Starting phenix.real_space_refine
on Tue Aug  4 16:25:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/10fj_75133/08_2026/10fj_75133_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/10fj_75133/08_2026/10fj_75133.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/10fj_75133/08_2026/10fj_75133.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/10fj_75133/08_2026/10fj_75133.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/10fj_75133/08_2026/10fj_75133_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/10fj_75133/08_2026/10fj_75133_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.109
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: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    2975      2.51       5
     N     789      2.21       5
     O     927      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4711
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1362
          Classifications: {'peptide': 172}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 157}
    Chain: "H"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1662
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 13, 'TRANS': 206}
    Chain: "L"
      Number of atoms: 1687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1687
          Classifications: {'peptide': 220}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 207}
  Time building chain proxies: 0.79, per 1000 atoms: 0.17
  Number of scatterers: 4711
  At special positions: 0
  Unit cell: (58.48, 83.42, 121.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O     927      8.00
     N     789      7.00
     C    2975      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  29 " - pdb=" SG  CYS A  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 110 " - pdb=" SG  CYS A 154 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  42 " - pdb=" SG  CYS L 112 " distance=1.86
    Simple disulfide: pdb=" SG  CYS L 158 " - pdb=" SG  CYS L 218 " 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: 0.24
  Conformation dependent library (CDL) restraints added in 167.3 milliseconds
  

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1136

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 13 sheets defined
      6.0% alpha, 24.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 47
    Processing helix  chain 'A' and resid 145 through 149
    Processing helix  chain 'H' and resid 47 through 51
      removed outlier: 3.708A  pdb=" N   TYR H  51 " --> pdb=" O   PHE H  48 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 198 through 203
      removed outlier: 4.093A  pdb=" N   TYR H 202 " --> pdb=" O   SER H 198 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 103 through 107
      removed outlier: 3.613A  pdb=" N   ASP L 106 " --> pdb=" O   GLU L 103 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   VAL L 107 " --> pdb=" O   ALA L 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 103 through 107'
    Processing helix  chain 'L' and resid 148 through 151
    Processing helix  chain 'L' and resid 207 through 213
      removed outlier: 3.525A  pdb=" N   HIS L 213 " --> pdb=" O   ASP L 209 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28
      removed outlier: 3.610A  pdb=" N   VAL A  25 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94
    Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 133
      removed outlier: 6.948A  pdb=" N   PHE A 123 " --> pdb=" O   GLN A 130 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   PHE A 132 " --> pdb=" O   VAL A 121 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   VAL A 121 " --> pdb=" O   PHE A 132 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ILE A 170 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 157 through 158
      removed outlier: 3.620A  pdb=" N   THR A 161 " --> pdb=" O   ILE A 158 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25
    Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31
      removed outlier: 3.824A  pdb=" N   THR H 136 " --> pdb=" O   GLU H  29 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   THR H 133 " --> pdb=" O   TYR H 113 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLY H  68 " --> pdb=" O   TRP H  55 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   LYS H  57 " --> pdb=" O   TRP H  66 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   TRP H  66 " --> pdb=" O   LYS H  57 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 37 through 38
      removed outlier: 3.818A  pdb=" N   SER H  90 " --> pdb=" O   TYR H  99 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLN H 101 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 179 through 180
    Processing sheet with id=AA9, first strand: chain 'L' and resid 29 through 32
    Processing sheet with id=AB1, first strand: chain 'L' and resid 38 through 42
      removed outlier: 3.559A  pdb=" N   CYS L  42 " --> pdb=" O   PHE L  95 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   PHE L  95 " --> pdb=" O   CYS L  42 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 77 through 78
      removed outlier: 6.721A  pdb=" N   TRP L  59 " --> pdb=" O   LEU L  71 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   TYR L  73 " --> pdb=" O   LEU L  57 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU L  57 " --> pdb=" O   TYR L  73 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 139 through 142
      removed outlier: 3.643A  pdb=" N   VAL L 157 " --> pdb=" O   PHE L 142 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   SER L 155 " --> pdb=" O   LEU L 205 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   LEU L 205 " --> pdb=" O   SER L 155 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   VAL L 157 " --> pdb=" O   LEU L 203 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   LEU L 203 " --> pdb=" O   VAL L 157 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   LEU L 159 " --> pdb=" O   SER L 201 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   SER L 201 " --> pdb=" O   LEU L 159 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   ASN L 161 " --> pdb=" O   LEU L 199 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   LEU L 199 " --> pdb=" O   ASN L 161 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   PHE L 163 " --> pdb=" O   TYR L 197 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 177 through 178
      removed outlier: 7.131A  pdb=" N   TYR L 216 " --> pdb=" O   SER L 232 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   SER L 232 " --> pdb=" O   TYR L 216 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   CYS L 218 " --> pdb=" O   THR L 230 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   THR L 230 " --> pdb=" O   CYS L 218 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   VAL L 220 " --> pdb=" O   PRO L 228 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   HIS L 222 " --> pdb=" O   SER L 226 " (cutoff:3.500A)

    94 hydrogen bonds defined for protein.
    204 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.35

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1320
        1.33 -     1.45: 867
        1.45 -     1.57: 2620
        1.57 -     1.69: 0
        1.69 -     1.81: 27
  Bond restraints: 4834
  Sorted by residual:
  bond pdb=" N   ILE A  40 "
       pdb=" CA  ILE A  40 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.15e-02 7.56e+03 1.05e+01
  bond pdb=" N   LYS H  32 "
       pdb=" CA  LYS H  32 "
    ideal  model  delta    sigma   weight residual
    1.453  1.490 -0.038 1.18e-02 7.18e+03 1.02e+01
  bond pdb=" N   VAL H 176 "
       pdb=" CA  VAL H 176 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.25e-02 6.40e+03 9.14e+00
  bond pdb=" N   VAL L 157 "
       pdb=" CA  VAL L 157 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 1.22e-02 6.72e+03 9.08e+00
  bond pdb=" N   ILE A 106 "
       pdb=" CA  ILE A 106 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.25e-02 6.40e+03 9.06e+00
  ... (remaining 4829 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 5889
        1.40 -     2.79: 527
        2.79 -     4.19: 132
        4.19 -     5.58: 31
        5.58 -     6.98: 6
  Bond angle restraints: 6585
  Sorted by residual:
  angle pdb=" C   SER H 146 "
        pdb=" CA  SER H 146 "
        pdb=" CB  SER H 146 "
      ideal   model   delta    sigma   weight residual
     116.54  111.07    5.47 1.15e+00 7.56e-01 2.26e+01
  angle pdb=" N   TYR H 120 "
        pdb=" CA  TYR H 120 "
        pdb=" CB  TYR H 120 "
      ideal   model   delta    sigma   weight residual
     110.90  104.60    6.30 1.33e+00 5.65e-01 2.24e+01
  angle pdb=" C   MET H 110 "
        pdb=" CA  MET H 110 "
        pdb=" CB  MET H 110 "
      ideal   model   delta    sigma   weight residual
     110.26  103.38    6.88 1.50e+00 4.44e-01 2.10e+01
  angle pdb=" CA  PHE L 163 "
        pdb=" CB  PHE L 163 "
        pdb=" CG  PHE L 163 "
      ideal   model   delta    sigma   weight residual
     113.80  118.38   -4.58 1.00e+00 1.00e+00 2.10e+01
  angle pdb=" N   TYR H 120 "
        pdb=" CA  TYR H 120 "
        pdb=" C   TYR H 120 "
      ideal   model   delta    sigma   weight residual
     114.31  108.59    5.72 1.29e+00 6.01e-01 1.96e+01
  ... (remaining 6580 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.38: 2524
       16.38 -    32.76: 268
       32.76 -    49.14: 67
       49.14 -    65.52: 22
       65.52 -    81.90: 3
  Dihedral angle restraints: 2884
    sinusoidal: 1115
      harmonic: 1769
  Sorted by residual:
  dihedral pdb=" CB  CYS A 110 "
           pdb=" SG  CYS A 110 "
           pdb=" SG  CYS A 154 "
           pdb=" CB  CYS A 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.90   43.10     1      1.00e+01 1.00e-02 2.59e+01
  dihedral pdb=" C   MET H 110 "
           pdb=" N   MET H 110 "
           pdb=" CA  MET H 110 "
           pdb=" CB  MET H 110 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.86  -11.74     0      2.50e+00 1.60e-01 2.21e+01
  dihedral pdb=" CA  LEU L 160 "
           pdb=" C   LEU L 160 "
           pdb=" N   ASN L 161 "
           pdb=" CA  ASN L 161 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.95  -21.05     0      5.00e+00 4.00e-02 1.77e+01
  ... (remaining 2881 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 559
       0.060 -    0.121: 128
       0.121 -    0.181: 34
       0.181 -    0.242: 7
       0.242 -    0.302: 7
  Chirality restraints: 735
  Sorted by residual:
  chirality pdb=" CA  MET H 110 "
            pdb=" N   MET H 110 "
            pdb=" C   MET H 110 "
            pdb=" CB  MET H 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CA  LYS H  32 "
            pdb=" N   LYS H  32 "
            pdb=" C   LYS H  32 "
            pdb=" CB  LYS H  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CA  TYR H 120 "
            pdb=" N   TYR H 120 "
            pdb=" C   TYR H 120 "
            pdb=" CB  TYR H 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.75e+00
  ... (remaining 732 not shown)

  Planarity restraints: 847
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 109 "   -0.270 9.50e-02 1.11e+02   1.21e-01 9.00e+00
        pdb=" NE  ARG A 109 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 109 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 109 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 109 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS H 235 "    0.009 2.00e-02 2.50e+03   1.81e-02 3.28e+00
        pdb=" C   LYS H 235 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   LYS H 235 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ARG H 236 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L 166 "    0.151 9.50e-02 1.11e+02   6.76e-02 2.81e+00
        pdb=" NE  ARG L 166 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG L 166 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG L 166 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG L 166 "    0.006 2.00e-02 2.50e+03
  ... (remaining 844 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 20
        2.56 -     3.15: 3684
        3.15 -     3.73: 6612
        3.73 -     4.32: 9304
        4.32 -     4.90: 15808
  Nonbonded interactions: 35428
  Sorted by model distance:
  nonbonded pdb=" O   PRO H 149 "
            pdb=" CD1 LEU H 150 "
     model   vdw
     1.980 3.460
  nonbonded pdb=" O   ASP L  84 "
            pdb=" OD1 ASP L  84 "
     model   vdw
     2.133 3.040
  nonbonded pdb=" CE1 PHE A  59 "
            pdb=" OD1 ASN A  62 "
     model   vdw
     2.207 3.340
  nonbonded pdb=" OD2 ASP H 124 "
            pdb=" OD2 ASP H 127 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" CD2 HIS A 134 "
            pdb=" O   ASN H  50 "
     model   vdw
     2.251 3.260
  ... (remaining 35423 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:             1.260
  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:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.960
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:0.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
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      :  0.008   0.173   4839  Z= 0.520
  Angle     :  0.923   6.977   6595  Z= 0.623
  Chirality :  0.063   0.302    735
  Planarity :  0.006   0.121    847
  Dihedral  : 14.690  81.899   1733
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 19.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.23 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 14.50 %
    Favored  : 84.01 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.58 (0.34), residues: 606
  helix: -0.46 (2.10), residues: 8
  sheet: -0.94 (0.39), residues: 215
  loop : -2.32 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H 117 
 TYR   0.014   0.001   TYR H 171 
 PHE   0.005   0.001   PHE H 114 
 TRP   0.010   0.001   TRP H  69 
 HIS   0.004   0.001   HIS A 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00712 /  0.51 ( 4834)
  covalent geometry    : angle       0.92199 /  0.62 ( 6585)
  SS BOND              : bond        0.07777 /  3.91 (    5)
  SS BOND              : angle       1.33830 /  0.85 (   10)
  hydrogen bonds       : bond        0.25618 / 16.60 (   94)
  hydrogen bonds       : angle      10.28171 /  6.84 (  204)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A  161 THR cc_start: 0.7393 (m) cc_final: 0.7020 (p)
REVERT: H   32 LYS cc_start: 0.7041 (mttt) cc_final: 0.6360 (mtmm)
REVERT: H  107 ASN cc_start: 0.8603 (t0) cc_final: 0.8279 (t0)
REVERT: H  236 ARG cc_start: 0.8176 (ttt90) cc_final: 0.7580 (ttp80)
REVERT: L  214 LYS cc_start: 0.7494 (tptt) cc_final: 0.7144 (mmmt)
  outliers start: 8
  outliers final: 7
  residues processed: 76
  average time/residue: 0.0494
  time to fit residues: 5.0114
Evaluate side-chains
  59 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue  120 TYR
Chi-restraints excluded: chain H residue  189 VAL
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain L residue  118 TYR
Chi-restraints excluded: chain L residue  163 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 56 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0170
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 58 optimal weight:    8.9990
   overall best weight:    0.5818

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.211584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.162067 restraints weight = 5420.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.165294 restraints weight = 3718.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.167076 restraints weight = 2906.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.168710 restraints weight = 2498.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.169195 restraints weight = 2266.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4839  Z= 0.128
  Angle     :  0.647  10.632   6595  Z= 0.321
  Chirality :  0.046   0.260    735
  Planarity :  0.004   0.035    847
  Dihedral  :  5.965  57.414    661
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.40 %
    Favored  : 89.60 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 16.54 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.32 (0.35), residues: 606
  helix: -0.30 (2.15), residues: 8
  sheet: -0.68 (0.38), residues: 228
  loop : -2.24 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 236 
 TYR   0.013   0.001   TYR L 118 
 PHE   0.011   0.001   PHE A  43 
 TRP   0.008   0.001   TRP H  66 
 HIS   0.005   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 4834)
  covalent geometry    : angle       0.64667 /  0.32 ( 6585)
  SS BOND              : bond        0.00348 /  0.17 (    5)
  SS BOND              : angle       0.77243 /  0.40 (   10)
  hydrogen bonds       : bond        0.03679 /  2.31 (   94)
  hydrogen bonds       : angle       7.04034 /  4.93 (  204)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 51
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  161 THR cc_start: 0.8014 (m) cc_final: 0.7750 (p)
REVERT: H  168 VAL cc_start: 0.6661 (OUTLIER) cc_final: 0.6417 (t)
REVERT: L  156 VAL cc_start: 0.5993 (OUTLIER) cc_final: 0.5675 (t)
  outliers start: 20
  outliers final: 16
  residues processed: 68
  average time/residue: 0.0425
  time to fit residues: 4.0777
Evaluate side-chains
  61 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 43
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  140 SER
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   77 SER
Chi-restraints excluded: chain H residue  120 TYR
Chi-restraints excluded: chain H residue  168 VAL
Chi-restraints excluded: chain H residue  189 VAL
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   51 THR
Chi-restraints excluded: chain L residue  118 TYR
Chi-restraints excluded: chain L residue  156 VAL
Chi-restraints excluded: chain L residue  163 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 6 optimal weight:    7.9990
   chunk 23 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 14 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.8582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.209660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.169989 restraints weight = 5481.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.167459 restraints weight = 7659.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.169450 restraints weight = 7667.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.168342 restraints weight = 4675.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.169652 restraints weight = 4246.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4839  Z= 0.149
  Angle     :  0.615   8.404   6595  Z= 0.314
  Chirality :  0.045   0.270    735
  Planarity :  0.004   0.045    847
  Dihedral  :  5.698  57.562    657
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 18.03 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.35), residues: 606
  helix: -0.43 (2.10), residues: 8
  sheet: -0.58 (0.38), residues: 224
  loop : -2.16 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 235 
 TYR   0.013   0.001   TYR H  51 
 PHE   0.008   0.001   PHE H  89 
 TRP   0.014   0.001   TRP L 172 
 HIS   0.007   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.15 ( 4834)
  covalent geometry    : angle       0.61505 /  0.31 ( 6585)
  SS BOND              : bond        0.00145 /  0.06 (    5)
  SS BOND              : angle       0.73310 /  0.39 (   10)
  hydrogen bonds       : bond        0.03570 /  2.29 (   94)
  hydrogen bonds       : angle       6.31126 /  4.52 (  204)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 42
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   18 ASN cc_start: 0.8363 (t0) cc_final: 0.8087 (t0)
REVERT: A  105 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8348 (t)
REVERT: A  161 THR cc_start: 0.7997 (m) cc_final: 0.7724 (p)
  outliers start: 22
  outliers final: 21
  residues processed: 60
  average time/residue: 0.0364
  time to fit residues: 3.2441
Evaluate side-chains
  64 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 42
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  140 SER
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   77 SER
Chi-restraints excluded: chain H residue  120 TYR
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  168 VAL
Chi-restraints excluded: chain H residue  189 VAL
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   51 THR
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain L residue  109 VAL
Chi-restraints excluded: chain L residue  118 TYR
Chi-restraints excluded: chain L residue  139 VAL
Chi-restraints excluded: chain L residue  156 VAL
Chi-restraints excluded: chain L residue  163 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 60 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  62 ASN ** 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 = 0.4341 r_free = 0.4341 target = 0.208785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.168170 restraints weight = 5423.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.165448 restraints weight = 7507.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.164409 restraints weight = 7983.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.162906 restraints weight = 4424.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.165456 restraints weight = 3542.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4839  Z= 0.148
  Angle     :  0.589   7.621   6595  Z= 0.301
  Chirality :  0.044   0.257    735
  Planarity :  0.004   0.048    847
  Dihedral  :  5.688  56.937    657
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.40 %
    Favored  : 89.60 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 18.22 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.19 (0.35), residues: 606
  helix: -0.43 (2.08), residues: 8
  sheet: -0.57 (0.38), residues: 224
  loop : -2.16 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 236 
 TYR   0.013   0.001   TYR H  51 
 PHE   0.007   0.001   PHE A  59 
 TRP   0.017   0.001   TRP L 172 
 HIS   0.008   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 ( 4834)
  covalent geometry    : angle       0.58886 /  0.30 ( 6585)
  SS BOND              : bond        0.00150 /  0.07 (    5)
  SS BOND              : angle       0.66031 /  0.35 (   10)
  hydrogen bonds       : bond        0.03228 /  2.11 (   94)
  hydrogen bonds       : angle       5.85553 /  4.15 (  204)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 47
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A   18 ASN cc_start: 0.8532 (t0) cc_final: 0.7912 (t0)
REVERT: A  105 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8304 (t)
REVERT: A  161 THR cc_start: 0.7954 (m) cc_final: 0.7615 (p)
REVERT: H  120 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.7987 (t80)
  outliers start: 27
  outliers final: 22
  residues processed: 68
  average time/residue: 0.0349
  time to fit residues: 3.4632
Evaluate side-chains
  69 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 45
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain H residue   22 GLN
Chi-restraints excluded: chain H residue   77 SER
Chi-restraints excluded: chain H residue  120 TYR
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  168 VAL
Chi-restraints excluded: chain H residue  189 VAL
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   51 THR
Chi-restraints excluded: chain L residue   72 ILE
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain L residue  109 VAL
Chi-restraints excluded: chain L residue  118 TYR
Chi-restraints excluded: chain L residue  139 VAL
Chi-restraints excluded: chain L residue  156 VAL
Chi-restraints excluded: chain L residue  163 PHE
Chi-restraints excluded: chain L residue  170 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 58 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 55 optimal weight:    0.1980
   chunk 1 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  21 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.221341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.182878 restraints weight = 5433.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.177509 restraints weight = 7682.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.173073 restraints weight = 5043.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.174861 restraints weight = 4212.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.176467 restraints weight = 3273.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4839  Z= 0.120
  Angle     :  0.565   7.015   6595  Z= 0.288
  Chirality :  0.044   0.236    735
  Planarity :  0.004   0.046    847
  Dihedral  :  5.581  56.929    655
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.23 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 18.59 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.08 (0.35), residues: 606
  helix: -0.33 (2.05), residues: 8
  sheet: -0.40 (0.38), residues: 218
  loop : -2.12 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 236 
 TYR   0.010   0.001   TYR H  51 
 PHE   0.008   0.001   PHE A  59 
 TRP   0.018   0.001   TRP L 172 
 HIS   0.004   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.12 ( 4834)
  covalent geometry    : angle       0.56501 /  0.29 ( 6585)
  SS BOND              : bond        0.00167 /  0.07 (    5)
  SS BOND              : angle       0.60108 /  0.33 (   10)
  hydrogen bonds       : bond        0.02992 /  1.95 (   94)
  hydrogen bonds       : angle       5.55151 /  3.92 (  204)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 47
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A   18 ASN cc_start: 0.8504 (t0) cc_final: 0.7882 (t0)
REVERT: A  105 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8261 (t)
REVERT: A  161 THR cc_start: 0.7934 (m) cc_final: 0.7619 (p)
REVERT: H  120 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.7999 (t80)
  outliers start: 24
  outliers final: 20
  residues processed: 65
  average time/residue: 0.0374
  time to fit residues: 3.5390
Evaluate side-chains
  67 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 45
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain H residue   22 GLN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   77 SER
Chi-restraints excluded: chain H residue  120 TYR
Chi-restraints excluded: chain H residue  168 VAL
Chi-restraints excluded: chain H residue  189 VAL
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   51 THR
Chi-restraints excluded: chain L residue   72 ILE
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain L residue  118 TYR
Chi-restraints excluded: chain L residue  156 VAL
Chi-restraints excluded: chain L residue  163 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0670
   chunk 14 optimal weight:    7.9990
   chunk 29 optimal weight:    0.0030
   chunk 50 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0070
   chunk 28 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   overall best weight:    0.6150

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.220420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.182408 restraints weight = 5536.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.178185 restraints weight = 8567.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.175580 restraints weight = 4860.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.176016 restraints weight = 4001.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.176939 restraints weight = 3281.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4839  Z= 0.118
  Angle     :  0.561   7.007   6595  Z= 0.288
  Chirality :  0.043   0.228    735
  Planarity :  0.004   0.045    847
  Dihedral  :  5.580  56.486    655
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.57 %
    Favored  : 90.43 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 18.96 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.35), residues: 606
  helix: -0.26 (2.03), residues: 8
  sheet: -0.40 (0.38), residues: 224
  loop : -2.08 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H 236 
 TYR   0.011   0.001   TYR H  51 
 PHE   0.008   0.001   PHE A  59 
 TRP   0.022   0.001   TRP L 172 
 HIS   0.004   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 ( 4834)
  covalent geometry    : angle       0.56065 /  0.29 ( 6585)
  SS BOND              : bond        0.00160 /  0.08 (    5)
  SS BOND              : angle       0.59622 /  0.33 (   10)
  hydrogen bonds       : bond        0.02897 /  1.90 (   94)
  hydrogen bonds       : angle       5.39880 /  3.80 (  204)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 44
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A   18 ASN cc_start: 0.8493 (t0) cc_final: 0.7901 (t0)
REVERT: A  105 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8270 (t)
REVERT: A  161 THR cc_start: 0.7920 (m) cc_final: 0.7586 (p)
REVERT: H  120 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.7997 (t80)
  outliers start: 25
  outliers final: 22
  residues processed: 63
  average time/residue: 0.0403
  time to fit residues: 3.7348
Evaluate side-chains
  67 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 43
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain H residue   22 GLN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   77 SER
Chi-restraints excluded: chain H residue  120 TYR
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  168 VAL
Chi-restraints excluded: chain H residue  189 VAL
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   51 THR
Chi-restraints excluded: chain L residue   72 ILE
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain L residue  118 TYR
Chi-restraints excluded: chain L residue  156 VAL
Chi-restraints excluded: chain L residue  163 PHE
Chi-restraints excluded: chain L residue  170 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 21 optimal weight:    0.3980
   chunk 58 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9990
   chunk 11 optimal weight:    0.3980
   chunk 33 optimal weight:    5.9990
   chunk 54 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    0.4980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  54 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.219087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.179372 restraints weight = 5349.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.178546 restraints weight = 7326.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.178921 restraints weight = 5199.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.177357 restraints weight = 4637.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.178755 restraints weight = 3888.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.4091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4839  Z= 0.118
  Angle     :  0.555   7.034   6595  Z= 0.285
  Chirality :  0.043   0.222    735
  Planarity :  0.004   0.044    847
  Dihedral  :  5.524  56.429    655
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 18.77 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.91 (0.35), residues: 606
  helix: -0.21 (2.04), residues: 8
  sheet: -0.35 (0.37), residues: 230
  loop : -1.99 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  43 
 TYR   0.011   0.001   TYR H  51 
 PHE   0.008   0.001   PHE A  59 
 TRP   0.027   0.001   TRP L 172 
 HIS   0.004   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.12 ( 4834)
  covalent geometry    : angle       0.55469 /  0.29 ( 6585)
  SS BOND              : bond        0.00184 /  0.09 (    5)
  SS BOND              : angle       0.61889 /  0.33 (   10)
  hydrogen bonds       : bond        0.02859 /  1.88 (   94)
  hydrogen bonds       : angle       5.24899 /  3.70 (  204)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 44
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A   18 ASN cc_start: 0.8460 (t0) cc_final: 0.7926 (t0)
REVERT: A  105 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8322 (t)
REVERT: A  161 THR cc_start: 0.7900 (m) cc_final: 0.7619 (p)
REVERT: H  120 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.7961 (t80)
  outliers start: 29
  outliers final: 23
  residues processed: 67
  average time/residue: 0.0400
  time to fit residues: 4.0031
Evaluate side-chains
  68 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 43
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain H residue   22 GLN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   77 SER
Chi-restraints excluded: chain H residue  120 TYR
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  168 VAL
Chi-restraints excluded: chain H residue  195 VAL
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   51 THR
Chi-restraints excluded: chain L residue   72 ILE
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain L residue  118 TYR
Chi-restraints excluded: chain L residue  156 VAL
Chi-restraints excluded: chain L residue  163 PHE
Chi-restraints excluded: chain L residue  170 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 4 optimal weight:    9.9990
   chunk 3 optimal weight:   20.0000
   chunk 56 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 41 optimal weight:    0.1980
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.219360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.180876 restraints weight = 5494.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.179004 restraints weight = 8233.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.177408 restraints weight = 5672.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.177971 restraints weight = 5786.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.178490 restraints weight = 4191.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4839  Z= 0.123
  Angle     :  0.575   7.211   6595  Z= 0.295
  Chirality :  0.044   0.221    735
  Planarity :  0.005   0.065    847
  Dihedral  :  5.439  56.947    654
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.41 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 18.96 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.84 (0.35), residues: 606
  helix: -0.27 (2.06), residues: 8
  sheet: -0.31 (0.37), residues: 230
  loop : -1.95 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H 236 
 TYR   0.012   0.001   TYR H  51 
 PHE   0.008   0.001   PHE A  59 
 TRP   0.021   0.001   TRP L 172 
 HIS   0.003   0.001   HIS A 153 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.12 ( 4834)
  covalent geometry    : angle       0.57483 /  0.29 ( 6585)
  SS BOND              : bond        0.00171 /  0.08 (    5)
  SS BOND              : angle       0.61161 /  0.33 (   10)
  hydrogen bonds       : bond        0.02837 /  1.85 (   94)
  hydrogen bonds       : angle       5.29096 /  3.76 (  204)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 46
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A   18 ASN cc_start: 0.8437 (t0) cc_final: 0.7934 (t0)
REVERT: A  105 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8317 (t)
REVERT: A  161 THR cc_start: 0.7922 (m) cc_final: 0.7632 (p)
REVERT: H  120 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.7873 (t80)
  outliers start: 28
  outliers final: 24
  residues processed: 68
  average time/residue: 0.0484
  time to fit residues: 4.6121
Evaluate side-chains
  69 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 43
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain H residue   22 GLN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   77 SER
Chi-restraints excluded: chain H residue  120 TYR
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  168 VAL
Chi-restraints excluded: chain H residue  189 VAL
Chi-restraints excluded: chain H residue  195 VAL
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   51 THR
Chi-restraints excluded: chain L residue   72 ILE
Chi-restraints excluded: chain L residue   74 ARG
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain L residue  118 TYR
Chi-restraints excluded: chain L residue  163 PHE
Chi-restraints excluded: chain L residue  170 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 3 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 54 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.215116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.177260 restraints weight = 5386.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.174783 restraints weight = 8296.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.174754 restraints weight = 7334.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.175576 restraints weight = 6563.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.176529 restraints weight = 4495.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.4044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4839  Z= 0.150
  Angle     :  0.600   7.693   6595  Z= 0.312
  Chirality :  0.044   0.240    735
  Planarity :  0.004   0.048    847
  Dihedral  :  5.542  58.844    654
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.07 %
    Favored  : 89.93 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 19.89 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.35), residues: 606
  helix: -0.07 (1.98), residues: 8
  sheet: -0.21 (0.38), residues: 214
  loop : -1.95 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L 235 
 TYR   0.014   0.001   TYR H  51 
 PHE   0.009   0.001   PHE A  59 
 TRP   0.024   0.001   TRP L 172 
 HIS   0.004   0.001   HIS A 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.15 ( 4834)
  covalent geometry    : angle       0.60002 /  0.31 ( 6585)
  SS BOND              : bond        0.00207 /  0.10 (    5)
  SS BOND              : angle       0.77180 /  0.42 (   10)
  hydrogen bonds       : bond        0.02961 /  1.93 (   94)
  hydrogen bonds       : angle       5.39738 /  3.84 (  204)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 40
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A   18 ASN cc_start: 0.8432 (t0) cc_final: 0.7910 (t0)
REVERT: A  161 THR cc_start: 0.7961 (m) cc_final: 0.7670 (p)
REVERT: H  120 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.7769 (t80)
  outliers start: 26
  outliers final: 24
  residues processed: 62
  average time/residue: 0.0390
  time to fit residues: 3.6223
Evaluate side-chains
  65 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 40
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain H residue   22 GLN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   77 SER
Chi-restraints excluded: chain H residue  120 TYR
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  168 VAL
Chi-restraints excluded: chain H residue  195 VAL
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   51 THR
Chi-restraints excluded: chain L residue   72 ILE
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain L residue  118 TYR
Chi-restraints excluded: chain L residue  139 VAL
Chi-restraints excluded: chain L residue  163 PHE
Chi-restraints excluded: chain L residue  170 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 54 optimal weight:    8.9990
   chunk 19 optimal weight:    0.0870
   chunk 11 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0980
   overall best weight:    0.5158

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.218765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.181243 restraints weight = 5443.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.177869 restraints weight = 8005.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.172164 restraints weight = 4644.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.173864 restraints weight = 4465.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.175066 restraints weight = 3464.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4839  Z= 0.112
  Angle     :  0.568   7.658   6595  Z= 0.293
  Chirality :  0.043   0.211    735
  Planarity :  0.004   0.043    847
  Dihedral  :  5.473  59.979    654
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.08 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 21.00 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.35), residues: 606
  helix: -0.11 (1.98), residues: 8
  sheet: -0.40 (0.36), residues: 236
  loop : -1.83 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H 236 
 TYR   0.011   0.001   TYR H  51 
 PHE   0.009   0.001   PHE A  59 
 TRP   0.020   0.001   TRP L 172 
 HIS   0.004   0.001   HIS A 153 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.11 ( 4834)
  covalent geometry    : angle       0.56831 /  0.29 ( 6585)
  SS BOND              : bond        0.00169 /  0.08 (    5)
  SS BOND              : angle       0.55239 /  0.30 (   10)
  hydrogen bonds       : bond        0.02676 /  1.74 (   94)
  hydrogen bonds       : angle       5.10216 /  3.62 (  204)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   18 ASN cc_start: 0.8475 (t0) cc_final: 0.7937 (t0)
REVERT: A  161 THR cc_start: 0.7874 (m) cc_final: 0.7531 (p)
REVERT: H  120 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.7730 (t80)
  outliers start: 21
  outliers final: 19
  residues processed: 59
  average time/residue: 0.0365
  time to fit residues: 3.2252
Evaluate side-chains
  63 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 43
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain H residue   22 GLN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   77 SER
Chi-restraints excluded: chain H residue  120 TYR
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  168 VAL
Chi-restraints excluded: chain H residue  195 VAL
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain L residue  118 TYR
Chi-restraints excluded: chain L residue  163 PHE
Chi-restraints excluded: chain L residue  170 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0980
   chunk 12 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.4580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.219403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.182070 restraints weight = 5457.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.177542 restraints weight = 7704.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.172977 restraints weight = 4605.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.174838 restraints weight = 3989.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.176062 restraints weight = 3194.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4839  Z= 0.105
  Angle     :  0.554   6.799   6595  Z= 0.285
  Chirality :  0.043   0.206    735
  Planarity :  0.004   0.042    847
  Dihedral  :  5.409  59.221    654
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.41 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 21.56 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.74 (0.35), residues: 606
  helix:  0.02 (2.02), residues: 8
  sheet: -0.38 (0.36), residues: 236
  loop : -1.79 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H 236 
 TYR   0.010   0.001   TYR H  51 
 PHE   0.008   0.001   PHE A  59 
 TRP   0.020   0.001   TRP L 172 
 HIS   0.004   0.001   HIS A 153 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.10 ( 4834)
  covalent geometry    : angle       0.55390 /  0.28 ( 6585)
  SS BOND              : bond        0.00175 /  0.08 (    5)
  SS BOND              : angle       0.58314 /  0.32 (   10)
  hydrogen bonds       : bond        0.02623 /  1.71 (   94)
  hydrogen bonds       : angle       4.98185 /  3.55 (  204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 821.02 seconds
wall clock time: 14 minutes 52.00 seconds (892.00 seconds total)