Starting phenix.real_space_refine
on Tue Jul 29 04:48:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8til_41295/07_2025/8til_41295.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8til_41295/07_2025/8til_41295.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8til_41295/07_2025/8til_41295.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8til_41295/07_2025/8til_41295.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8til_41295/07_2025/8til_41295.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8til_41295/07_2025/8til_41295.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.020
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    3512      2.51       5
     N     931      2.21       5
     O    1045      1.98       5
     H    5472      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10983
  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: "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: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 121
          Classifications: {'peptide': 7}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'TPO:plan-1': 2}
          Unresolved non-hydrogen planarities: 2
    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
  Time building chain proxies: 5.74, per 1000 atoms: 0.52
  Number of scatterers: 10983
  At special positions: 0
  Unit cell: (57.97, 102.238, 118.048, 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    1045      8.00
     N     931      7.00
     C    3512      6.00
     H    5472      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=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.77
  Conformation dependent library (CDL) restraints added in 937.0 milliseconds
  

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1336

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 18 sheets defined
      5.0% alpha, 44.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'H' and resid 204 through 208
    Processing helix  chain 'L' and resid 122 through 129
      removed outlier: 3.511A  pdb=" N   SER L 128 " --> pdb=" O   SER L 124 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 190
      removed outlier: 3.632A  pdb=" N   HIS L 190 " --> pdb=" O   ASP L 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.869A  pdb=" N   LEU A  49 " --> pdb=" O   ASP A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 108
      removed outlier: 3.637A  pdb=" N   LYS A 108 " --> pdb=" O   ARG A 104 " (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: 5.367A  pdb=" N   TRP H  50 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ARG H  41 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 3.893A  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: 5.367A  pdb=" N   TRP H  50 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
      removed outlier: 6.304A  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: 5.933A  pdb=" N   TYR H 195 " --> pdb=" O   ASP H 163 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL H 200 " --> pdb=" O   HIS H 183 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 139 through 143
      removed outlier: 5.933A  pdb=" N   TYR H 195 " --> pdb=" O   ASP H 163 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 172 through 173
    Processing sheet with id=AA7, first strand: chain 'L' and resid 6 through 8
      removed outlier: 3.663A  pdb=" N   VAL L  20 " --> pdb=" O   ILE L  76 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 11 through 12
    Processing sheet with id=AA9, first strand: chain 'L' and resid 35 through 39
      removed outlier: 3.887A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 49 through 50
    Processing sheet with id=AB2, first strand: chain 'L' and resid 115 through 119
      removed outlier: 5.840A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   THR L 179 " --> pdb=" O   GLN L 161 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 145 through 150
    Processing sheet with id=AB4, first strand: chain 'R' and resid 353 through 355
      removed outlier: 3.843A  pdb=" N   LYS A  11 " --> pdb=" O   GLY R 353 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   TPO R 355 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   VAL A   9 " --> pdb=" O   TPO R 355 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 28 through 29
      removed outlier: 6.004A  pdb=" N   PHE A  28 " --> pdb=" O   VAL A 172 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'A' and resid 78 through 88
      removed outlier: 4.643A  pdb=" N   ASP A  79 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   PHE A  62 " --> pdb=" O   ASP A  79 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   PHE A  81 " --> pdb=" O   CYS A  60 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   VAL A  54 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 128 through 130
    Processing sheet with id=AB8, first strand: chain 'A' and resid 184 through 188
    Processing sheet with id=AB9, first strand: chain 'A' and resid 253 through 259
      removed outlier: 6.887A  pdb=" N   GLN A 238 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ALA A 255 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL A 234 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LYS A 231 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)

    235 hydrogen bonds defined for protein.
    615 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: 4.27

  Time building geometry restraints manager: 3.41 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: 5456
        1.03 -     1.23: 56
        1.23 -     1.43: 2317
        1.43 -     1.62: 3247
        1.62 -     1.82: 26
  Bond restraints: 11102
  Sorted by residual:
  bond pdb=" CG2 TPO R 355 "
       pdb="HG21 TPO R 355 "
    ideal  model  delta    sigma   weight residual
    0.970  1.091 -0.121 2.00e-02 2.50e+03 3.64e+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 3.61e+01
  bond pdb=" CG2 TPO R 355 "
       pdb="HG23 TPO R 355 "
    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  1.090 -0.120 2.00e-02 2.50e+03 3.58e+01
  bond pdb=" CB  TPO R 355 "
       pdb=" HB  TPO R 355 "
    ideal  model  delta    sigma   weight residual
    0.970  1.088 -0.118 2.00e-02 2.50e+03 3.50e+01
  ... (remaining 11097 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 19927
        2.15 -     4.30: 96
        4.30 -     6.45: 9
        6.45 -     8.60: 1
        8.60 -    10.75: 4
  Bond angle restraints: 20037
  Sorted by residual:
  angle pdb=" OG1 TPO R 355 "
        pdb=" P   TPO R 355 "
        pdb=" O1P TPO R 355 "
      ideal   model   delta    sigma   weight residual
     100.43  111.18  -10.75 3.00e+00 1.11e-01 1.28e+01
  angle pdb=" CB  TPO R 352 "
        pdb=" OG1 TPO R 352 "
        pdb=" P   TPO R 352 "
      ideal   model   delta    sigma   weight residual
     119.31  108.62   10.69 3.00e+00 1.11e-01 1.27e+01
  angle pdb=" CB  TPO R 355 "
        pdb=" OG1 TPO R 355 "
        pdb=" P   TPO R 355 "
      ideal   model   delta    sigma   weight residual
     119.31  109.12   10.19 3.00e+00 1.11e-01 1.15e+01
  angle pdb=" N   LEU A  32 "
        pdb=" CA  LEU A  32 "
        pdb=" CB  LEU A  32 "
      ideal   model   delta    sigma   weight residual
     114.17  110.79    3.38 1.14e+00 7.69e-01 8.77e+00
  angle pdb=" OG1 TPO R 352 "
        pdb=" P   TPO R 352 "
        pdb=" O1P TPO R 352 "
      ideal   model   delta    sigma   weight residual
     100.43  109.25   -8.82 3.00e+00 1.11e-01 8.65e+00
  ... (remaining 20032 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4875
       17.94 -    35.88: 306
       35.88 -    53.82: 91
       53.82 -    71.76: 17
       71.76 -    89.70: 3
  Dihedral angle restraints: 5292
    sinusoidal: 2847
      harmonic: 2445
  Sorted by residual:
  dihedral pdb=" CA  ALA H  95 "
           pdb=" C   ALA H  95 "
           pdb=" N   VAL H  96 "
           pdb=" CA  VAL H  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.52   22.48     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  ASP L 171 "
           pdb=" C   ASP L 171 "
           pdb=" N   SER L 172 "
           pdb=" CA  SER L 172 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.72   22.28     0      5.00e+00 4.00e-02 1.99e+01
  dihedral pdb=" CA  TRP H 111 "
           pdb=" CB  TRP H 111 "
           pdb=" CG  TRP H 111 "
           pdb=" CD1 TRP H 111 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -179.70   89.70     2      2.00e+01 2.50e-03 1.20e+01
  ... (remaining 5289 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 467
       0.027 -    0.054: 266
       0.054 -    0.082: 56
       0.082 -    0.109: 54
       0.109 -    0.136: 32
  Chirality restraints: 875
  Sorted by residual:
  chirality pdb=" CA  VAL H 203 "
            pdb=" N   VAL H 203 "
            pdb=" C   VAL H 203 "
            pdb=" CB  VAL H 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.63e-01
  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    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  VAL A 165 "
            pdb=" N   VAL A 165 "
            pdb=" C   VAL A 165 "
            pdb=" CB  VAL A 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.47e-01
  ... (remaining 872 not shown)

  Planarity restraints: 1583
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 167 "   -0.027 5.00e-02 4.00e+02   4.02e-02 2.58e+00
        pdb=" N   PRO H 168 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO H 168 "   -0.023 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 H 141 "    0.021 5.00e-02 4.00e+02   3.20e-02 1.64e+00
        pdb=" N   PRO H 142 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO H 142 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO H 142 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H 220 "   -0.021 5.00e-02 4.00e+02   3.19e-02 1.63e+00
        pdb=" N   PRO H 221 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO H 221 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO H 221 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1580 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.14: 364
        2.14 -     2.75: 20960
        2.75 -     3.37: 29451
        3.37 -     3.98: 39898
        3.98 -     4.60: 61426
  Nonbonded interactions: 152099
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN H  42 "
            pdb="HE22 GLN L  39 "
     model   vdw
     1.521 2.450
  nonbonded pdb=" HE1 TRP H  50 "
            pdb=" OG  SER H  53 "
     model   vdw
     1.552 2.450
  nonbonded pdb=" OE2 GLU H   9 "
            pdb=" H   CYS H  99 "
     model   vdw
     1.564 2.450
  nonbonded pdb=" H   ASP L 168 "
            pdb=" O   THR L 173 "
     model   vdw
     1.578 2.450
  nonbonded pdb=" OE1 GLU H   9 "
            pdb=" H   GLY H 125 "
     model   vdw
     1.590 2.450
  ... (remaining 152094 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.710
  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:             0.210
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     27.560
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6068
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      :  0.005   0.106   5634  Z= 0.233
  Angle     :  0.679  10.751   7644  Z= 0.358
  Chirality :  0.045   0.136    875
  Planarity :  0.004   0.040    951
  Dihedral  : 12.238  89.701   2034
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  :  8.35 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.33), residues: 666
  helix: -0.97 (0.97), residues: 29
  sheet: -1.04 (0.28), residues: 350
  loop : -1.43 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  50 
 HIS   0.004   0.001   HIS H  38 
 PHE   0.013   0.002   PHE A 145 
 TYR   0.012   0.001   TYR H  36 
 ARG   0.003   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14898 (  204)
  hydrogen bonds       : angle       7.05742 (  615)
  SS BOND              : bond        0.00276 (    4)
  SS BOND              : angle       0.81007 (    8)
  covalent geometry    : bond        0.00478 ( 5630)
  covalent geometry    : angle       0.67898 ( 7636)

*********************** 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
  164 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 124
  time to evaluate  : 0.798 
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: H  157 LEU cc_start: 0.5294 (OUTLIER) cc_final: 0.4793 (pp)
REVERT: L  136 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7892 (tp)
REVERT: L  166 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6381 (tp30)
REVERT: A  284 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6911 (pp20)
REVERT: A  291 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7411 (m-30)
REVERT: A  318 ILE cc_start: 0.5436 (mt) cc_final: 0.5195 (tt)
  outliers start: 40
  outliers final: 23
  residues processed: 156
  average time/residue: 0.4136
  time to fit residues: 81.6642
Evaluate side-chains
  113 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 85
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue    2 ASP
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  173 THR
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  345 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0770
   chunk 40 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.6740

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

Flipped N/Q/H residues before XYZ refinement:
L  28 GLN
L 211 ASN
A 182 GLN
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.190885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.159788 restraints weight = 17805.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.166449 restraints weight = 10297.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.170967 restraints weight = 6717.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6067
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5634  Z= 0.167
  Angle     :  0.582   4.747   7644  Z= 0.306
  Chirality :  0.046   0.151    875
  Planarity :  0.005   0.046    951
  Dihedral  :  9.354  89.751    807
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 14.61 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.33), residues: 666
  helix: -1.04 (0.90), residues: 31
  sheet: -0.86 (0.28), residues: 342
  loop : -1.34 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  50 
 HIS   0.009   0.002   HIS A 346 
 PHE   0.015   0.002   PHE A 116 
 TYR   0.011   0.001   TYR H  36 
 ARG   0.004   0.000   ARG A  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  204)
  hydrogen bonds       : angle       5.89595 (  615)
  SS BOND              : bond        0.00210 (    4)
  SS BOND              : angle       0.93610 (    8)
  covalent geometry    : bond        0.00370 ( 5630)
  covalent geometry    : angle       0.58161 ( 7636)

*********************** 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
  121 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 86
  time to evaluate  : 0.778 
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: H  157 LEU cc_start: 0.5080 (OUTLIER) cc_final: 0.4608 (pp)
REVERT: L   93 TYR cc_start: 0.7748 (t80) cc_final: 0.7497 (t80)
REVERT: L  136 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7841 (tp)
REVERT: L  164 VAL cc_start: 0.9216 (t) cc_final: 0.8891 (p)
REVERT: L  166 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6324 (tp30)
REVERT: A  284 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6915 (pp20)
  outliers start: 35
  outliers final: 25
  residues processed: 112
  average time/residue: 0.3602
  time to fit residues: 53.6948
Evaluate side-chains
  111 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 82
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  338 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 15 optimal weight:    0.3980
   chunk 9 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 3 optimal weight:    0.1980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A 182 GLN
** A 300 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 = 0.4440 r_free = 0.4440 target = 0.191041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.158578 restraints weight = 18042.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.165622 restraints weight = 10301.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.170481 restraints weight = 6657.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.4230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6044
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5634  Z= 0.152
  Angle     :  0.576   8.052   7644  Z= 0.303
  Chirality :  0.046   0.151    875
  Planarity :  0.004   0.042    951
  Dihedral  :  8.785  89.030    794
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 15.73 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.33), residues: 666
  helix: -1.04 (0.86), residues: 31
  sheet: -0.66 (0.29), residues: 337
  loop : -1.37 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  50 
 HIS   0.007   0.001   HIS A 346 
 PHE   0.013   0.002   PHE A 116 
 TYR   0.012   0.001   TYR A  22 
 ARG   0.004   0.000   ARG H  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03477 (  204)
  hydrogen bonds       : angle       5.76021 (  615)
  SS BOND              : bond        0.00534 (    4)
  SS BOND              : angle       2.01323 (    8)
  covalent geometry    : bond        0.00338 ( 5630)
  covalent geometry    : angle       0.57304 ( 7636)

*********************** 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
  115 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 78
  time to evaluate  : 0.875 
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  157 LEU cc_start: 0.5065 (OUTLIER) cc_final: 0.4576 (pp)
REVERT: H  164 TYR cc_start: 0.7790 (p90) cc_final: 0.7339 (p90)
REVERT: L   92 SER cc_start: 0.7813 (OUTLIER) cc_final: 0.7427 (t)
REVERT: L  137 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7494 (mp)
REVERT: L  164 VAL cc_start: 0.9206 (t) cc_final: 0.8892 (p)
REVERT: L  166 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6332 (tp30)
REVERT: A  284 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6940 (pp20)
  outliers start: 37
  outliers final: 28
  residues processed: 106
  average time/residue: 0.3592
  time to fit residues: 50.2968
Evaluate side-chains
  109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 76
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  345 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0980
   chunk 15 optimal weight:    0.2980
   chunk 23 optimal weight:    2.9990
   chunk 24 optimal weight:    0.4980
   chunk 27 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    0.2980
   chunk 7 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
H  42 GLN
L  39 GLN
A  86 GLN
** A 300 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 = 0.4434 r_free = 0.4434 target = 0.191268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.162393 restraints weight = 17694.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.168943 restraints weight = 10177.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.173452 restraints weight = 6564.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.4238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6028
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5634  Z= 0.114
  Angle     :  0.532   7.362   7644  Z= 0.276
  Chirality :  0.045   0.143    875
  Planarity :  0.004   0.040    951
  Dihedral  :  8.488  88.846    793
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 16.69 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.33), residues: 666
  helix: -0.88 (0.85), residues: 31
  sheet: -0.54 (0.29), residues: 337
  loop : -1.24 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.009   0.001   HIS A 346 
 PHE   0.009   0.001   PHE A 116 
 TYR   0.010   0.001   TYR A  22 
 ARG   0.004   0.000   ARG H  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03000 (  204)
  hydrogen bonds       : angle       5.40190 (  615)
  SS BOND              : bond        0.00394 (    4)
  SS BOND              : angle       1.68431 (    8)
  covalent geometry    : bond        0.00256 ( 5630)
  covalent geometry    : angle       0.52992 ( 7636)

*********************** 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
  115 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 78
  time to evaluate  : 1.029 
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  139 SER cc_start: 0.6032 (OUTLIER) cc_final: 0.5789 (m)
REVERT: H  157 LEU cc_start: 0.5048 (OUTLIER) cc_final: 0.4601 (pp)
REVERT: H  164 TYR cc_start: 0.7679 (p90) cc_final: 0.7474 (p90)
REVERT: L   92 SER cc_start: 0.7744 (OUTLIER) cc_final: 0.7476 (t)
REVERT: L   99 PHE cc_start: 0.5232 (m-80) cc_final: 0.4868 (m-80)
REVERT: L  166 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6420 (tp30)
REVERT: L  168 ASP cc_start: 0.8667 (t0) cc_final: 0.8379 (m-30)
REVERT: A  284 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6864 (pp20)
  outliers start: 37
  outliers final: 28
  residues processed: 103
  average time/residue: 0.3714
  time to fit residues: 51.1099
Evaluate side-chains
  110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 77
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  120 ASP
Chi-restraints excluded: chain H residue  139 SER
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   39 GLN
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  318 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   chunk 17 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
L  39 GLN
** A 300 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 = 0.4401 r_free = 0.4401 target = 0.188248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.160245 restraints weight = 17973.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.166399 restraints weight = 10662.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.170398 restraints weight = 7045.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.4212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6135
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5634  Z= 0.160
  Angle     :  0.567   7.659   7644  Z= 0.297
  Chirality :  0.045   0.149    875
  Planarity :  0.005   0.052    951
  Dihedral  :  8.457  89.201    788
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 16.53 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.33), residues: 666
  helix: -0.94 (0.84), residues: 31
  sheet: -0.61 (0.29), residues: 343
  loop : -1.35 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  50 
 HIS   0.005   0.001   HIS A 346 
 PHE   0.014   0.002   PHE A 116 
 TYR   0.010   0.001   TYR H  36 
 ARG   0.005   0.000   ARG H  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03267 (  204)
  hydrogen bonds       : angle       5.55896 (  615)
  SS BOND              : bond        0.00573 (    4)
  SS BOND              : angle       1.44251 (    8)
  covalent geometry    : bond        0.00361 ( 5630)
  covalent geometry    : angle       0.56534 ( 7636)

*********************** 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
  114 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 76
  time to evaluate  : 0.795 
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  139 SER cc_start: 0.6109 (OUTLIER) cc_final: 0.5872 (m)
REVERT: H  157 LEU cc_start: 0.5086 (OUTLIER) cc_final: 0.4678 (pp)
REVERT: H  164 TYR cc_start: 0.7787 (p90) cc_final: 0.7570 (p90)
REVERT: L   92 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7512 (t)
REVERT: L  166 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6452 (tp30)
REVERT: L  168 ASP cc_start: 0.8609 (t0) cc_final: 0.8306 (m-30)
REVERT: A  284 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6828 (pp20)
  outliers start: 38
  outliers final: 30
  residues processed: 101
  average time/residue: 0.3522
  time to fit residues: 47.1444
Evaluate side-chains
  108 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 73
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  120 ASP
Chi-restraints excluded: chain H residue  139 SER
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  170 THR
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  345 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 63 optimal weight:    0.2980
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
H  42 GLN
L  39 GLN
** A 300 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 = 0.4392 r_free = 0.4392 target = 0.187576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.159713 restraints weight = 18298.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.165801 restraints weight = 10842.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.169937 restraints weight = 7164.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6172
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5634  Z= 0.173
  Angle     :  0.580   7.474   7644  Z= 0.304
  Chirality :  0.046   0.150    875
  Planarity :  0.005   0.040    951
  Dihedral  :  8.370  88.107    786
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 16.85 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.33), residues: 666
  helix: -1.03 (0.83), residues: 31
  sheet: -0.70 (0.28), residues: 343
  loop : -1.40 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  50 
 HIS   0.006   0.001   HIS A 346 
 PHE   0.014   0.002   PHE A 116 
 TYR   0.009   0.001   TYR H  36 
 ARG   0.006   0.000   ARG H  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03321 (  204)
  hydrogen bonds       : angle       5.65958 (  615)
  SS BOND              : bond        0.00582 (    4)
  SS BOND              : angle       1.37188 (    8)
  covalent geometry    : bond        0.00388 ( 5630)
  covalent geometry    : angle       0.57816 ( 7636)

*********************** 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
  116 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 76
  time to evaluate  : 0.926 
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  139 SER cc_start: 0.6182 (OUTLIER) cc_final: 0.5976 (m)
REVERT: H  157 LEU cc_start: 0.5268 (OUTLIER) cc_final: 0.4792 (pp)
REVERT: H  164 TYR cc_start: 0.7836 (p90) cc_final: 0.7607 (p90)
REVERT: L  166 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6185 (tp30)
REVERT: L  168 ASP cc_start: 0.8626 (t0) cc_final: 0.8310 (m-30)
REVERT: A  165 VAL cc_start: 0.4157 (OUTLIER) cc_final: 0.3863 (t)
REVERT: A  284 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6827 (pp20)
  outliers start: 40
  outliers final: 34
  residues processed: 102
  average time/residue: 0.3859
  time to fit residues: 51.3085
Evaluate side-chains
  114 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 75
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  120 ASP
Chi-restraints excluded: chain H residue  139 SER
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  170 THR
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   22 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  345 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 11 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** H  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.187051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.157309 restraints weight = 18351.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.163580 restraints weight = 10776.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.168034 restraints weight = 7109.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6173
moved from start:          0.3643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5634  Z= 0.179
  Angle     :  0.583   7.155   7644  Z= 0.306
  Chirality :  0.046   0.149    875
  Planarity :  0.005   0.041    951
  Dihedral  :  8.457  87.886    786
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  7.22 %
    Allowed  : 16.85 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.33), residues: 666
  helix: -0.99 (0.84), residues: 31
  sheet: -0.73 (0.28), residues: 343
  loop : -1.45 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  50 
 HIS   0.005   0.001   HIS A 346 
 PHE   0.013   0.002   PHE A 116 
 TYR   0.010   0.001   TYR H  36 
 ARG   0.007   0.000   ARG H  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03333 (  204)
  hydrogen bonds       : angle       5.74573 (  615)
  SS BOND              : bond        0.00602 (    4)
  SS BOND              : angle       1.23659 (    8)
  covalent geometry    : bond        0.00401 ( 5630)
  covalent geometry    : angle       0.58220 ( 7636)

*********************** 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
  124 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 79
  time to evaluate  : 1.233 
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  157 LEU cc_start: 0.5255 (OUTLIER) cc_final: 0.4825 (pp)
REVERT: L  166 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6391 (tp30)
REVERT: L  168 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8223 (m-30)
  outliers start: 45
  outliers final: 36
  residues processed: 106
  average time/residue: 0.5165
  time to fit residues: 74.3618
Evaluate side-chains
  117 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 78
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  170 THR
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   22 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  168 ASP
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  126 CYS
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  345 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0970
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.188726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.160328 restraints weight = 18159.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.166150 restraints weight = 10976.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.170104 restraints weight = 7365.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6187
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5634  Z= 0.156
  Angle     :  0.566   6.836   7644  Z= 0.296
  Chirality :  0.046   0.146    875
  Planarity :  0.004   0.045    951
  Dihedral  :  8.393  87.391    786
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  6.90 %
    Allowed  : 17.34 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.33), residues: 666
  helix: -0.94 (0.84), residues: 31
  sheet: -0.74 (0.28), residues: 343
  loop : -1.42 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  50 
 HIS   0.007   0.001   HIS A 346 
 PHE   0.011   0.002   PHE A 116 
 TYR   0.019   0.001   TYR H 164 
 ARG   0.006   0.000   ARG H  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03181 (  204)
  hydrogen bonds       : angle       5.63778 (  615)
  SS BOND              : bond        0.00546 (    4)
  SS BOND              : angle       1.18206 (    8)
  covalent geometry    : bond        0.00351 ( 5630)
  covalent geometry    : angle       0.56544 ( 7636)

*********************** 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
  120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 77
  time to evaluate  : 0.939 
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: H  157 LEU cc_start: 0.5195 (OUTLIER) cc_final: 0.4783 (pp)
REVERT: L    4 GLN cc_start: 0.7243 (mp10) cc_final: 0.6897 (mm-40)
REVERT: L  166 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6358 (tp30)
REVERT: L  168 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8261 (m-30)
REVERT: A  284 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6874 (pp20)
REVERT: A  342 PHE cc_start: 0.5460 (p90) cc_final: 0.5111 (p90)
  outliers start: 43
  outliers final: 37
  residues processed: 102
  average time/residue: 0.3752
  time to fit residues: 50.0572
Evaluate side-chains
  117 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 76
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  170 THR
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   22 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  168 ASP
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain R residue  356 LYS
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  126 CYS
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  345 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 17 optimal weight:    0.0770
   chunk 54 optimal weight:    0.1980
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 15 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.5742

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

Flipped N/Q/H residues before XYZ refinement:
** H  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.189531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.161063 restraints weight = 18187.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.166914 restraints weight = 10917.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.171078 restraints weight = 7309.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.4227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6168
moved from start:          0.3987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5634  Z= 0.138
  Angle     :  0.543   6.498   7644  Z= 0.283
  Chirality :  0.045   0.144    875
  Planarity :  0.004   0.046    951
  Dihedral  :  8.204  87.583    784
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 18.46 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.33), residues: 666
  helix: -0.79 (0.86), residues: 31
  sheet: -0.65 (0.29), residues: 342
  loop : -1.40 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H  50 
 HIS   0.007   0.001   HIS A 346 
 PHE   0.010   0.002   PHE A 116 
 TYR   0.013   0.001   TYR H 164 
 ARG   0.007   0.000   ARG H  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02977 (  204)
  hydrogen bonds       : angle       5.50875 (  615)
  SS BOND              : bond        0.00532 (    4)
  SS BOND              : angle       1.07006 (    8)
  covalent geometry    : bond        0.00313 ( 5630)
  covalent geometry    : angle       0.54230 ( 7636)

*********************** 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
  111 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 74
  time to evaluate  : 0.911 
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  157 LEU cc_start: 0.5236 (OUTLIER) cc_final: 0.4824 (pp)
REVERT: L    4 GLN cc_start: 0.7220 (mp10) cc_final: 0.6920 (mm-40)
REVERT: L  166 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6408 (tp30)
REVERT: L  168 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8280 (m-30)
  outliers start: 37
  outliers final: 33
  residues processed: 95
  average time/residue: 0.3515
  time to fit residues: 44.3311
Evaluate side-chains
  110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 74
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  170 THR
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  168 ASP
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  126 CYS
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  318 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    0.3980
   chunk 67 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.187863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.159994 restraints weight = 18232.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.165591 restraints weight = 11065.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.169634 restraints weight = 7487.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6214
moved from start:          0.4104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5634  Z= 0.162
  Angle     :  0.569   6.781   7644  Z= 0.298
  Chirality :  0.046   0.147    875
  Planarity :  0.005   0.046    951
  Dihedral  :  8.260  87.541    784
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 17.98 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.33), residues: 666
  helix: -0.79 (0.87), residues: 31
  sheet: -0.52 (0.29), residues: 330
  loop : -1.59 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  50 
 HIS   0.005   0.001   HIS A 346 
 PHE   0.012   0.002   PHE A 116 
 TYR   0.011   0.001   TYR H 164 
 ARG   0.006   0.000   ARG H  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03217 (  204)
  hydrogen bonds       : angle       5.65463 (  615)
  SS BOND              : bond        0.00570 (    4)
  SS BOND              : angle       1.16849 (    8)
  covalent geometry    : bond        0.00363 ( 5630)
  covalent geometry    : angle       0.56846 ( 7636)

********************** 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
  116 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 76
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  157 LEU cc_start: 0.5233 (OUTLIER) cc_final: 0.4828 (pp)
REVERT: L    4 GLN cc_start: 0.7223 (mp10) cc_final: 0.6949 (mm-40)
REVERT: L  166 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6534 (tp30)
REVERT: L  168 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8224 (m-30)
  outliers start: 40
  outliers final: 34
  residues processed: 98
  average time/residue: 0.3856
  time to fit residues: 49.4313
Evaluate side-chains
  110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 73
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  104 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  116 TYR
Chi-restraints excluded: chain H residue  157 LEU
Chi-restraints excluded: chain H residue  159 CYS
Chi-restraints excluded: chain H residue  170 THR
Chi-restraints excluded: chain H residue  189 LEU
Chi-restraints excluded: chain H residue  196 SER
Chi-restraints excluded: chain H residue  201 VAL
Chi-restraints excluded: chain H residue  216 ASN
Chi-restraints excluded: chain L residue   22 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  168 ASP
Chi-restraints excluded: chain L residue  180 LEU
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  126 CYS
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  284 GLU
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  318 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 54 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.185502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.158020 restraints weight = 18104.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.163531 restraints weight = 11051.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.167459 restraints weight = 7482.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6247
moved from start:          0.4326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5634  Z= 0.194
  Angle     :  0.604   7.270   7644  Z= 0.318
  Chirality :  0.047   0.147    875
  Planarity :  0.005   0.045    951
  Dihedral  :  8.385  87.767    784
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 17.66 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.33), residues: 666
  helix: -0.86 (0.87), residues: 31
  sheet: -0.62 (0.29), residues: 330
  loop : -1.70 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  50 
 HIS   0.006   0.001   HIS A 211 
 PHE   0.018   0.002   PHE A 116 
 TYR   0.011   0.002   TYR H  36 
 ARG   0.007   0.001   ARG H  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03452 (  204)
  hydrogen bonds       : angle       5.88364 (  615)
  SS BOND              : bond        0.00624 (    4)
  SS BOND              : angle       1.24778 (    8)
  covalent geometry    : bond        0.00435 ( 5630)
  covalent geometry    : angle       0.60271 ( 7636)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5052.20 seconds
wall clock time: 88 minutes 54.98 seconds (5334.98 seconds total)