Starting phenix.real_space_refine
on Tue May 13 20:58:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tin_41296/05_2025/8tin_41296.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tin_41296/05_2025/8tin_41296.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tin_41296/05_2025/8tin_41296.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tin_41296/05_2025/8tin_41296.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tin_41296/05_2025/8tin_41296.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tin_41296/05_2025/8tin_41296.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      21      5.16       5
     C    3513      2.51       5
     N     929      2.21       5
     O    1050      1.98       5
     H    5456      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 10971
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 3182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 3182
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 4565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 4565
          Classifications: {'peptide': 282}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 263}
          Chain breaks: 9
    Chain: "L"
      Number of atoms: 3115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 3115
          Classifications: {'peptide': 204}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 192}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 109
          Classifications: {'peptide': 7}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 5.91, per 1000 atoms: 0.54
  Number of scatterers: 10971
  At special positions: 0
  Unit cell: (54.808, 103.292, 119.102, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      21     16.00
     P       2     15.00
     O    1050      8.00
     N     929      7.00
     C    3513      6.00
     H    5456      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 215 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.92
  Conformation dependent library (CDL) restraints added in 686.9 milliseconds
  

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1338

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 16 sheets defined
      5.0% alpha, 40.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'H' and resid 204 through 208
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.676A  pdb=" N   LEU A  49 " --> pdb=" O   ASP A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 108
      removed outlier: 3.715A  pdb=" N   LYS A 108 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 122 through 129
    Processing helix  chain 'L' and resid 184 through 190
      removed outlier: 3.952A  pdb=" N   HIS L 190 " --> pdb=" O   ASP L 186 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'H' and resid 60 through 63
      removed outlier: 5.324A  pdb=" N   TRP H  50 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ARG H  41 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   TYR H 121 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 60 through 63
      removed outlier: 5.324A  pdb=" N   TRP H  50 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ARG H  41 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 139 through 143
      removed outlier: 4.667A  pdb=" N   ALA H 156 " --> pdb=" O   VAL H 203 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL H 203 " --> pdb=" O   ALA H 156 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   GLY H 158 " --> pdb=" O   VAL H 201 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   VAL H 201 " --> pdb=" O   GLY H 158 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   LEU H 160 " --> pdb=" O   SER H 199 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   SER H 199 " --> pdb=" O   LEU H 160 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   LYS H 162 " --> pdb=" O   LEU H 197 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LEU H 197 " --> pdb=" O   LYS H 162 " (cutoff:3.500A)
      removed outlier: 5.706A  pdb=" N   SER H 196 " --> pdb=" O   ALA H 187 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   ALA H 187 " --> pdb=" O   SER H 196 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   SER H 198 " --> pdb=" O   PHE H 185 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   VAL H 200 " --> pdb=" O   HIS H 183 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   HIS H 183 " --> pdb=" O   VAL H 200 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 172 through 173
    Processing sheet with id=AA6, first strand: chain 'A' and resid 113 through 118
    Processing sheet with id=AA7, first strand: chain 'A' and resid 28 through 29
      removed outlier: 6.016A  pdb=" N   PHE A  28 " --> pdb=" O   VAL A 172 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 82 through 88
      removed outlier: 5.846A  pdb=" N   ASN A  84 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   LEU A  58 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   GLN A  86 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   VAL A  56 " --> pdb=" O   GLN A  86 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 62 through 63
      removed outlier: 3.544A  pdb=" N   ARG A  63 " --> pdb=" O   GLY A 142 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLY A 142 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 184 through 188
      removed outlier: 3.590A  pdb=" N   LYS A 271 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 253 through 259
      removed outlier: 6.997A  pdb=" N   GLN A 238 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   ALA A 255 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 6 through 8
    Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 12
      removed outlier: 3.752A  pdb=" N   LEU L  12 " --> pdb=" O   LYS L 104 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'L' and resid 35 through 39
      removed outlier: 4.223A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 115 through 119
      removed outlier: 4.302A  pdb=" N   ASN L 139 " --> pdb=" O   TYR L 174 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 145 through 150

    208 hydrogen bonds defined for protein.
    537 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: 3.66

  Time building geometry restraints manager: 3.48 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5444
        1.03 -     1.23: 27
        1.23 -     1.42: 2354
        1.42 -     1.62: 3240
        1.62 -     1.81: 26
  Bond restraints: 11091
  Sorted by residual:
  bond pdb=" CB  TPO R 352 "
       pdb=" HB  TPO R 352 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.59e+01
  bond pdb=" CG2 TPO R 352 "
       pdb="HG23 TPO R 352 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.58e+01
  bond pdb=" CG2 TPO R 352 "
       pdb="HG21 TPO R 352 "
    ideal  model  delta    sigma   weight residual
    0.970  1.089 -0.119 2.00e-02 2.50e+03 3.57e+01
  bond pdb=" CG2 TPO R 352 "
       pdb="HG22 TPO R 352 "
    ideal  model  delta    sigma   weight residual
    0.970  1.089 -0.119 2.00e-02 2.50e+03 3.56e+01
  bond pdb=" OG1 TPO R 352 "
       pdb=" P   TPO R 352 "
    ideal  model  delta    sigma   weight residual
    1.717  1.612  0.105 2.00e-02 2.50e+03 2.76e+01
  ... (remaining 11086 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 19909
        2.15 -     4.30: 91
        4.30 -     6.46: 6
        6.46 -     8.61: 0
        8.61 -    10.76: 2
  Bond angle restraints: 20008
  Sorted by residual:
  angle pdb=" CB  TPO R 352 "
        pdb=" OG1 TPO R 352 "
        pdb=" P   TPO R 352 "
      ideal   model   delta    sigma   weight residual
     119.31  108.55   10.76 3.00e+00 1.11e-01 1.29e+01
  angle pdb=" OG1 TPO R 352 "
        pdb=" P   TPO R 352 "
        pdb=" O1P TPO R 352 "
      ideal   model   delta    sigma   weight residual
     100.43  110.04   -9.61 3.00e+00 1.11e-01 1.03e+01
  angle pdb=" CA  VAL H 203 "
        pdb=" C   VAL H 203 "
        pdb=" N   PRO H 204 "
      ideal   model   delta    sigma   weight residual
     116.57  119.45   -2.88 9.80e-01 1.04e+00 8.61e+00
  angle pdb=" C   VAL H 203 "
        pdb=" CA  VAL H 203 "
        pdb=" CB  VAL H 203 "
      ideal   model   delta    sigma   weight residual
     109.33  111.52   -2.19 9.80e-01 1.04e+00 4.99e+00
  angle pdb=" N   VAL H  32 "
        pdb=" CA  VAL H  32 "
        pdb=" C   VAL H  32 "
      ideal   model   delta    sigma   weight residual
     112.50  109.52    2.98 1.39e+00 5.18e-01 4.59e+00
  ... (remaining 20003 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.56: 4810
       16.56 -    33.12: 348
       33.12 -    49.68: 102
       49.68 -    66.24: 29
       66.24 -    82.80: 2
  Dihedral angle restraints: 5291
    sinusoidal: 2839
      harmonic: 2452
  Sorted by residual:
  dihedral pdb=" CA  ASN A 224 "
           pdb=" C   ASN A 224 "
           pdb=" N   SER A 225 "
           pdb=" CA  SER A 225 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.33  -22.67     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  HIS H 106 "
           pdb=" C   HIS H 106 "
           pdb=" N   ARG H 107 "
           pdb=" CA  ARG H 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.25   19.75     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  PHE L 119 "
           pdb=" C   PHE L 119 "
           pdb=" N   PRO L 120 "
           pdb=" CA  PRO L 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.16   18.84     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 5288 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 541
       0.033 -    0.067: 222
       0.067 -    0.100: 47
       0.100 -    0.133: 63
       0.133 -    0.166: 1
  Chirality restraints: 874
  Sorted by residual:
  chirality pdb=" CA  ILE A 147 "
            pdb=" N   ILE A 147 "
            pdb=" C   ILE A 147 "
            pdb=" CB  ILE A 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.92e-01
  chirality pdb=" CA  VAL H  40 "
            pdb=" N   VAL H  40 "
            pdb=" C   VAL H  40 "
            pdb=" CB  VAL H  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.28e-01
  chirality pdb=" CA  VAL A 326 "
            pdb=" N   VAL A 326 "
            pdb=" C   VAL A 326 "
            pdb=" CB  VAL A 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.27e-01
  ... (remaining 871 not shown)

  Planarity restraints: 1586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 167 "    0.026 5.00e-02 4.00e+02   3.97e-02 2.52e+00
        pdb=" N   PRO H 168 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO H 168 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO H 168 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE L 119 "    0.024 5.00e-02 4.00e+02   3.62e-02 2.10e+00
        pdb=" N   PRO L 120 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO L 120 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO L 120 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H 165 "    0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO H 166 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO H 166 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H 166 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1583 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.10: 274
        2.10 -     2.73: 19466
        2.73 -     3.35: 30454
        3.35 -     3.98: 39819
        3.98 -     4.60: 61653
  Nonbonded interactions: 151666
  Sorted by model distance:
  nonbonded pdb=" HE1 TRP H  50 "
            pdb=" OG  SER H  53 "
     model   vdw
     1.476 2.450
  nonbonded pdb=" O   ALA A 289 "
            pdb=" H   ALA A 302 "
     model   vdw
     1.523 2.450
  nonbonded pdb=" OE2 GLU H   9 "
            pdb=" H   CYS H  99 "
     model   vdw
     1.537 2.450
  nonbonded pdb="HE21 GLN H  42 "
            pdb=" O   LYS H  46 "
     model   vdw
     1.579 2.450
  nonbonded pdb=" OE1 GLN H  42 "
            pdb="HE22 GLN L  39 "
     model   vdw
     1.594 2.450
  ... (remaining 151661 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.900
  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:             0.190
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.910
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5273
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105   5639  Z= 0.197
  Angle     :  0.640  10.762   7653  Z= 0.348
  Chirality :  0.046   0.166    874
  Planarity :  0.004   0.040    954
  Dihedral  : 12.418  82.796   2035
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 14.85
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.96 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  :  8.35 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.33), residues: 666
  helix:  0.03 (1.06), residues: 30
  sheet: -0.63 (0.30), residues: 325
  loop : -1.70 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.004   0.001   HIS A 346 
 PHE   0.015   0.002   PHE A  62 
 TYR   0.011   0.001   TYR H  98 
 ARG   0.003   0.000   ARG L 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14398 (  192)
  hydrogen bonds       : angle       7.35998 (  537)
  SS BOND              : bond        0.00210 (    4)
  SS BOND              : angle       0.85093 (    8)
  covalent geometry    : bond        0.00391 ( 5635)
  covalent geometry    : angle       0.63954 ( 7645)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 104
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  167 GLU cc_start: 0.6532 (mm-30) cc_final: 0.6308 (mt-10)
REVERT: H  173 TRP cc_start: 0.5007 (m100) cc_final: 0.4382 (m100)
REVERT: L   88 TYR cc_start: 0.3284 (OUTLIER) cc_final: 0.2174 (m-80)
  outliers start: 41
  outliers final: 28
  residues processed: 140
  average time/residue: 0.4424
  time to fit residues: 76.8699
Evaluate side-chains
  95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 66
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   36 TYR
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  119 MET
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain H residue  218 ASN
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   79 ASP
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   88 TYR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue  132 SER
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  168 ASP
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  354 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 224 ASN
A 281 ASN
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 346 HIS ** 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 = 0.4707 r_free = 0.4707 target = 0.233070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.223746 restraints weight = 20738.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.226852 restraints weight = 12030.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.228840 restraints weight = 7405.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.4665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5273
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   5639  Z= 0.254
  Angle     :  0.721   7.364   7653  Z= 0.382
  Chirality :  0.050   0.186    874
  Planarity :  0.006   0.043    954
  Dihedral  : 10.168  58.986    809
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 17.94
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.51 %
    Favored  : 89.34 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 13.32 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.32), residues: 666
  helix: -0.16 (1.03), residues: 29
  sheet: -0.86 (0.29), residues: 323
  loop : -2.21 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP H  50 
 HIS   0.008   0.001   HIS A 211 
 PHE   0.030   0.003   PHE A  62 
 TYR   0.020   0.002   TYR L  37 
 ARG   0.004   0.001   ARG L 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04804 (  192)
  hydrogen bonds       : angle       7.19135 (  537)
  SS BOND              : bond        0.00575 (    4)
  SS BOND              : angle       1.68338 (    8)
  covalent geometry    : bond        0.00579 ( 5635)
  covalent geometry    : angle       0.71911 ( 7645)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 68
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  167 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6377 (mt-10)
REVERT: A   47 ASP cc_start: 0.2994 (OUTLIER) cc_final: 0.0440 (t70)
REVERT: A  208 LEU cc_start: 0.3363 (OUTLIER) cc_final: 0.2810 (tt)
REVERT: L   88 TYR cc_start: 0.3547 (OUTLIER) cc_final: 0.1931 (m-80)
REVERT: R  354 TYR cc_start: 0.5337 (OUTLIER) cc_final: 0.3889 (m-80)
  outliers start: 40
  outliers final: 27
  residues processed: 102
  average time/residue: 0.3990
  time to fit residues: 52.6573
Evaluate side-chains
  89 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 58
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   36 TYR
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  113 SER
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   88 TYR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue  132 SER
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  168 ASP
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  354 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0870
   chunk 10 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
H 216 ASN
A 220 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4726 r_free = 0.4726 target = 0.236163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.228774 restraints weight = 20781.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.231291 restraints weight = 12244.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.232962 restraints weight = 7503.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.4680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5198
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5639  Z= 0.160
  Angle     :  0.613   5.052   7653  Z= 0.323
  Chirality :  0.047   0.173    874
  Planarity :  0.005   0.049    954
  Dihedral  :  9.765  58.496    799
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.66 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 15.89 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.32), residues: 666
  helix:  0.31 (1.08), residues: 29
  sheet: -0.74 (0.30), residues: 318
  loop : -1.99 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  50 
 HIS   0.007   0.001   HIS A 346 
 PHE   0.021   0.002   PHE A 342 
 TYR   0.011   0.002   TYR H 213 
 ARG   0.004   0.001   ARG A 189 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03881 (  192)
  hydrogen bonds       : angle       6.69181 (  537)
  SS BOND              : bond        0.00378 (    4)
  SS BOND              : angle       1.25511 (    8)
  covalent geometry    : bond        0.00362 ( 5635)
  covalent geometry    : angle       0.61167 ( 7645)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 64
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  101 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6889 (ppt170)
REVERT: H  167 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6235 (mt-10)
REVERT: A   47 ASP cc_start: 0.2812 (OUTLIER) cc_final: 0.0382 (t70)
REVERT: A  208 LEU cc_start: 0.3306 (OUTLIER) cc_final: 0.2776 (tt)
REVERT: L   88 TYR cc_start: 0.3258 (OUTLIER) cc_final: 0.1785 (m-80)
REVERT: R  354 TYR cc_start: 0.5447 (OUTLIER) cc_final: 0.4273 (m-80)
  outliers start: 41
  outliers final: 28
  residues processed: 99
  average time/residue: 0.3477
  time to fit residues: 45.6160
Evaluate side-chains
  92 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 59
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   36 TYR
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  113 SER
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  119 MET
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   88 TYR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue  132 SER
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  168 ASP
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  354 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0870
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
L 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.235415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.227552 restraints weight = 20925.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.230235 restraints weight = 12265.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.232000 restraints weight = 7532.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.4691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5217
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   5639  Z= 0.158
  Angle     :  0.598   4.874   7653  Z= 0.317
  Chirality :  0.047   0.170    874
  Planarity :  0.005   0.045    954
  Dihedral  :  9.694  59.957    799
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.41 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  6.26 %
    Allowed  : 16.85 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.33), residues: 666
  helix:  0.30 (1.07), residues: 30
  sheet: -0.79 (0.30), residues: 321
  loop : -1.90 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  50 
 HIS   0.006   0.001   HIS A 346 
 PHE   0.018   0.002   PHE A 342 
 TYR   0.015   0.002   TYR H 213 
 ARG   0.005   0.001   ARG A 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03958 (  192)
  hydrogen bonds       : angle       6.51659 (  537)
  SS BOND              : bond        0.00170 (    4)
  SS BOND              : angle       1.41087 (    8)
  covalent geometry    : bond        0.00362 ( 5635)
  covalent geometry    : angle       0.59683 ( 7645)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 60
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  101 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6920 (ppt170)
REVERT: H  167 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6232 (mt-10)
REVERT: H  216 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6154 (p0)
REVERT: A   47 ASP cc_start: 0.2941 (OUTLIER) cc_final: 0.0798 (t70)
REVERT: A  208 LEU cc_start: 0.3323 (OUTLIER) cc_final: 0.2767 (tt)
REVERT: L   88 TYR cc_start: 0.3103 (OUTLIER) cc_final: 0.1835 (m-80)
REVERT: R  354 TYR cc_start: 0.5406 (OUTLIER) cc_final: 0.3757 (m-80)
  outliers start: 39
  outliers final: 27
  residues processed: 94
  average time/residue: 0.3500
  time to fit residues: 43.4771
Evaluate side-chains
  91 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 58
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain H residue  113 SER
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  119 MET
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain H residue  231 GLU
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   88 TYR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue  132 SER
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  168 ASP
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  354 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 41 optimal weight:    0.4980
   chunk 59 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
H 216 ASN
A 220 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.235270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.227910 restraints weight = 20851.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.230357 restraints weight = 12367.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.232021 restraints weight = 7749.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.4689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5240
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5639  Z= 0.164
  Angle     :  0.602   5.543   7653  Z= 0.318
  Chirality :  0.047   0.157    874
  Planarity :  0.005   0.053    954
  Dihedral  :  9.320  58.043    795
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.61 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 17.34 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.33), residues: 666
  helix:  0.35 (1.06), residues: 30
  sheet: -0.70 (0.30), residues: 314
  loop : -1.95 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.005   0.001   HIS A 346 
 PHE   0.019   0.002   PHE A  62 
 TYR   0.012   0.002   TYR L  37 
 ARG   0.008   0.001   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03608 (  192)
  hydrogen bonds       : angle       6.46303 (  537)
  SS BOND              : bond        0.00469 (    4)
  SS BOND              : angle       0.95971 (    8)
  covalent geometry    : bond        0.00376 ( 5635)
  covalent geometry    : angle       0.60170 ( 7645)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 66
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   98 TYR cc_start: 0.3014 (OUTLIER) cc_final: 0.2695 (m-80)
REVERT: H  101 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6946 (ppt170)
REVERT: H  167 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6240 (mt-10)
REVERT: A   47 ASP cc_start: 0.3153 (OUTLIER) cc_final: 0.0980 (t70)
REVERT: A  208 LEU cc_start: 0.3345 (OUTLIER) cc_final: 0.2765 (tt)
REVERT: L   88 TYR cc_start: 0.3128 (OUTLIER) cc_final: 0.1902 (m-80)
REVERT: R  354 TYR cc_start: 0.6017 (OUTLIER) cc_final: 0.4720 (m-80)
  outliers start: 40
  outliers final: 29
  residues processed: 100
  average time/residue: 0.3506
  time to fit residues: 46.3016
Evaluate side-chains
  96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 61
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   98 TYR
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain H residue  113 SER
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  119 MET
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  214 ILE
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain H residue  231 GLU
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   88 TYR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue  132 SER
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  168 ASP
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  354 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0570
   chunk 30 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
H 216 ASN
A 220 HIS
** A 224 ASN ** 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 = 0.4732 r_free = 0.4732 target = 0.235366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.230736 restraints weight = 21059.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.232342 restraints weight = 13181.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4708 r_free = 0.4708 target = 0.233177 restraints weight = 8644.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.4710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5199
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5639  Z= 0.144
  Angle     :  0.584   5.211   7653  Z= 0.308
  Chirality :  0.046   0.144    874
  Planarity :  0.005   0.050    954
  Dihedral  :  9.087  57.050    794
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.96 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 18.30 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.33), residues: 666
  helix:  0.46 (1.07), residues: 30
  sheet: -0.68 (0.30), residues: 314
  loop : -1.84 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.005   0.001   HIS A 346 
 PHE   0.016   0.002   PHE A 342 
 TYR   0.013   0.001   TYR H 213 
 ARG   0.005   0.000   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03444 (  192)
  hydrogen bonds       : angle       6.34202 (  537)
  SS BOND              : bond        0.00543 (    4)
  SS BOND              : angle       0.88950 (    8)
  covalent geometry    : bond        0.00331 ( 5635)
  covalent geometry    : angle       0.58374 ( 7645)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 59
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   98 TYR cc_start: 0.2902 (OUTLIER) cc_final: 0.2553 (m-80)
REVERT: H  101 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6867 (ppt170)
REVERT: H  167 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6352 (mt-10)
REVERT: A   47 ASP cc_start: 0.3057 (OUTLIER) cc_final: 0.0989 (t70)
REVERT: A  208 LEU cc_start: 0.3317 (OUTLIER) cc_final: 0.2753 (tt)
REVERT: L   88 TYR cc_start: 0.2975 (OUTLIER) cc_final: 0.1873 (m-80)
REVERT: R  354 TYR cc_start: 0.6008 (OUTLIER) cc_final: 0.5180 (m-80)
  outliers start: 37
  outliers final: 26
  residues processed: 91
  average time/residue: 0.3536
  time to fit residues: 42.6613
Evaluate side-chains
  91 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 59
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   98 TYR
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain H residue  113 SER
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  119 MET
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  231 GLU
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   88 TYR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue  132 SER
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  168 ASP
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  354 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 42 optimal weight:    0.4980
   chunk 48 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 36 optimal weight:    0.4980
   chunk 12 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
H 216 ASN
A 220 HIS
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  38 GLN
** L  39 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 = 0.4735 r_free = 0.4735 target = 0.235439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.227356 restraints weight = 21128.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4686 r_free = 0.4686 target = 0.230083 restraints weight = 12445.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.231586 restraints weight = 7779.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.4706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5220
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5639  Z= 0.141
  Angle     :  0.578   5.300   7653  Z= 0.303
  Chirality :  0.046   0.145    874
  Planarity :  0.005   0.048    954
  Dihedral  :  8.950  55.500    793
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.71 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  6.26 %
    Allowed  : 18.30 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.33), residues: 666
  helix:  0.49 (1.07), residues: 30
  sheet: -0.67 (0.30), residues: 316
  loop : -1.84 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.005   0.001   HIS A 346 
 PHE   0.017   0.002   PHE A 342 
 TYR   0.009   0.001   TYR L  37 
 ARG   0.004   0.000   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03318 (  192)
  hydrogen bonds       : angle       6.15323 (  537)
  SS BOND              : bond        0.00453 (    4)
  SS BOND              : angle       0.83627 (    8)
  covalent geometry    : bond        0.00325 ( 5635)
  covalent geometry    : angle       0.57780 ( 7645)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 60
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   98 TYR cc_start: 0.2737 (OUTLIER) cc_final: 0.2381 (m-80)
REVERT: A   47 ASP cc_start: 0.3184 (OUTLIER) cc_final: 0.1220 (t70)
REVERT: A  208 LEU cc_start: 0.3277 (OUTLIER) cc_final: 0.2826 (mp)
REVERT: L   88 TYR cc_start: 0.3045 (OUTLIER) cc_final: 0.2061 (m-80)
REVERT: L   99 PHE cc_start: 0.3242 (OUTLIER) cc_final: 0.1828 (m-80)
REVERT: R  354 TYR cc_start: 0.6172 (OUTLIER) cc_final: 0.5347 (m-80)
  outliers start: 39
  outliers final: 30
  residues processed: 93
  average time/residue: 0.3303
  time to fit residues: 41.6569
Evaluate side-chains
  94 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 58
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   98 TYR
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain H residue  113 SER
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  119 MET
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  214 ILE
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain H residue  231 GLU
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain L residue   88 TYR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   99 PHE
Chi-restraints excluded: chain L residue  132 SER
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  168 ASP
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  354 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0970
   chunk 44 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0670
   chunk 58 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.9920

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

Flipped N/Q/H residues before XYZ refinement:
** H  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  39 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 = 0.4739 r_free = 0.4739 target = 0.236380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.221130 restraints weight = 220131.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.225741 restraints weight = 121548.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.225888 restraints weight = 97957.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.4545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5475
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   5639  Z= 0.196
  Angle     :  0.626   5.402   7653  Z= 0.331
  Chirality :  0.047   0.155    874
  Planarity :  0.006   0.045    954
  Dihedral  :  8.690  55.104    790
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.06 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 18.62 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.33), residues: 666
  helix:  0.45 (1.07), residues: 30
  sheet: -0.79 (0.30), residues: 316
  loop : -1.98 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP H  50 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.022   0.002   PHE A  62 
 TYR   0.015   0.002   TYR L  37 
 ARG   0.004   0.001   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03772 (  192)
  hydrogen bonds       : angle       6.41159 (  537)
  SS BOND              : bond        0.00351 (    4)
  SS BOND              : angle       1.10381 (    8)
  covalent geometry    : bond        0.00453 ( 5635)
  covalent geometry    : angle       0.62495 ( 7645)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 59
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   98 TYR cc_start: 0.2984 (OUTLIER) cc_final: 0.2590 (m-80)
REVERT: H  101 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7198 (ppt170)
REVERT: A   47 ASP cc_start: 0.3403 (OUTLIER) cc_final: 0.1431 (t70)
REVERT: A  208 LEU cc_start: 0.2831 (OUTLIER) cc_final: 0.2498 (mp)
REVERT: L   88 TYR cc_start: 0.3171 (OUTLIER) cc_final: 0.2024 (m-80)
REVERT: L   99 PHE cc_start: 0.3484 (OUTLIER) cc_final: 0.1780 (m-80)
REVERT: R  354 TYR cc_start: 0.5999 (OUTLIER) cc_final: 0.5147 (m-80)
  outliers start: 38
  outliers final: 27
  residues processed: 92
  average time/residue: 0.3284
  time to fit residues: 40.7396
Evaluate side-chains
  92 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 58
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   98 TYR
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain H residue  113 SER
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  119 MET
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  231 GLU
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  224 ASN
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   88 TYR
Chi-restraints excluded: chain L residue   99 PHE
Chi-restraints excluded: chain L residue  132 SER
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  168 ASP
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  354 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** H  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 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 = 0.4755 r_free = 0.4755 target = 0.237758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.221694 restraints weight = 221377.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4618 r_free = 0.4618 target = 0.226335 restraints weight = 126382.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.226938 restraints weight = 93525.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.4549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5468
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5639  Z= 0.155
  Angle     :  0.598   5.485   7653  Z= 0.315
  Chirality :  0.046   0.142    874
  Planarity :  0.005   0.049    954
  Dihedral  :  8.259  54.122    787
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.16 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 19.58 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.33), residues: 666
  helix:  0.54 (1.08), residues: 30
  sheet: -0.71 (0.30), residues: 313
  loop : -1.96 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.016   0.002   PHE A 342 
 TYR   0.023   0.002   TYR L  37 
 ARG   0.004   0.000   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03437 (  192)
  hydrogen bonds       : angle       6.30022 (  537)
  SS BOND              : bond        0.00426 (    4)
  SS BOND              : angle       0.91120 (    8)
  covalent geometry    : bond        0.00358 ( 5635)
  covalent geometry    : angle       0.59765 ( 7645)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 60
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   98 TYR cc_start: 0.2705 (OUTLIER) cc_final: 0.2347 (m-80)
REVERT: A   47 ASP cc_start: 0.3364 (OUTLIER) cc_final: 0.1415 (t70)
REVERT: A  208 LEU cc_start: 0.2538 (OUTLIER) cc_final: 0.2219 (mp)
REVERT: L   88 TYR cc_start: 0.3123 (OUTLIER) cc_final: 0.2200 (m-80)
REVERT: L   99 PHE cc_start: 0.3281 (OUTLIER) cc_final: 0.1665 (m-80)
REVERT: R  354 TYR cc_start: 0.5931 (OUTLIER) cc_final: 0.5199 (m-80)
  outliers start: 32
  outliers final: 24
  residues processed: 87
  average time/residue: 0.3423
  time to fit residues: 40.0076
Evaluate side-chains
  88 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 58
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   98 TYR
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain H residue  113 SER
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  119 MET
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  231 GLU
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain L residue   88 TYR
Chi-restraints excluded: chain L residue   99 PHE
Chi-restraints excluded: chain L residue  132 SER
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  354 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0170
   chunk 61 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.7218

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

Flipped N/Q/H residues before XYZ refinement:
** H  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  38 GLN
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 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 = 0.4749 r_free = 0.4749 target = 0.236980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.220919 restraints weight = 219238.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.225386 restraints weight = 121116.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.226234 restraints weight = 94490.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.4540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5499
moved from start:          0.3584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5639  Z= 0.161
  Angle     :  0.600   5.452   7653  Z= 0.316
  Chirality :  0.047   0.142    874
  Planarity :  0.005   0.049    954
  Dihedral  :  7.959  53.120    784
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.21 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 19.58 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.33), residues: 666
  helix:  0.50 (1.06), residues: 30
  sheet: -0.73 (0.30), residues: 313
  loop : -1.99 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 173 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.017   0.002   PHE A  62 
 TYR   0.017   0.002   TYR L  37 
 ARG   0.004   0.000   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03457 (  192)
  hydrogen bonds       : angle       6.26801 (  537)
  SS BOND              : bond        0.00430 (    4)
  SS BOND              : angle       1.23122 (    8)
  covalent geometry    : bond        0.00371 ( 5635)
  covalent geometry    : angle       0.59927 ( 7645)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 56
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   98 TYR cc_start: 0.2753 (OUTLIER) cc_final: 0.2388 (m-80)
REVERT: H  101 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7195 (ppt170)
REVERT: A    8 ARG cc_start: 0.6864 (ptm160) cc_final: 0.6259 (ttt180)
REVERT: A   47 ASP cc_start: 0.3265 (OUTLIER) cc_final: 0.1383 (t70)
REVERT: A  208 LEU cc_start: 0.2318 (OUTLIER) cc_final: 0.1851 (tt)
REVERT: L   88 TYR cc_start: 0.3311 (OUTLIER) cc_final: 0.2365 (m-80)
REVERT: L   99 PHE cc_start: 0.3239 (OUTLIER) cc_final: 0.1555 (m-80)
  outliers start: 31
  outliers final: 24
  residues processed: 83
  average time/residue: 0.3334
  time to fit residues: 37.0898
Evaluate side-chains
  84 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 54
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   98 TYR
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain H residue  113 SER
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  119 MET
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  231 GLU
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   88 TYR
Chi-restraints excluded: chain L residue   99 PHE
Chi-restraints excluded: chain L residue  132 SER
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  198 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 1 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0010
   chunk 18 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
** H  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  38 GLN
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 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 = 0.4755 r_free = 0.4755 target = 0.237739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.221157 restraints weight = 219818.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.227379 restraints weight = 124027.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.227232 restraints weight = 90119.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.4547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5486
moved from start:          0.3575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   5639  Z= 0.181
  Angle     :  1.048  59.195   7653  Z= 0.621
  Chirality :  0.049   0.429    874
  Planarity :  0.005   0.050    954
  Dihedral  :  7.740  53.158    782
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.21 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 19.42 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.33), residues: 666
  helix:  0.49 (1.06), residues: 30
  sheet: -0.73 (0.30), residues: 313
  loop : -1.98 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 173 
 HIS   0.003   0.001   HIS A 346 
 PHE   0.017   0.002   PHE A  62 
 TYR   0.011   0.001   TYR H  58 
 ARG   0.003   0.000   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03454 (  192)
  hydrogen bonds       : angle       6.26646 (  537)
  SS BOND              : bond        0.00402 (    4)
  SS BOND              : angle       1.11122 (    8)
  covalent geometry    : bond        0.00401 ( 5635)
  covalent geometry    : angle       1.04812 ( 7645)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4082.33 seconds
wall clock time: 71 minutes 15.48 seconds (4275.48 seconds total)