Starting phenix.real_space_refine
on Sat Aug 23 08:48:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tin_41296/08_2025/8tin_41296.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tin_41296/08_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_41296/08_2025/8tin_41296.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tin_41296/08_2025/8tin_41296.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tin_41296/08_2025/8tin_41296.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tin_41296/08_2025/8tin_41296.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.90, per 1000 atoms: 0.17
  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: 0.77
  Conformation dependent library (CDL) restraints added in 182.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.29
  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: 1.90

  Time building geometry restraints manager: 1.02 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:             3.950
  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:             0.070
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.060
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.510
-------------------------------------------------------------------------------
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 : 14.67
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.003   0.000   ARG L 212 
 TYR   0.011   0.001   TYR H  98 
 PHE   0.015   0.002   PHE A  62 
 TRP   0.007   0.001   TRP H  50 
 HIS   0.004   0.001   HIS A 346 

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

*********************** 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  : 0.189 
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: H  173 TRP cc_start: 0.5007 (m100) cc_final: 0.4381 (m100)
REVERT: A   44 VAL cc_start: 0.0799 (OUTLIER) cc_final: 0.0591 (t)
REVERT: L   88 TYR cc_start: 0.3284 (OUTLIER) cc_final: 0.2217 (m-80)
  outliers start: 41
  outliers final: 28
  residues processed: 140
  average time/residue: 0.1934
  time to fit residues: 33.6529
Evaluate side-chains
  96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 66
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
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   44 VAL
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 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.1980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
H  87 ASN
A 281 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.236172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.227364 restraints weight = 20658.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.230406 restraints weight = 12073.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.232196 restraints weight = 7460.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.233416 restraints weight = 4835.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4716 r_free = 0.4716 target = 0.234058 restraints weight = 3250.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.4722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5142
moved from start:          0.1816

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= 0.168
  Angle     :  0.630   7.120   7653  Z= 0.329
  Chirality :  0.047   0.176    874
  Planarity :  0.005   0.039    954
  Dihedral  :  9.911  58.826    810
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.71 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  6.26 %
    Allowed  : 12.04 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.33), residues: 666
  helix:  0.16 (1.06), residues: 29
  sheet: -0.64 (0.30), residues: 323
  loop : -1.85 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L 212 
 TYR   0.016   0.002   TYR H 213 
 PHE   0.019   0.002   PHE A  62 
 TRP   0.008   0.002   TRP H  50 
 HIS   0.007   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 5635)
  covalent geometry    : angle       0.62766 ( 7645)
  SS BOND              : bond        0.00286 (    4)
  SS BOND              : angle       1.75713 (    8)
  hydrogen bonds       : bond        0.04072 (  192)
  hydrogen bonds       : angle       6.72601 (  537)

*********************** 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: 39
    poor density    : 69
  time to evaluate  : 0.282 
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: H  173 TRP cc_start: 0.5188 (m100) cc_final: 0.4336 (m100)
REVERT: A   44 VAL cc_start: 0.1030 (OUTLIER) cc_final: 0.0814 (t)
REVERT: A   47 ASP cc_start: 0.2829 (OUTLIER) cc_final: 0.0361 (t70)
REVERT: A  208 LEU cc_start: 0.3317 (OUTLIER) cc_final: 0.2784 (tt)
REVERT: L   88 TYR cc_start: 0.3141 (OUTLIER) cc_final: 0.1738 (m-80)
REVERT: L  101 GLN cc_start: 0.6293 (mp10) cc_final: 0.6062 (mp10)
REVERT: R  354 TYR cc_start: 0.5335 (OUTLIER) cc_final: 0.3916 (m-80)
  outliers start: 39
  outliers final: 28
  residues processed: 101
  average time/residue: 0.1697
  time to fit residues: 22.0061
Evaluate side-chains
  96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 63
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
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  104 MET
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 A residue   19 LEU
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   44 VAL
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  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  188 GLU
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 52 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
H  87 ASN
H 216 ASN
A 220 HIS
A 224 ASN
L 167 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.233353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.224229 restraints weight = 21024.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.227352 restraints weight = 12242.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.229082 restraints weight = 7509.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.230445 restraints weight = 4979.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.231089 restraints weight = 3328.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.4691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5238
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5639  Z= 0.207
  Angle     :  0.657   5.869   7653  Z= 0.347
  Chirality :  0.048   0.178    874
  Planarity :  0.005   0.038    954
  Dihedral  : 10.026  58.594    803
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  6.90 %
    Allowed  : 14.77 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.05 (0.32), residues: 666
  helix:  0.20 (1.06), residues: 29
  sheet: -0.81 (0.30), residues: 321
  loop : -2.07 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  63 
 TYR   0.016   0.002   TYR L  37 
 PHE   0.026   0.002   PHE A  62 
 TRP   0.007   0.002   TRP H  50 
 HIS   0.006   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 5635)
  covalent geometry    : angle       0.65490 ( 7645)
  SS BOND              : bond        0.00562 (    4)
  SS BOND              : angle       1.80100 (    8)
  hydrogen bonds       : bond        0.04270 (  192)
  hydrogen bonds       : angle       6.85659 (  537)

*********************** 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
  110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 67
  time to evaluate  : 0.284 
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: 0.7390 (OUTLIER) cc_final: 0.6969 (ppt170)
REVERT: A   44 VAL cc_start: 0.0907 (OUTLIER) cc_final: 0.0670 (t)
REVERT: A   47 ASP cc_start: 0.3074 (OUTLIER) cc_final: 0.0567 (t70)
REVERT: A  208 LEU cc_start: 0.3217 (OUTLIER) cc_final: 0.2661 (tt)
REVERT: L   88 TYR cc_start: 0.3433 (OUTLIER) cc_final: 0.2043 (m-80)
REVERT: L  101 GLN cc_start: 0.6353 (mp10) cc_final: 0.6137 (mp10)
REVERT: R  354 TYR cc_start: 0.5482 (OUTLIER) cc_final: 0.4341 (m-80)
  outliers start: 43
  outliers final: 28
  residues processed: 103
  average time/residue: 0.1704
  time to fit residues: 22.8237
Evaluate side-chains
  94 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 60
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
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  104 MET
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 H residue  216 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   44 VAL
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 25 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0970
   chunk 13 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
H  87 ASN
** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.237226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.229990 restraints weight = 20921.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.232421 restraints weight = 12356.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4708 r_free = 0.4708 target = 0.234085 restraints weight = 7673.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4716 r_free = 0.4716 target = 0.234955 restraints weight = 4911.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.235476 restraints weight = 3384.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.4709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5154
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5639  Z= 0.138
  Angle     :  0.579   4.639   7653  Z= 0.306
  Chirality :  0.047   0.166    874
  Planarity :  0.005   0.046    954
  Dihedral  :  9.525  59.832    798
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  6.26 %
    Allowed  : 16.37 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.81 (0.33), residues: 666
  helix:  0.27 (1.06), residues: 30
  sheet: -0.64 (0.30), residues: 306
  loop : -1.89 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 170 
 TYR   0.014   0.001   TYR H 213 
 PHE   0.016   0.002   PHE A 342 
 TRP   0.007   0.001   TRP H 173 
 HIS   0.006   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5635)
  covalent geometry    : angle       0.57745 ( 7645)
  SS BOND              : bond        0.00153 (    4)
  SS BOND              : angle       1.30441 (    8)
  hydrogen bonds       : bond        0.03735 (  192)
  hydrogen bonds       : angle       6.41875 (  537)

*********************** 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
  102 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 63
  time to evaluate  : 0.219 
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: H  101 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6894 (ppt170)
REVERT: H  216 ASN cc_start: 0.6927 (OUTLIER) cc_final: 0.6062 (p0)
REVERT: A   44 VAL cc_start: 0.0907 (OUTLIER) cc_final: 0.0647 (t)
REVERT: A   47 ASP cc_start: 0.2836 (OUTLIER) cc_final: 0.0700 (t70)
REVERT: A  208 LEU cc_start: 0.3327 (OUTLIER) cc_final: 0.2778 (tt)
REVERT: L   88 TYR cc_start: 0.3000 (OUTLIER) cc_final: 0.1834 (m-80)
REVERT: R  354 TYR cc_start: 0.5468 (OUTLIER) cc_final: 0.4328 (m-80)
  outliers start: 39
  outliers final: 26
  residues processed: 96
  average time/residue: 0.1602
  time to fit residues: 20.1901
Evaluate side-chains
  93 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 60
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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  104 MET
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   23 LEU
Chi-restraints excluded: chain A residue   44 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 1 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
H  87 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 = 0.4757 r_free = 0.4757 target = 0.237720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.221350 restraints weight = 219613.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.226166 restraints weight = 126142.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.226429 restraints weight = 94456.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.227425 restraints weight = 92007.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.227992 restraints weight = 86077.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.4570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5389
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5639  Z= 0.154
  Angle     :  0.593   5.333   7653  Z= 0.313
  Chirality :  0.046   0.153    874
  Planarity :  0.005   0.046    954
  Dihedral  :  9.166  57.904    795
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.86 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 17.17 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.80 (0.33), residues: 666
  helix:  0.30 (1.04), residues: 30
  sheet: -0.69 (0.30), residues: 314
  loop : -1.85 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A   8 
 TYR   0.012   0.002   TYR H 213 
 PHE   0.017   0.002   PHE A  62 
 TRP   0.006   0.001   TRP H  50 
 HIS   0.005   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5635)
  covalent geometry    : angle       0.59136 ( 7645)
  SS BOND              : bond        0.00506 (    4)
  SS BOND              : angle       1.61868 (    8)
  hydrogen bonds       : bond        0.03481 (  192)
  hydrogen bonds       : angle       6.37111 (  537)

*********************** 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
  100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 62
  time to evaluate  : 0.356 
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: 0.2808 (OUTLIER) cc_final: 0.2484 (m-80)
REVERT: H  101 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7091 (ppt170)
REVERT: A   44 VAL cc_start: 0.0692 (OUTLIER) cc_final: 0.0475 (t)
REVERT: A   47 ASP cc_start: 0.3081 (OUTLIER) cc_final: 0.1081 (t70)
REVERT: A  208 LEU cc_start: 0.2962 (OUTLIER) cc_final: 0.2431 (tt)
REVERT: L   88 TYR cc_start: 0.3271 (OUTLIER) cc_final: 0.1902 (m-80)
REVERT: R  354 TYR cc_start: 0.5703 (OUTLIER) cc_final: 0.4159 (m-80)
  outliers start: 38
  outliers final: 27
  residues processed: 94
  average time/residue: 0.1361
  time to fit residues: 17.1596
Evaluate side-chains
  91 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 57
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
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  104 MET
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   23 LEU
Chi-restraints excluded: chain A residue   44 VAL
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  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 2 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0170
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
H  87 ASN
H 216 ASN
A 220 HIS
** A 224 ASN ** 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 = 0.4730 r_free = 0.4730 target = 0.234508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.230010 restraints weight = 20952.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.231581 restraints weight = 12902.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.232407 restraints weight = 8498.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.4712 r_free = 0.4712 target = 0.233046 restraints weight = 5893.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.4717 r_free = 0.4717 target = 0.233435 restraints weight = 4263.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.4720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5207
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5639  Z= 0.150
  Angle     :  0.580   4.949   7653  Z= 0.304
  Chirality :  0.046   0.146    874
  Planarity :  0.005   0.046    954
  Dihedral  :  9.090  56.884    795
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.81 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 17.82 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.33), residues: 666
  helix:  0.44 (1.07), residues: 30
  sheet: -0.69 (0.30), residues: 319
  loop : -1.82 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A   8 
 TYR   0.011   0.002   TYR H 213 
 PHE   0.016   0.002   PHE A  62 
 TRP   0.006   0.001   TRP H  50 
 HIS   0.004   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 5635)
  covalent geometry    : angle       0.57946 ( 7645)
  SS BOND              : bond        0.00466 (    4)
  SS BOND              : angle       1.18771 (    8)
  hydrogen bonds       : bond        0.03382 (  192)
  hydrogen bonds       : angle       6.27783 (  537)

*********************** 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
  97 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 59
  time to evaluate  : 0.218 
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: H   98 TYR cc_start: 0.2722 (OUTLIER) cc_final: 0.2397 (m-80)
REVERT: A   44 VAL cc_start: 0.0979 (OUTLIER) cc_final: 0.0727 (t)
REVERT: A   47 ASP cc_start: 0.3343 (OUTLIER) cc_final: 0.1284 (t70)
REVERT: A  208 LEU cc_start: 0.3388 (OUTLIER) cc_final: 0.2815 (tt)
REVERT: L   88 TYR cc_start: 0.3149 (OUTLIER) cc_final: 0.1962 (m-80)
REVERT: R  354 TYR cc_start: 0.5890 (OUTLIER) cc_final: 0.5142 (m-80)
  outliers start: 38
  outliers final: 29
  residues processed: 91
  average time/residue: 0.1498
  time to fit residues: 17.9831
Evaluate side-chains
  94 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 59
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
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  104 MET
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   44 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0670
   chunk 30 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
H  87 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 = 0.4731 r_free = 0.4731 target = 0.235044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4663 r_free = 0.4663 target = 0.227783 restraints weight = 21155.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4686 r_free = 0.4686 target = 0.230224 restraints weight = 12538.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.231601 restraints weight = 7900.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4706 r_free = 0.4706 target = 0.232570 restraints weight = 5298.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.233271 restraints weight = 3740.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.4719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5171
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5639  Z= 0.140
  Angle     :  0.565   4.950   7653  Z= 0.297
  Chirality :  0.046   0.150    874
  Planarity :  0.005   0.047    954
  Dihedral  :  8.989  55.922    794
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.71 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 17.66 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.75 (0.34), residues: 666
  helix:  0.49 (1.07), residues: 30
  sheet: -0.69 (0.30), residues: 321
  loop : -1.79 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A   8 
 TYR   0.010   0.001   TYR H 213 
 PHE   0.014   0.002   PHE A  62 
 TRP   0.006   0.001   TRP H  50 
 HIS   0.004   0.001   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 5635)
  covalent geometry    : angle       0.56426 ( 7645)
  SS BOND              : bond        0.00206 (    4)
  SS BOND              : angle       1.08747 (    8)
  hydrogen bonds       : bond        0.03408 (  192)
  hydrogen bonds       : angle       6.18103 (  537)

*********************** 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
  98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 61
  time to evaluate  : 0.273 
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: H   98 TYR cc_start: 0.2679 (OUTLIER) cc_final: 0.2361 (m-80)
REVERT: A   44 VAL cc_start: 0.0875 (OUTLIER) cc_final: 0.0624 (t)
REVERT: A   47 ASP cc_start: 0.3268 (OUTLIER) cc_final: 0.1303 (t70)
REVERT: A  208 LEU cc_start: 0.3273 (OUTLIER) cc_final: 0.2718 (tt)
REVERT: L   88 TYR cc_start: 0.3172 (OUTLIER) cc_final: 0.2077 (m-80)
REVERT: R  354 TYR cc_start: 0.5919 (OUTLIER) cc_final: 0.5223 (m-80)
  outliers start: 37
  outliers final: 30
  residues processed: 93
  average time/residue: 0.1499
  time to fit residues: 18.6393
Evaluate side-chains
  95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 59
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
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  104 MET
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  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   44 VAL
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 17 optimal weight:    0.1980
   chunk 58 optimal weight:    0.3980
   chunk 0 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0040
   chunk 30 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.3992

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

Flipped N/Q/H residues before XYZ refinement:
H  87 ASN
H 216 ASN
A 220 HIS
L  38 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4754 r_free = 0.4754 target = 0.237185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.229979 restraints weight = 20849.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.232477 restraints weight = 12200.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.233725 restraints weight = 7595.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.234811 restraints weight = 5215.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.235471 restraints weight = 3542.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.4743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5113
moved from start:          0.3192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5639  Z= 0.114
  Angle     :  0.532   5.008   7653  Z= 0.278
  Chirality :  0.045   0.138    874
  Planarity :  0.005   0.048    954
  Dihedral  :  8.681  53.883    794
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.21 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 18.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.63 (0.34), residues: 666
  helix:  0.60 (1.07), residues: 30
  sheet: -0.62 (0.30), residues: 316
  loop : -1.70 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A   8 
 TYR   0.008   0.001   TYR H  98 
 PHE   0.015   0.001   PHE A 342 
 TRP   0.006   0.001   TRP H  50 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 5635)
  covalent geometry    : angle       0.53182 ( 7645)
  SS BOND              : bond        0.00475 (    4)
  SS BOND              : angle       0.81188 (    8)
  hydrogen bonds       : bond        0.02953 (  192)
  hydrogen bonds       : angle       5.85165 (  537)

*********************** 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
  96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 65
  time to evaluate  : 0.242 
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: A    8 ARG cc_start: 0.6438 (mtp-110) cc_final: 0.5919 (ttt180)
REVERT: A   44 VAL cc_start: 0.0871 (OUTLIER) cc_final: 0.0598 (t)
REVERT: A   47 ASP cc_start: 0.3021 (OUTLIER) cc_final: 0.1200 (t70)
REVERT: A  208 LEU cc_start: 0.3215 (OUTLIER) cc_final: 0.2805 (mp)
REVERT: L   88 TYR cc_start: 0.3039 (OUTLIER) cc_final: 0.2283 (m-80)
REVERT: L  101 GLN cc_start: 0.6119 (mp10) cc_final: 0.5791 (mp10)
  outliers start: 31
  outliers final: 25
  residues processed: 92
  average time/residue: 0.1481
  time to fit residues: 17.9933
Evaluate side-chains
  92 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 63
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain H residue  104 MET
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   23 LEU
Chi-restraints excluded: chain A residue   44 VAL
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   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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 ** 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 = 0.4759 r_free = 0.4759 target = 0.237837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.221179 restraints weight = 223355.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.226214 restraints weight = 123295.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.226378 restraints weight = 102549.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.227117 restraints weight = 90594.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.227238 restraints weight = 86977.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.4556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5433
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5639  Z= 0.165
  Angle     :  0.588   5.916   7653  Z= 0.310
  Chirality :  0.046   0.143    874
  Planarity :  0.005   0.044    954
  Dihedral  :  8.202  53.960    788
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.76 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 18.62 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.34), residues: 666
  helix:  0.58 (1.06), residues: 30
  sheet: -0.71 (0.30), residues: 321
  loop : -1.82 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A   8 
 TYR   0.012   0.002   TYR L  37 
 PHE   0.019   0.002   PHE A  62 
 TRP   0.009   0.002   TRP H 173 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 5635)
  covalent geometry    : angle       0.58760 ( 7645)
  SS BOND              : bond        0.00833 (    4)
  SS BOND              : angle       1.11709 (    8)
  hydrogen bonds       : bond        0.03465 (  192)
  hydrogen bonds       : angle       6.15235 (  537)

*********************** 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
  95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 62
  time to evaluate  : 0.193 
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   98 TYR cc_start: 0.2626 (OUTLIER) cc_final: 0.2300 (m-80)
REVERT: A   44 VAL cc_start: 0.0636 (OUTLIER) cc_final: 0.0380 (t)
REVERT: A   47 ASP cc_start: 0.3405 (OUTLIER) cc_final: 0.1524 (t70)
REVERT: L   88 TYR cc_start: 0.3322 (OUTLIER) cc_final: 0.2210 (m-80)
REVERT: L  101 GLN cc_start: 0.6156 (mp10) cc_final: 0.5841 (mp10)
  outliers start: 33
  outliers final: 25
  residues processed: 91
  average time/residue: 0.1625
  time to fit residues: 19.5371
Evaluate side-chains
  90 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 61
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
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  104 MET
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   23 LEU
Chi-restraints excluded: chain A residue   44 VAL
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  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   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  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 35 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 14 optimal weight:    0.3980
   chunk 56 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
** 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 = 0.4754 r_free = 0.4754 target = 0.237477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.221326 restraints weight = 220734.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.226204 restraints weight = 123424.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.226547 restraints weight = 98742.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.227174 restraints weight = 88431.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.227407 restraints weight = 84745.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.4554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5444
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5639  Z= 0.155
  Angle     :  0.585   5.199   7653  Z= 0.307
  Chirality :  0.046   0.150    874
  Planarity :  0.005   0.047    954
  Dihedral  :  8.026  53.537    786
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.71 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 18.94 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.82 (0.33), residues: 666
  helix:  0.64 (1.07), residues: 30
  sheet: -0.70 (0.30), residues: 318
  loop : -1.91 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A   8 
 TYR   0.012   0.002   TYR H  58 
 PHE   0.016   0.002   PHE A  62 
 TRP   0.009   0.001   TRP H 173 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 5635)
  covalent geometry    : angle       0.58432 ( 7645)
  SS BOND              : bond        0.00538 (    4)
  SS BOND              : angle       1.09342 (    8)
  hydrogen bonds       : bond        0.03414 (  192)
  hydrogen bonds       : angle       6.19224 (  537)

********************** 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
  92 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 62
  time to evaluate  : 0.282 
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: H   98 TYR cc_start: 0.2589 (OUTLIER) cc_final: 0.2243 (m-80)
REVERT: A    8 ARG cc_start: 0.6648 (mtp-110) cc_final: 0.6022 (ttt180)
REVERT: A   44 VAL cc_start: 0.0537 (OUTLIER) cc_final: 0.0287 (t)
REVERT: A   47 ASP cc_start: 0.3230 (OUTLIER) cc_final: 0.1468 (t70)
REVERT: L   88 TYR cc_start: 0.3323 (OUTLIER) cc_final: 0.2194 (m-80)
REVERT: L  101 GLN cc_start: 0.6195 (mp10) cc_final: 0.5847 (mp10)
  outliers start: 30
  outliers final: 25
  residues processed: 88
  average time/residue: 0.1504
  time to fit residues: 17.6512
Evaluate side-chains
  89 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 60
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
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  104 MET
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   23 LEU
Chi-restraints excluded: chain A residue   44 VAL
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  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   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  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 38 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 65 optimal weight:    0.3980
   chunk 4 optimal weight:    0.0570
   chunk 49 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
** 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 = 0.4772 r_free = 0.4772 target = 0.239420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.223032 restraints weight = 220575.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.228503 restraints weight = 124119.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.229063 restraints weight = 92569.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.230074 restraints weight = 81819.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.230161 restraints weight = 79197.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.4596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5394
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5639  Z= 0.131
  Angle     :  0.556   5.154   7653  Z= 0.291
  Chirality :  0.046   0.150    874
  Planarity :  0.005   0.047    954
  Dihedral  :  7.838  52.632    786
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.01 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 19.26 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.75 (0.34), residues: 666
  helix:  0.70 (1.06), residues: 30
  sheet: -0.68 (0.30), residues: 317
  loop : -1.83 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A   8 
 TYR   0.010   0.001   TYR H  58 
 PHE   0.015   0.002   PHE A 342 
 TRP   0.008   0.001   TRP H 173 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5635)
  covalent geometry    : angle       0.55516 ( 7645)
  SS BOND              : bond        0.00432 (    4)
  SS BOND              : angle       1.23605 (    8)
  hydrogen bonds       : bond        0.03129 (  192)
  hydrogen bonds       : angle       5.97669 (  537)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2239.50 seconds
wall clock time: 39 minutes 3.99 seconds (2343.99 seconds total)