual
    1.528  1.422  0.105 1.32e-02 5.74e+03 6.33e+01
  bond pdb=" CA  ASN C 203 "
       pdb=" C   ASN C 203 "
    ideal  model  delta    sigma   weight residual
    1.528  1.422  0.105 1.32e-02 5.74e+03 6.33e+01
  bond pdb=" CA  PHE C 201 "
       pdb=" C   PHE C 201 "
    ideal  model  delta    sigma   weight residual
    1.527  1.438  0.089 1.30e-02 5.92e+03 4.71e+01
  ... (remaining 7955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.90: 10342
        2.90 -     5.81: 371
        5.81 -     8.71: 33
        8.71 -    11.62: 10
       11.62 -    14.52: 8
  Bond angle restraints: 10764
  Sorted by residual:
  angle pdb=" N   LEU A 162 "
        pdb=" CA  LEU A 162 "
        pdb=" C   LEU A 162 "
      ideal   model   delta    sigma   weight residual
     114.04  102.26   11.78 1.24e+00 6.50e-01 9.02e+01
  angle pdb=" N   LEU C 162 "
        pdb=" CA  LEU C 162 "
        pdb=" C   LEU C 162 "
      ideal   model   delta    sigma   weight residual
     114.04  102.34   11.70 1.24e+00 6.50e-01 8.90e+01
  angle pdb=" N   PHE C 201 "
        pdb=" CA  PHE C 201 "
        pdb=" C   PHE C 201 "
      ideal   model   delta    sigma   weight residual
     111.39  123.75  -12.36 1.38e+00 5.25e-01 8.02e+01
  angle pdb=" N   PHE A 201 "
        pdb=" CA  PHE A 201 "
        pdb=" C   PHE A 201 "
      ideal   model   delta    sigma   weight residual
     111.39  123.73  -12.34 1.38e+00 5.25e-01 8.00e+01
  angle pdb=" N   SER A 166 "
        pdb=" CA  SER A 166 "
        pdb=" C   SER A 166 "
      ideal   model   delta    sigma   weight residual
     110.80   98.72   12.08 2.13e+00 2.20e-01 3.22e+01
  ... (remaining 10759 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 4002
       17.69 -    35.37: 468
       35.37 -    53.06: 88
       53.06 -    70.75: 38
       70.75 -    88.43: 8
  Dihedral angle restraints: 4604
    sinusoidal: 1934
      harmonic: 2670
  Sorted by residual:
  dihedral pdb=" C   PHE A 201 "
           pdb=" N   PHE A 201 "
           pdb=" CA  PHE A 201 "
           pdb=" CB  PHE A 201 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -155.63   33.03     0      2.50e+00 1.60e-01 1.75e+02
  dihedral pdb=" C   PHE C 201 "
           pdb=" N   PHE C 201 "
           pdb=" CA  PHE C 201 "
           pdb=" CB  PHE C 201 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -155.61   33.01     0      2.50e+00 1.60e-01 1.74e+02
  dihedral pdb=" N   PHE A 201 "
           pdb=" C   PHE A 201 "
           pdb=" CA  PHE A 201 "
           pdb=" CB  PHE A 201 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  155.76  -32.96     0      2.50e+00 1.60e-01 1.74e+02
  ... (remaining 4601 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.326: 1132
       0.326 -    0.652: 6
       0.652 -    0.978: 0
       0.978 -    1.304: 0
       1.304 -    1.630: 2
  Chirality restraints: 1140
  Sorted by residual:
  chirality pdb=" CA  PHE C 201 "
            pdb=" N   PHE C 201 "
            pdb=" C   PHE C 201 "
            pdb=" CB  PHE C 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.88    1.63 2.00e-01 2.50e+01 6.65e+01
  chirality pdb=" CA  PHE A 201 "
            pdb=" N   PHE A 201 "
            pdb=" C   PHE A 201 "
            pdb=" CB  PHE A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.88    1.63 2.00e-01 2.50e+01 6.64e+01
  chirality pdb=" CB  VAL C 164 "
            pdb=" CA  VAL C 164 "
            pdb=" CG1 VAL C 164 "
            pdb=" CG2 VAL C 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.21   -0.42 2.00e-01 2.50e+01 4.39e+00
  ... (remaining 1137 not shown)

  Planarity restraints: 1298
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 201 "    0.046 2.00e-02 2.50e+03   3.54e-02 2.19e+01
        pdb=" CG  PHE C 201 "   -0.080 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 201 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 201 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 201 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 201 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 201 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 201 "   -0.046 2.00e-02 2.50e+03   3.52e-02 2.17e+01
        pdb=" CG  PHE A 201 "    0.079 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 201 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 201 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 201 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 201 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 201 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 106 "    0.015 2.00e-02 2.50e+03   3.09e-02 9.54e+00
        pdb=" C   LYS C 106 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   LYS C 106 "    0.020 2.00e-02 2.50e+03
        pdb=" N   THR C 107 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1295 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 83
        2.58 -     3.16: 6758
        3.16 -     3.74: 11804
        3.74 -     4.32: 16487
        4.32 -     4.90: 27540
  Nonbonded interactions: 62672
  Sorted by model distance:
  nonbonded pdb=" O   THR A 204 "
            pdb=" N   ALA A 206 "
     model   vdw
     1.998 3.120
  nonbonded pdb=" O   THR C 204 "
            pdb=" N   ALA C 206 "
     model   vdw
     1.999 3.120
  nonbonded pdb=" OH  TYR A 224 "
            pdb=" OG  SER A 266 "
     model   vdw
     2.041 3.040
  nonbonded pdb=" OH  TYR C 224 "
            pdb=" OG  SER C 266 "
     model   vdw
     2.041 3.040
  nonbonded pdb=" O   LEU A 261 "
            pdb=" OG  SER A 265 "
     model   vdw
     2.091 3.040
  ... (remaining 62667 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             1.670
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.730
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
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      :  0.011   0.118   7964  Z= 0.558
  Angle     :  1.212  14.522  10772  Z= 0.686
  Chirality :  0.096   1.630   1140
  Planarity :  0.006   0.050   1298
  Dihedral  : 15.982  88.432   2880
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 17.33
  Ramachandran Plot:
    Outliers :  1.58 %
    Allowed  :  6.76 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  :  3.21 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.28), residues: 888
  helix:  0.49 (0.22), residues: 556
  sheet: -0.40 (0.73), residues: 58
  loop : -2.40 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  78 
 TYR   0.023   0.002   TYR D 114 
 PHE   0.080   0.003   PHE C 201 
 TRP   0.010   0.002   TRP A 200 
 HIS   0.008   0.002   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.01082 ( 7960)
  covalent geometry    : angle       1.21273 (10764)
  SS BOND              : bond        0.00604 (    4)
  SS BOND              : angle       0.27511 (    8)
  hydrogen bonds       : bond        0.12579 (  485)
  hydrogen bonds       : angle       6.58689 ( 1431)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 MET cc_start: 0.6931 (mmt) cc_final: 0.6708 (mtt)
REVERT: A  177 MET cc_start: 0.6893 (mmt) cc_final: 0.6231 (tpt)
REVERT: A  193 CYS cc_start: 0.7390 (t) cc_final: 0.6802 (m)
REVERT: A  375 ILE cc_start: 0.5444 (OUTLIER) cc_final: 0.5129 (mm)
REVERT: A  377 ARG cc_start: 0.6510 (ttp-170) cc_final: 0.5528 (tpt90)
REVERT: C   89 MET cc_start: 0.6967 (mmt) cc_final: 0.6750 (mtt)
REVERT: C  177 MET cc_start: 0.6838 (mmt) cc_final: 0.6173 (tpt)
REVERT: C  193 CYS cc_start: 0.7383 (t) cc_final: 0.6821 (m)
REVERT: C  375 ILE cc_start: 0.5458 (OUTLIER) cc_final: 0.5127 (mm)
REVERT: C  377 ARG cc_start: 0.6486 (ttp-170) cc_final: 0.5574 (tpt90)
REVERT: D  136 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7678 (tp30)
  outliers start: 24
  outliers final: 2
  residues processed: 155
  average time/residue: 0.1126
  time to fit residues: 22.5183
Evaluate side-chains
  106 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  371 TRP
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain C residue  371 TRP
Chi-restraints excluded: chain C residue  375 ILE
Chi-restraints excluded: chain D residue  136 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0770
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 163 HIS
A 338 ASN
A 365 GLN
C 163 HIS
C 338 ASN
C 365 GLN
D 149 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.166286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.133088 restraints weight = 9542.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 2.22
r_work: 0.3411 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   7964  Z= 0.171
  Angle     :  0.702   8.235  10772  Z= 0.386
  Chirality :  0.048   0.253   1140
  Planarity :  0.006   0.050   1298
  Dihedral  : 11.201  61.138   1173
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.64 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  :  9.63 %
    Favored  : 87.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.28), residues: 888
  helix:  0.81 (0.22), residues: 560
  sheet: -0.35 (0.66), residues: 58
  loop : -2.13 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  25 
 TYR   0.039   0.002   TYR C 182 
 PHE   0.019   0.001   PHE C 135 
 TRP   0.012   0.001   TRP D  68 
 HIS   0.018   0.002   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 7960)
  covalent geometry    : angle       0.70228 (10764)
  SS BOND              : bond        0.00297 (    4)
  SS BOND              : angle       0.33987 (    8)
  hydrogen bonds       : bond        0.05612 (  485)
  hydrogen bonds       : angle       5.55463 ( 1431)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  177 MET cc_start: 0.7319 (mmt) cc_final: 0.6678 (tpt)
REVERT: A  193 CYS cc_start: 0.7507 (t) cc_final: 0.7024 (m)
REVERT: A  371 TRP cc_start: 0.6008 (OUTLIER) cc_final: 0.5352 (m-90)
REVERT: A  375 ILE cc_start: 0.6381 (OUTLIER) cc_final: 0.5888 (mt)
REVERT: A  377 ARG cc_start: 0.6712 (ttp-170) cc_final: 0.5773 (tpt90)
REVERT: B  134 ASP cc_start: 0.8567 (p0) cc_final: 0.8323 (p0)
REVERT: C   89 MET cc_start: 0.7472 (mmt) cc_final: 0.7266 (mtt)
REVERT: C  177 MET cc_start: 0.7305 (mmt) cc_final: 0.6639 (tpt)
REVERT: C  193 CYS cc_start: 0.7480 (t) cc_final: 0.7040 (m)
REVERT: C  205 LYS cc_start: 0.7692 (tmtt) cc_final: 0.6829 (mmtt)
REVERT: C  371 TRP cc_start: 0.6018 (OUTLIER) cc_final: 0.5333 (m-90)
REVERT: C  375 ILE cc_start: 0.6367 (OUTLIER) cc_final: 0.5868 (mt)
REVERT: C  377 ARG cc_start: 0.6822 (ttp-170) cc_final: 0.5894 (tpt90)
REVERT: C  379 LEU cc_start: 0.7522 (tp) cc_final: 0.7315 (pp)
REVERT: D  134 ASP cc_start: 0.8563 (p0) cc_final: 0.8317 (p0)
REVERT: D  136 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.8000 (tp30)
  outliers start: 21
  outliers final: 6
  residues processed: 127
  average time/residue: 0.0969
  time to fit residues: 16.4214
Evaluate side-chains
  117 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 MET
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  338 ASN
Chi-restraints excluded: chain A residue  371 TRP
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain B residue  108 ASN
Chi-restraints excluded: chain C residue  338 ASN
Chi-restraints excluded: chain C residue  371 TRP
Chi-restraints excluded: chain C residue  375 ILE
Chi-restraints excluded: chain D residue  108 ASN
Chi-restraints excluded: chain D residue  136 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0030
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.7590

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

Flipped N/Q/H residues before XYZ refinement:
B  47 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.162118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.132557 restraints weight = 9421.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.77
r_work: 0.3394 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7964  Z= 0.162
  Angle     :  0.635   7.261  10772  Z= 0.348
  Chirality :  0.045   0.235   1140
  Planarity :  0.005   0.051   1298
  Dihedral  : 10.882  58.847   1173
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  5.29 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 11.23 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.00 (0.28), residues: 888
  helix:  0.91 (0.21), residues: 568
  sheet: -0.39 (0.63), residues: 58
  loop : -1.88 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  70 
 TYR   0.029   0.002   TYR C 182 
 PHE   0.019   0.001   PHE A 135 
 TRP   0.009   0.001   TRP D  68 
 HIS   0.005   0.001   HIS C 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7960)
  covalent geometry    : angle       0.63529 (10764)
  SS BOND              : bond        0.00253 (    4)
  SS BOND              : angle       0.27164 (    8)
  hydrogen bonds       : bond        0.05229 (  485)
  hydrogen bonds       : angle       5.31925 ( 1431)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  177 MET cc_start: 0.7419 (mmt) cc_final: 0.6705 (tpt)
REVERT: A  193 CYS cc_start: 0.7648 (t) cc_final: 0.6966 (m)
REVERT: A  205 LYS cc_start: 0.7832 (tmtt) cc_final: 0.6785 (mmtt)
REVERT: A  224 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.7169 (t80)
REVERT: A  293 LYS cc_start: 0.6292 (mtpt) cc_final: 0.5995 (tttm)
REVERT: A  371 TRP cc_start: 0.5783 (OUTLIER) cc_final: 0.5240 (m-90)
REVERT: A  375 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5627 (mt)
REVERT: A  377 ARG cc_start: 0.6570 (ttp80) cc_final: 0.5646 (tpt90)
REVERT: B  134 ASP cc_start: 0.8478 (p0) cc_final: 0.8102 (p0)
REVERT: C   89 MET cc_start: 0.7668 (mmt) cc_final: 0.7364 (mtt)
REVERT: C  177 MET cc_start: 0.7413 (mmt) cc_final: 0.6694 (tpt)
REVERT: C  205 LYS cc_start: 0.7762 (tmtt) cc_final: 0.6768 (mmtt)
REVERT: C  224 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.7164 (t80)
REVERT: C  371 TRP cc_start: 0.5718 (OUTLIER) cc_final: 0.5157 (m-90)
REVERT: C  375 ILE cc_start: 0.6124 (OUTLIER) cc_final: 0.5655 (mt)
REVERT: C  377 ARG cc_start: 0.6678 (ttp80) cc_final: 0.5777 (tpt90)
REVERT: D  134 ASP cc_start: 0.8617 (p0) cc_final: 0.8231 (p0)
  outliers start: 30
  outliers final: 11
  residues processed: 141
  average time/residue: 0.0944
  time to fit residues: 17.8169
Evaluate side-chains
  135 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 MET
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  201 PHE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  371 TRP
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain B residue  108 ASN
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  201 PHE
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  371 TRP
Chi-restraints excluded: chain C residue  375 ILE
Chi-restraints excluded: chain D residue  108 ASN
Chi-restraints excluded: chain D residue  136 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 24 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 338 ASN
B  47 ASN
C 338 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.162025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.132464 restraints weight = 9507.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 1.72
r_work: 0.3378 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7964  Z= 0.159
  Angle     :  0.603   6.973  10772  Z= 0.332
  Chirality :  0.045   0.228   1140
  Planarity :  0.005   0.051   1298
  Dihedral  : 10.580  59.573   1173
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.29 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 12.22 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.28), residues: 888
  helix:  1.04 (0.21), residues: 568
  sheet: -0.46 (0.62), residues: 58
  loop : -1.86 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  78 
 TYR   0.031   0.001   TYR C 182 
 PHE   0.019   0.001   PHE A 135 
 TRP   0.009   0.001   TRP D  68 
 HIS   0.005   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7960)
  covalent geometry    : angle       0.60351 (10764)
  SS BOND              : bond        0.00269 (    4)
  SS BOND              : angle       0.31623 (    8)
  hydrogen bonds       : bond        0.05012 (  485)
  hydrogen bonds       : angle       5.23173 ( 1431)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 123
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   78 ILE cc_start: 0.4923 (OUTLIER) cc_final: 0.4469 (mt)
REVERT: A  177 MET cc_start: 0.7379 (mmt) cc_final: 0.6735 (tpt)
REVERT: A  193 CYS cc_start: 0.7656 (t) cc_final: 0.6904 (m)
REVERT: A  205 LYS cc_start: 0.7814 (tmtt) cc_final: 0.6776 (mmtt)
REVERT: A  224 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.7232 (t80)
REVERT: A  371 TRP cc_start: 0.5625 (OUTLIER) cc_final: 0.5158 (m-90)
REVERT: A  375 ILE cc_start: 0.6092 (OUTLIER) cc_final: 0.5660 (mt)
REVERT: A  377 ARG cc_start: 0.6570 (ttp80) cc_final: 0.5615 (tpt90)
REVERT: B  134 ASP cc_start: 0.8568 (p0) cc_final: 0.8143 (p0)
REVERT: C   78 ILE cc_start: 0.4897 (OUTLIER) cc_final: 0.4468 (mt)
REVERT: C   89 MET cc_start: 0.7666 (mmt) cc_final: 0.7381 (mtt)
REVERT: C  177 MET cc_start: 0.7372 (mmt) cc_final: 0.6717 (tpt)
REVERT: C  193 CYS cc_start: 0.7647 (t) cc_final: 0.6907 (m)
REVERT: C  224 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.7230 (t80)
REVERT: C  371 TRP cc_start: 0.5685 (OUTLIER) cc_final: 0.5158 (m-90)
REVERT: C  375 ILE cc_start: 0.6051 (OUTLIER) cc_final: 0.5608 (mt)
REVERT: C  377 ARG cc_start: 0.6731 (ttp80) cc_final: 0.5700 (tpt90)
REVERT: D  134 ASP cc_start: 0.8570 (p0) cc_final: 0.8155 (p0)
  outliers start: 38
  outliers final: 13
  residues processed: 147
  average time/residue: 0.0917
  time to fit residues: 18.4489
Evaluate side-chains
  137 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  151 MET
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  201 PHE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  371 TRP
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain B residue  108 ASN
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  201 PHE
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  371 TRP
Chi-restraints excluded: chain C residue  375 ILE
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain D residue  108 ASN
Chi-restraints excluded: chain D residue  136 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 23 optimal weight:    0.0970
   chunk 9 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 71 optimal weight:    0.5980
   chunk 34 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.166734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.137235 restraints weight = 9481.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.75
r_work: 0.3392 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
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      :  0.003   0.061   7964  Z= 0.134
  Angle     :  0.563   7.199  10772  Z= 0.310
  Chirality :  0.043   0.195   1140
  Planarity :  0.005   0.052   1298
  Dihedral  :  9.981  58.096   1173
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.73 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 14.07 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.28), residues: 888
  helix:  1.31 (0.21), residues: 560
  sheet: -0.35 (0.62), residues: 58
  loop : -1.85 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 112 
 TYR   0.031   0.001   TYR C 182 
 PHE   0.020   0.001   PHE A 135 
 TRP   0.009   0.001   TRP B  68 
 HIS   0.006   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7960)
  covalent geometry    : angle       0.56323 (10764)
  SS BOND              : bond        0.00195 (    4)
  SS BOND              : angle       0.34482 (    8)
  hydrogen bonds       : bond        0.04641 (  485)
  hydrogen bonds       : angle       5.08622 ( 1431)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   78 ILE cc_start: 0.5004 (OUTLIER) cc_final: 0.4527 (mt)
REVERT: A  171 LYS cc_start: 0.7795 (tppt) cc_final: 0.7470 (tmtt)
REVERT: A  174 MET cc_start: 0.5813 (OUTLIER) cc_final: 0.5517 (ptm)
REVERT: A  177 MET cc_start: 0.7352 (mmt) cc_final: 0.6702 (tpt)
REVERT: A  193 CYS cc_start: 0.7625 (t) cc_final: 0.6827 (m)
REVERT: A  224 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.7212 (t80)
REVERT: A  279 TYR cc_start: 0.7588 (m-10) cc_final: 0.7247 (m-10)
REVERT: A  371 TRP cc_start: 0.5353 (OUTLIER) cc_final: 0.5047 (m-90)
REVERT: A  375 ILE cc_start: 0.6256 (OUTLIER) cc_final: 0.5859 (mt)
REVERT: A  377 ARG cc_start: 0.6453 (ttp80) cc_final: 0.5508 (tpt90)
REVERT: B   97 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7651 (tt0)
REVERT: B  108 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8466 (p0)
REVERT: B  134 ASP cc_start: 0.8595 (p0) cc_final: 0.8120 (p0)
REVERT: C   78 ILE cc_start: 0.4939 (OUTLIER) cc_final: 0.4507 (mt)
REVERT: C   89 MET cc_start: 0.7655 (mmt) cc_final: 0.7362 (mtt)
REVERT: C  171 LYS cc_start: 0.7715 (tppt) cc_final: 0.7386 (tmtt)
REVERT: C  174 MET cc_start: 0.6017 (OUTLIER) cc_final: 0.5727 (ptm)
REVERT: C  177 MET cc_start: 0.7324 (mmt) cc_final: 0.6690 (tpt)
REVERT: C  193 CYS cc_start: 0.7614 (t) cc_final: 0.6840 (m)
REVERT: C  224 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.7232 (t80)
REVERT: C  279 TYR cc_start: 0.7575 (m-10) cc_final: 0.7235 (m-10)
REVERT: C  371 TRP cc_start: 0.5318 (OUTLIER) cc_final: 0.4987 (m-90)
REVERT: C  375 ILE cc_start: 0.6161 (OUTLIER) cc_final: 0.5760 (mt)
REVERT: C  377 ARG cc_start: 0.6562 (ttp80) cc_final: 0.5605 (tpt90)
REVERT: D   19 LYS cc_start: 0.7525 (ptpp) cc_final: 0.6801 (pttt)
REVERT: D   97 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7644 (tt0)
REVERT: D  108 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8462 (p0)
REVERT: D  134 ASP cc_start: 0.8588 (p0) cc_final: 0.8156 (p0)
  outliers start: 33
  outliers final: 12
  residues processed: 138
  average time/residue: 0.0881
  time to fit residues: 16.8284
Evaluate side-chains
  137 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  201 PHE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  371 TRP
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  108 ASN
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  201 PHE
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  273 LYS
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  371 TRP
Chi-restraints excluded: chain C residue  375 ILE
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain D residue  108 ASN
Chi-restraints excluded: chain D residue  136 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 32 optimal weight:    5.9990
   chunk 80 optimal weight:    0.0040
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
A 256 HIS
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 GLN
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.162049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.131940 restraints weight = 9518.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 1.81
r_work: 0.3414 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7964  Z= 0.140
  Angle     :  0.566   6.986  10772  Z= 0.310
  Chirality :  0.043   0.204   1140
  Planarity :  0.005   0.052   1298
  Dihedral  :  9.689  57.096   1173
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.62 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 15.43 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.28), residues: 888
  helix:  1.30 (0.21), residues: 566
  sheet: -0.21 (0.62), residues: 58
  loop : -1.77 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  70 
 TYR   0.032   0.001   TYR A 182 
 PHE   0.019   0.001   PHE C 135 
 TRP   0.008   0.001   TRP D  68 
 HIS   0.006   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7960)
  covalent geometry    : angle       0.56611 (10764)
  SS BOND              : bond        0.00215 (    4)
  SS BOND              : angle       0.28828 (    8)
  hydrogen bonds       : bond        0.04696 (  485)
  hydrogen bonds       : angle       5.04377 ( 1431)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 118
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A   78 ILE cc_start: 0.4888 (OUTLIER) cc_final: 0.4404 (mt)
REVERT: A  123 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7458 (p)
REVERT: A  171 LYS cc_start: 0.7708 (tppt) cc_final: 0.7446 (tmtt)
REVERT: A  177 MET cc_start: 0.7433 (mmt) cc_final: 0.6772 (tpt)
REVERT: A  193 CYS cc_start: 0.7699 (t) cc_final: 0.6929 (m)
REVERT: A  201 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7178 (m-80)
REVERT: A  224 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.7162 (t80)
REVERT: A  371 TRP cc_start: 0.5234 (OUTLIER) cc_final: 0.4943 (m-90)
REVERT: A  375 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5733 (mt)
REVERT: A  377 ARG cc_start: 0.6332 (ttp80) cc_final: 0.5324 (tpt90)
REVERT: B   19 LYS cc_start: 0.7320 (ptpp) cc_final: 0.6597 (pttt)
REVERT: B   97 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7591 (tt0)
REVERT: B  108 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8446 (p0)
REVERT: B  134 ASP cc_start: 0.8608 (p0) cc_final: 0.8135 (p0)
REVERT: C   78 ILE cc_start: 0.4815 (OUTLIER) cc_final: 0.4374 (mt)
REVERT: C   89 MET cc_start: 0.7599 (mmt) cc_final: 0.7331 (mtt)
REVERT: C  123 THR cc_start: 0.7783 (OUTLIER) cc_final: 0.7416 (p)
REVERT: C  171 LYS cc_start: 0.7621 (tppt) cc_final: 0.7332 (tmtt)
REVERT: C  177 MET cc_start: 0.7403 (mmt) cc_final: 0.6740 (tpt)
REVERT: C  193 CYS cc_start: 0.7645 (t) cc_final: 0.6850 (m)
REVERT: C  224 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.7162 (t80)
REVERT: C  371 TRP cc_start: 0.5156 (OUTLIER) cc_final: 0.4839 (m-90)
REVERT: C  375 ILE cc_start: 0.5994 (OUTLIER) cc_final: 0.5654 (mt)
REVERT: C  377 ARG cc_start: 0.6362 (ttp80) cc_final: 0.5416 (tpt90)
REVERT: D   19 LYS cc_start: 0.7251 (ptpp) cc_final: 0.6491 (pttt)
REVERT: D   97 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7648 (tt0)
REVERT: D  108 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8437 (p0)
REVERT: D  134 ASP cc_start: 0.8613 (p0) cc_final: 0.8170 (p0)
  outliers start: 38
  outliers final: 16
  residues processed: 139
  average time/residue: 0.0866
  time to fit residues: 16.5089
Evaluate side-chains
  145 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 114
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  106 LYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  151 MET
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  201 PHE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  371 TRP
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  108 ASN
Chi-restraints excluded: chain B residue  131 TYR
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  201 PHE
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  273 LYS
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  371 TRP
Chi-restraints excluded: chain C residue  375 ILE
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain D residue  108 ASN
Chi-restraints excluded: chain D residue  131 TYR
Chi-restraints excluded: chain D residue  136 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 52 optimal weight:    0.1980
   chunk 58 optimal weight:    0.2980
   chunk 38 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0770
   chunk 34 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0980
   chunk 44 optimal weight:   10.0000
   chunk 23 optimal weight:    0.3980
   overall best weight:    0.2138

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN
A 256 HIS
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 GLN
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.168121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.139163 restraints weight = 9489.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 1.73
r_work: 0.3458 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7964  Z= 0.118
  Angle     :  0.532   7.170  10772  Z= 0.291
  Chirality :  0.042   0.167   1140
  Planarity :  0.005   0.052   1298
  Dihedral  :  9.163  58.819   1173
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.84 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 15.19 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.28), residues: 888
  helix:  1.41 (0.21), residues: 568
  sheet:  0.01 (0.63), residues: 58
  loop : -1.71 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 112 
 TYR   0.029   0.001   TYR C 182 
 PHE   0.019   0.001   PHE A 230 
 TRP   0.008   0.001   TRP B  68 
 HIS   0.007   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 7960)
  covalent geometry    : angle       0.53223 (10764)
  SS BOND              : bond        0.00137 (    4)
  SS BOND              : angle       0.45513 (    8)
  hydrogen bonds       : bond        0.04295 (  485)
  hydrogen bonds       : angle       4.92254 ( 1431)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 121
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A   78 ILE cc_start: 0.4916 (OUTLIER) cc_final: 0.4445 (mt)
REVERT: A  123 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7578 (p)
REVERT: A  161 ARG cc_start: 0.6824 (tpt90) cc_final: 0.6225 (tmt170)
REVERT: A  171 LYS cc_start: 0.7765 (tppt) cc_final: 0.7419 (tmtt)
REVERT: A  177 MET cc_start: 0.7463 (mmt) cc_final: 0.6898 (tpt)
REVERT: A  193 CYS cc_start: 0.7575 (t) cc_final: 0.6777 (m)
REVERT: A  201 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6915 (m-80)
REVERT: A  224 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7187 (t80)
REVERT: A  279 TYR cc_start: 0.7484 (m-10) cc_final: 0.7182 (m-10)
REVERT: A  371 TRP cc_start: 0.5276 (OUTLIER) cc_final: 0.5035 (m-90)
REVERT: A  375 ILE cc_start: 0.6208 (OUTLIER) cc_final: 0.5975 (mt)
REVERT: A  377 ARG cc_start: 0.6401 (ttp80) cc_final: 0.5396 (tpt90)
REVERT: B   19 LYS cc_start: 0.7371 (ptpp) cc_final: 0.6590 (mtmt)
REVERT: B   97 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7700 (tt0)
REVERT: B  134 ASP cc_start: 0.8633 (p0) cc_final: 0.8142 (p0)
REVERT: C   78 ILE cc_start: 0.4913 (OUTLIER) cc_final: 0.4458 (mt)
REVERT: C   89 MET cc_start: 0.7519 (mmt) cc_final: 0.7293 (mtt)
REVERT: C  123 THR cc_start: 0.7841 (OUTLIER) cc_final: 0.7511 (p)
REVERT: C  171 LYS cc_start: 0.7659 (tppt) cc_final: 0.7398 (tmtt)
REVERT: C  177 MET cc_start: 0.7428 (mmt) cc_final: 0.6882 (tpt)
REVERT: C  193 CYS cc_start: 0.7629 (t) cc_final: 0.6968 (m)
REVERT: C  224 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7195 (t80)
REVERT: C  279 TYR cc_start: 0.7467 (m-10) cc_final: 0.7174 (m-10)
REVERT: C  371 TRP cc_start: 0.5251 (OUTLIER) cc_final: 0.4985 (m-90)
REVERT: C  375 ILE cc_start: 0.6058 (OUTLIER) cc_final: 0.5796 (mt)
REVERT: C  377 ARG cc_start: 0.6469 (ttp80) cc_final: 0.5529 (tpt90)
REVERT: D   19 LYS cc_start: 0.7362 (ptpp) cc_final: 0.6610 (mtmt)
REVERT: D   97 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7743 (tt0)
REVERT: D  136 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8001 (tp30)
REVERT: D  140 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7887 (mm-30)
  outliers start: 42
  outliers final: 12
  residues processed: 145
  average time/residue: 0.0899
  time to fit residues: 17.9105
Evaluate side-chains
  137 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  201 PHE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  371 TRP
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  131 TYR
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  241 GLN
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  371 TRP
Chi-restraints excluded: chain C residue  375 ILE
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain D residue  131 TYR
Chi-restraints excluded: chain D residue  136 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 70 optimal weight:    0.7980
   chunk 83 optimal weight:    0.4980
   chunk 15 optimal weight:    0.8980
   chunk 13 optimal weight:    0.2980
   chunk 2 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 GLN
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.164218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.134801 restraints weight = 9471.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 1.80
r_work: 0.3448 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7964  Z= 0.143
  Angle     :  0.555   6.776  10772  Z= 0.303
  Chirality :  0.043   0.198   1140
  Planarity :  0.005   0.052   1298
  Dihedral  :  9.161  58.286   1173
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.18 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 17.04 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.28), residues: 888
  helix:  1.42 (0.21), residues: 570
  sheet:  0.04 (0.63), residues: 58
  loop : -1.56 (0.39), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  70 
 TYR   0.035   0.001   TYR C 182 
 PHE   0.016   0.001   PHE C 135 
 TRP   0.007   0.001   TRP D  68 
 HIS   0.007   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7960)
  covalent geometry    : angle       0.55557 (10764)
  SS BOND              : bond        0.00246 (    4)
  SS BOND              : angle       0.28622 (    8)
  hydrogen bonds       : bond        0.04550 (  485)
  hydrogen bonds       : angle       4.93597 ( 1431)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 111
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A   78 ILE cc_start: 0.4798 (OUTLIER) cc_final: 0.4332 (mt)
REVERT: A  123 THR cc_start: 0.7857 (OUTLIER) cc_final: 0.7504 (p)
REVERT: A  171 LYS cc_start: 0.7695 (tppt) cc_final: 0.7427 (tmtt)
REVERT: A  177 MET cc_start: 0.7404 (mmt) cc_final: 0.6805 (tpt)
REVERT: A  193 CYS cc_start: 0.7850 (t) cc_final: 0.7116 (m)
REVERT: A  201 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.7157 (m-80)
REVERT: A  224 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.7139 (t80)
REVERT: A  279 TYR cc_start: 0.7484 (m-10) cc_final: 0.7147 (m-10)
REVERT: A  371 TRP cc_start: 0.5051 (OUTLIER) cc_final: 0.4801 (m-90)
REVERT: A  375 ILE cc_start: 0.6051 (OUTLIER) cc_final: 0.5816 (mt)
REVERT: A  377 ARG cc_start: 0.6351 (ttp80) cc_final: 0.5313 (tpt90)
REVERT: B   19 LYS cc_start: 0.7134 (ptpp) cc_final: 0.6451 (mtmt)
REVERT: B   97 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7614 (tt0)
REVERT: B  134 ASP cc_start: 0.8625 (p0) cc_final: 0.8128 (p0)
REVERT: C   78 ILE cc_start: 0.4814 (OUTLIER) cc_final: 0.4368 (mt)
REVERT: C   89 MET cc_start: 0.7538 (mmt) cc_final: 0.7262 (mtt)
REVERT: C  123 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7468 (p)
REVERT: C  171 LYS cc_start: 0.7530 (tppt) cc_final: 0.7275 (tmtt)
REVERT: C  177 MET cc_start: 0.7406 (mmt) cc_final: 0.6831 (tpt)
REVERT: C  193 CYS cc_start: 0.7701 (t) cc_final: 0.6958 (m)
REVERT: C  224 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.7130 (t80)
REVERT: C  279 TYR cc_start: 0.7491 (m-10) cc_final: 0.7150 (m-10)
REVERT: C  371 TRP cc_start: 0.5033 (OUTLIER) cc_final: 0.4761 (m-90)
REVERT: C  375 ILE cc_start: 0.5926 (OUTLIER) cc_final: 0.5657 (mt)
REVERT: C  377 ARG cc_start: 0.6394 (ttp80) cc_final: 0.5414 (tpt90)
REVERT: D   19 LYS cc_start: 0.7135 (ptpp) cc_final: 0.6397 (mtmt)
REVERT: D   97 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7625 (tt0)
REVERT: D  136 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7945 (tp30)
REVERT: D  140 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7924 (mm-30)
  outliers start: 32
  outliers final: 16
  residues processed: 131
  average time/residue: 0.0896
  time to fit residues: 16.1124
Evaluate side-chains
  141 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  201 PHE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  371 TRP
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  131 TYR
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  273 LYS
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  371 TRP
Chi-restraints excluded: chain C residue  375 ILE
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain D residue   74 SER
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain D residue  131 TYR
Chi-restraints excluded: chain D residue  136 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 84 optimal weight:    0.3980
   chunk 7 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 256 HIS
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 GLN
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.164920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.136385 restraints weight = 9533.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 1.69
r_work: 0.3426 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7964  Z= 0.145
  Angle     :  0.567   6.803  10772  Z= 0.311
  Chirality :  0.043   0.204   1140
  Planarity :  0.005   0.053   1298
  Dihedral  :  9.180  56.593   1173
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.73 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 17.65 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.28), residues: 888
  helix:  1.48 (0.21), residues: 560
  sheet:  0.07 (0.63), residues: 58
  loop : -1.62 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  70 
 TYR   0.021   0.001   TYR A 182 
 PHE   0.016   0.001   PHE C 135 
 TRP   0.007   0.001   TRP D  68 
 HIS   0.008   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 7960)
  covalent geometry    : angle       0.56724 (10764)
  SS BOND              : bond        0.00235 (    4)
  SS BOND              : angle       0.29459 (    8)
  hydrogen bonds       : bond        0.04630 (  485)
  hydrogen bonds       : angle       4.96541 ( 1431)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 108
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A   78 ILE cc_start: 0.4991 (OUTLIER) cc_final: 0.4495 (mt)
REVERT: A  171 LYS cc_start: 0.7806 (tppt) cc_final: 0.7572 (tmtt)
REVERT: A  177 MET cc_start: 0.7508 (mmt) cc_final: 0.6925 (tpt)
REVERT: A  193 CYS cc_start: 0.7799 (t) cc_final: 0.7154 (m)
REVERT: A  224 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7290 (t80)
REVERT: A  279 TYR cc_start: 0.7585 (m-10) cc_final: 0.7252 (m-10)
REVERT: A  371 TRP cc_start: 0.5355 (OUTLIER) cc_final: 0.5103 (m-90)
REVERT: A  375 ILE cc_start: 0.6154 (OUTLIER) cc_final: 0.5940 (mt)
REVERT: A  377 ARG cc_start: 0.6384 (ttp80) cc_final: 0.5322 (tpt90)
REVERT: B   19 LYS cc_start: 0.7306 (ptpp) cc_final: 0.6601 (mtmt)
REVERT: B   97 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7699 (tt0)
REVERT: B  134 ASP cc_start: 0.8594 (p0) cc_final: 0.8074 (p0)
REVERT: C   78 ILE cc_start: 0.5004 (OUTLIER) cc_final: 0.4526 (mt)
REVERT: C   89 MET cc_start: 0.7501 (mmt) cc_final: 0.7259 (mtt)
REVERT: C  171 LYS cc_start: 0.7616 (tppt) cc_final: 0.7296 (tmtt)
REVERT: C  177 MET cc_start: 0.7375 (mmt) cc_final: 0.6796 (tpt)
REVERT: C  193 CYS cc_start: 0.7711 (t) cc_final: 0.7093 (m)
REVERT: C  200 TRP cc_start: 0.7947 (t-100) cc_final: 0.7716 (t-100)
REVERT: C  224 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7303 (t80)
REVERT: C  279 TYR cc_start: 0.7571 (m-10) cc_final: 0.7234 (m-10)
REVERT: C  371 TRP cc_start: 0.5258 (OUTLIER) cc_final: 0.4984 (m-90)
REVERT: C  375 ILE cc_start: 0.6094 (OUTLIER) cc_final: 0.5858 (mt)
REVERT: C  377 ARG cc_start: 0.6462 (ttp80) cc_final: 0.5480 (tpt90)
REVERT: D   97 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7682 (tt0)
  outliers start: 30
  outliers final: 18
  residues processed: 128
  average time/residue: 0.0878
  time to fit residues: 15.5244
Evaluate side-chains
  137 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  201 PHE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  371 TRP
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  131 TYR
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  241 GLN
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  371 TRP
Chi-restraints excluded: chain C residue  375 ILE
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain D residue   74 SER
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain D residue  131 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 82 optimal weight:    0.2980
   chunk 23 optimal weight:    0.2980
   chunk 10 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 57 optimal weight:    0.4980
   chunk 33 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 256 HIS
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 GLN
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.165838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.137443 restraints weight = 9460.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 1.67
r_work: 0.3441 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.3516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7964  Z= 0.132
  Angle     :  0.556   6.906  10772  Z= 0.305
  Chirality :  0.043   0.194   1140
  Planarity :  0.005   0.052   1298
  Dihedral  :  8.970  57.175   1170
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.84 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 17.90 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.28), residues: 888
  helix:  1.52 (0.21), residues: 560
  sheet:  0.21 (0.63), residues: 58
  loop : -1.61 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 112 
 TYR   0.018   0.001   TYR C 182 
 PHE   0.016   0.001   PHE C 135 
 TRP   0.008   0.001   TRP B  68 
 HIS   0.008   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7960)
  covalent geometry    : angle       0.55601 (10764)
  SS BOND              : bond        0.00190 (    4)
  SS BOND              : angle       0.30112 (    8)
  hydrogen bonds       : bond        0.04529 (  485)
  hydrogen bonds       : angle       4.95324 ( 1431)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A   78 ILE cc_start: 0.5010 (OUTLIER) cc_final: 0.4520 (mt)
REVERT: A  171 LYS cc_start: 0.7746 (tppt) cc_final: 0.7443 (tmtt)
REVERT: A  177 MET cc_start: 0.7502 (mmt) cc_final: 0.6919 (tpt)
REVERT: A  193 CYS cc_start: 0.7812 (t) cc_final: 0.7191 (m)
REVERT: A  224 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.7272 (t80)
REVERT: A  279 TYR cc_start: 0.7539 (m-10) cc_final: 0.7259 (m-10)
REVERT: A  371 TRP cc_start: 0.5374 (OUTLIER) cc_final: 0.5137 (m-90)
REVERT: A  375 ILE cc_start: 0.6163 (OUTLIER) cc_final: 0.5962 (mt)
REVERT: A  377 ARG cc_start: 0.6398 (ttp80) cc_final: 0.5338 (tpt90)
REVERT: B   19 LYS cc_start: 0.7321 (ptpp) cc_final: 0.6614 (mtmt)
REVERT: B   97 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7715 (tt0)
REVERT: C   78 ILE cc_start: 0.5024 (OUTLIER) cc_final: 0.4546 (mt)
REVERT: C   89 MET cc_start: 0.7471 (mmt) cc_final: 0.7237 (mtt)
REVERT: C  171 LYS cc_start: 0.7604 (tppt) cc_final: 0.7302 (tmtt)
REVERT: C  177 MET cc_start: 0.7494 (mmt) cc_final: 0.6912 (tpt)
REVERT: C  193 CYS cc_start: 0.7728 (t) cc_final: 0.7127 (m)
REVERT: C  200 TRP cc_start: 0.7935 (t-100) cc_final: 0.7698 (t-100)
REVERT: C  224 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7282 (t80)
REVERT: C  279 TYR cc_start: 0.7525 (m-10) cc_final: 0.7239 (m-10)
REVERT: C  371 TRP cc_start: 0.5272 (OUTLIER) cc_final: 0.5018 (m-90)
REVERT: C  375 ILE cc_start: 0.6108 (OUTLIER) cc_final: 0.5882 (mt)
REVERT: C  377 ARG cc_start: 0.6476 (ttp80) cc_final: 0.5497 (tpt90)
REVERT: D   97 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7701 (tt0)
  outliers start: 29
  outliers final: 18
  residues processed: 125
  average time/residue: 0.0837
  time to fit residues: 14.3884
Evaluate side-chains
  132 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  201 PHE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  371 TRP
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  131 TYR
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  371 TRP
Chi-restraints excluded: chain C residue  375 ILE
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain D residue   74 SER
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain D residue  131 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0170
   chunk 16 optimal weight:    0.0980
   chunk 3 optimal weight:    0.0060
   chunk 73 optimal weight:    0.9990
   chunk 57 optimal weight:    0.4980
   overall best weight:    0.2834

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

Flipped N/Q/H residues before XYZ refinement:
A 256 HIS
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.165793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.137387 restraints weight = 9666.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 1.70
r_work: 0.3457 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7964  Z= 0.119
  Angle     :  0.540   7.016  10772  Z= 0.296
  Chirality :  0.042   0.172   1140
  Planarity :  0.004   0.052   1298
  Dihedral  :  8.635  59.623   1170
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.95 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.78 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.28), residues: 888
  helix:  1.53 (0.21), residues: 572
  sheet:  0.43 (0.64), residues: 58
  loop : -1.59 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 112 
 TYR   0.019   0.001   TYR C 182 
 PHE   0.018   0.001   PHE A 135 
 TRP   0.008   0.001   TRP B  68 
 HIS   0.008   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 7960)
  covalent geometry    : angle       0.54042 (10764)
  SS BOND              : bond        0.00143 (    4)
  SS BOND              : angle       0.41465 (    8)
  hydrogen bonds       : bond        0.04253 (  485)
  hydrogen bonds       : angle       4.88095 ( 1431)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2377.01 seconds
wall clock time: 41 minutes 24.76 seconds (2484.76 seconds total)