Starting phenix.real_space_refine
on Tue Feb  3 16:46:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m08_63539/02_2026/9m08_63539.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m08_63539/02_2026/9m08_63539.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m08_63539/02_2026/9m08_63539.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m08_63539/02_2026/9m08_63539.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m08_63539/02_2026/9m08_63539.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m08_63539/02_2026/9m08_63539.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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    3154      2.51       5
     N     940      2.21       5
     O     971      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5085
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1313
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 1313
          Classifications: {'peptide': 163}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 155}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 1314
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 1314
          Classifications: {'peptide': 163}
          Link IDs: {'PTRANS': 7, 'TRANS': 155}
    Chain: "C"
      Number of atoms: 1229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1229
          Classifications: {'peptide': 156}
          Link IDs: {'PTRANS': 3, 'TRANS': 152}
    Chain: "D"
      Number of atoms: 1229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1229
          Classifications: {'peptide': 156}
          Link IDs: {'PTRANS': 3, 'TRANS': 152}
  Time building chain proxies: 1.21, per 1000 atoms: 0.24
  Number of scatterers: 5085
  At special positions: 0
  Unit cell: (47.7, 64.66, 196.1, 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     971      8.00
     N     940      7.00
     C    3154      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  67 " - pdb=" SG  CYS A  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  67 " - pdb=" SG  CYS B  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  76 " - pdb=" SG  CYS C 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  76 " - pdb=" SG  CYS D 126 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.28
  Conformation dependent library (CDL) restraints added in 264.4 milliseconds
  

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1244

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 0 sheets defined
      84.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 73
      removed outlier: 4.131A  pdb=" N   ILE A  70 " --> pdb=" O   ALA A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 95
      removed outlier: 3.731A  pdb=" N   ASP A  93 " --> pdb=" O   ILE A  89 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ARG A  94 " --> pdb=" O   ASP A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 106
      removed outlier: 4.189A  pdb=" N   ALA A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 124
      removed outlier: 3.964A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 145
      removed outlier: 3.787A  pdb=" N   ARG A 132 " --> pdb=" O   THR A 128 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   GLU A 140 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   ALA A 141 " --> pdb=" O   THR A 137 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU A 142 " --> pdb=" O   ARG A 138 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLN A 145 " --> pdb=" O   ALA A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 220
      removed outlier: 3.917A  pdb=" N   LYS A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 74
      removed outlier: 3.804A  pdb=" N   ARG B  74 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'B' and resid 96 through 106
      removed outlier: 3.804A  pdb=" N   SER B 100 " --> pdb=" O   MET B  96 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ALA B 106 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 122
    Processing helix  chain 'B' and resid 128 through 142
    Processing helix  chain 'B' and resid 143 through 146
      removed outlier: 3.858A  pdb=" N   ILE B 146 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 143 through 146'
    Processing helix  chain 'B' and resid 150 through 220
      removed outlier: 3.615A  pdb=" N   LYS B 220 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 79
    Processing helix  chain 'C' and resid 80 through 100
    Processing helix  chain 'C' and resid 108 through 121
    Processing helix  chain 'C' and resid 132 through 179
    Processing helix  chain 'D' and resid 27 through 78
    Processing helix  chain 'D' and resid 80 through 100
    Processing helix  chain 'D' and resid 107 through 121
      removed outlier: 3.928A  pdb=" N   TYR D 111 " --> pdb=" O   ASP D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 132 through 179

    440 hydrogen bonds defined for protein.
    1320 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: 0.54

  Time building geometry restraints manager: 0.38 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1784
        1.34 -     1.46: 1022
        1.46 -     1.58: 2323
        1.58 -     1.70: 0
        1.70 -     1.81: 32
  Bond restraints: 5161
  Sorted by residual:
  bond pdb=" C   PRO B 129 "
       pdb=" N   PRO B 130 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.033 2.34e-02 1.83e+03 1.99e+00
  bond pdb=" CB  ASP A 186 "
       pdb=" CG  ASP A 186 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.08e+00
  bond pdb=" CG  LYS D  92 "
       pdb=" CD  LYS D  92 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.08e+00
  bond pdb=" CB  ASP B 186 "
       pdb=" CG  ASP B 186 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 1.01e+00
  bond pdb=" CA  ASP C  96 "
       pdb=" C   ASP C  96 "
    ideal  model  delta    sigma   weight residual
    1.524  1.512  0.012 1.27e-02 6.20e+03 8.81e-01
  ... (remaining 5156 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 6831
        1.99 -     3.99: 121
        3.99 -     5.98: 32
        5.98 -     7.98: 11
        7.98 -     9.97: 6
  Bond angle restraints: 7001
  Sorted by residual:
  angle pdb=" CA  TYR C 158 "
        pdb=" CB  TYR C 158 "
        pdb=" CG  TYR C 158 "
      ideal   model   delta    sigma   weight residual
     113.90  121.08   -7.18 1.80e+00 3.09e-01 1.59e+01
  angle pdb=" N   PRO A 129 "
        pdb=" CA  PRO A 129 "
        pdb=" C   PRO A 129 "
      ideal   model   delta    sigma   weight residual
     110.70  115.04   -4.34 1.22e+00 6.72e-01 1.26e+01
  angle pdb=" C   TRP B  85 "
        pdb=" N   LEU B  86 "
        pdb=" CA  LEU B  86 "
      ideal   model   delta    sigma   weight residual
     120.28  116.28    4.00 1.34e+00 5.57e-01 8.93e+00
  angle pdb=" CA  PRO A 129 "
        pdb=" C   PRO A 129 "
        pdb=" N   PRO A 130 "
      ideal   model   delta    sigma   weight residual
     117.93  121.40   -3.47 1.20e+00 6.94e-01 8.38e+00
  angle pdb=" CA  GLN D 162 "
        pdb=" CB  GLN D 162 "
        pdb=" CG  GLN D 162 "
      ideal   model   delta    sigma   weight residual
     114.10  119.88   -5.78 2.00e+00 2.50e-01 8.34e+00
  ... (remaining 6996 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 2690
       17.95 -    35.89: 377
       35.89 -    53.84: 119
       53.84 -    71.78: 13
       71.78 -    89.73: 6
  Dihedral angle restraints: 3205
    sinusoidal: 1307
      harmonic: 1898
  Sorted by residual:
  dihedral pdb=" CB  CYS B  67 "
           pdb=" SG  CYS B  67 "
           pdb=" SG  CYS B  91 "
           pdb=" CB  CYS B  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   19.80   73.20     1      1.00e+01 1.00e-02 6.82e+01
  dihedral pdb=" CB  CYS A  67 "
           pdb=" SG  CYS A  67 "
           pdb=" SG  CYS A  91 "
           pdb=" CB  CYS A  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   40.48   52.52     1      1.00e+01 1.00e-02 3.76e+01
  dihedral pdb=" CB  CYS D  76 "
           pdb=" SG  CYS D  76 "
           pdb=" SG  CYS D 126 "
           pdb=" CB  CYS D 126 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  142.18  -49.18     1      1.00e+01 1.00e-02 3.32e+01
  ... (remaining 3202 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 703
       0.060 -    0.121: 75
       0.121 -    0.181: 8
       0.181 -    0.242: 5
       0.242 -    0.302: 1
  Chirality restraints: 792
  Sorted by residual:
  chirality pdb=" CG  LEU A 163 "
            pdb=" CB  LEU A 163 "
            pdb=" CD1 LEU A 163 "
            pdb=" CD2 LEU A 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CB  ILE A 212 "
            pdb=" CA  ILE A 212 "
            pdb=" CG1 ILE A 212 "
            pdb=" CG2 ILE A 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CG  LEU B  86 "
            pdb=" CB  LEU B  86 "
            pdb=" CD1 LEU B  86 "
            pdb=" CD2 LEU B  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 789 not shown)

  Planarity restraints: 924
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 129 "    0.056 5.00e-02 4.00e+02   8.32e-02 1.11e+01
        pdb=" N   PRO A 130 "   -0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO A 130 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 130 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A  96 "   -0.038 5.00e-02 4.00e+02   5.82e-02 5.41e+00
        pdb=" N   PRO A  97 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A  97 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  97 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B  96 "    0.031 5.00e-02 4.00e+02   4.66e-02 3.48e+00
        pdb=" N   PRO B  97 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B  97 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B  97 "    0.026 5.00e-02 4.00e+02
  ... (remaining 921 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 620
        2.74 -     3.28: 5602
        3.28 -     3.82: 9511
        3.82 -     4.36: 9393
        4.36 -     4.90: 16150
  Nonbonded interactions: 41276
  Sorted by model distance:
  nonbonded pdb=" O   LEU D  37 "
            pdb=" OG  SER D  41 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OD2 ASP D  80 "
            pdb=" OG1 THR D  82 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   GLN D  43 "
            pdb=" OG1 THR D  47 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OE1 GLN D  88 "
            pdb=" NH2 ARG D  91 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" OE1 GLN C  88 "
            pdb=" NH2 ARG C  91 "
     model   vdw
     2.309 3.120
  ... (remaining 41271 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 58 through 207 or (resid 208 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 209 through 220))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             5.420
  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:             0.020
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     4.990
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
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      :  0.003   0.033   5165  Z= 0.158
  Angle     :  0.754   9.974   7009  Z= 0.372
  Chirality :  0.042   0.302    792
  Planarity :  0.005   0.083    924
  Dihedral  : 17.935  89.728   1949
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 34.84 %
    Favored  : 64.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.77 (0.33), residues: 630
  helix:  2.32 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -1.10 (0.62), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  49 
 TYR   0.028   0.002   TYR C 158 
 PHE   0.011   0.001   PHE C 142 
 TRP   0.011   0.001   TRP A 157 
 HIS   0.004   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 5161)
  covalent geometry    : angle       0.75434 ( 7001)
  SS BOND              : bond        0.00092 (    4)
  SS BOND              : angle       0.72609 (    8)
  hydrogen bonds       : bond        0.07237 (  440)
  hydrogen bonds       : angle       4.06367 ( 1320)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0700
  time to fit residues: 8.4516
Evaluate side-chains
  89 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 48 optimal weight:    0.1980
   chunk 56 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:   10.0000
   chunk 61 optimal weight:    0.7980
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  58 GLN
B 113 GLN
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 178 GLN
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.146474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.110046 restraints weight = 9247.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.112296 restraints weight = 4975.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.113657 restraints weight = 3182.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.113790 restraints weight = 2143.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.113989 restraints weight = 2096.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.1012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5165  Z= 0.171
  Angle     :  0.659   7.819   7009  Z= 0.331
  Chirality :  0.039   0.178    792
  Planarity :  0.005   0.082    924
  Dihedral  :  3.410  14.902    712
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 32.02 %
    Favored  : 65.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.89 (0.32), residues: 630
  helix:  2.38 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.97 (0.60), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  49 
 TYR   0.023   0.002   TYR C 158 
 PHE   0.013   0.001   PHE C 142 
 TRP   0.008   0.001   TRP B  85 
 HIS   0.003   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 5161)
  covalent geometry    : angle       0.65910 ( 7001)
  SS BOND              : bond        0.00207 (    4)
  SS BOND              : angle       0.92417 (    8)
  hydrogen bonds       : bond        0.04549 (  440)
  hydrogen bonds       : angle       3.73044 ( 1320)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  179 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8283 (tm-30)
REVERT: B  180 MET cc_start: 0.8201 (mmm) cc_final: 0.7503 (mmm)
  outliers start: 15
  outliers final: 9
  residues processed: 110
  average time/residue: 0.0688
  time to fit residues: 9.7582
Evaluate side-chains
  99 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  179 GLN
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  177 TRP
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   77 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0470
   chunk 38 optimal weight:    0.4980
   chunk 37 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN
C 144 ASN
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.147621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.107314 restraints weight = 9277.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.111025 restraints weight = 4822.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.113393 restraints weight = 3009.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.114912 restraints weight = 2180.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.115711 restraints weight = 1763.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5165  Z= 0.150
  Angle     :  0.645   9.684   7009  Z= 0.321
  Chirality :  0.038   0.197    792
  Planarity :  0.005   0.082    924
  Dihedral  :  3.366  14.853    712
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 31.64 %
    Favored  : 64.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.05 (0.32), residues: 630
  helix:  2.49 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.91 (0.61), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  87 
 TYR   0.036   0.002   TYR C 158 
 PHE   0.011   0.001   PHE C 142 
 TRP   0.013   0.001   TRP A  71 
 HIS   0.004   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 5161)
  covalent geometry    : angle       0.64443 ( 7001)
  SS BOND              : bond        0.00149 (    4)
  SS BOND              : angle       0.82593 (    8)
  hydrogen bonds       : bond        0.04413 (  440)
  hydrogen bonds       : angle       3.60478 ( 1320)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8529 (ttm170)
REVERT: B  154 TYR cc_start: 0.8040 (t80) cc_final: 0.7785 (t80)
REVERT: B  179 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8236 (tm-30)
REVERT: B  180 MET cc_start: 0.8297 (mmm) cc_final: 0.7734 (mmm)
REVERT: C  140 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6739 (tm-30)
  outliers start: 21
  outliers final: 14
  residues processed: 111
  average time/residue: 0.0664
  time to fit residues: 9.5083
Evaluate side-chains
  104 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 GLU
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  173 ARG
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  179 GLN
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  177 TRP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   77 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.147588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.107584 restraints weight = 9175.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.111022 restraints weight = 4947.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.113279 restraints weight = 3152.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.114755 restraints weight = 2321.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.115357 restraints weight = 1888.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.4086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5165  Z= 0.167
  Angle     :  0.678  11.828   7009  Z= 0.335
  Chirality :  0.040   0.213    792
  Planarity :  0.006   0.083    924
  Dihedral  :  3.320  15.012    712
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 30.51 %
    Favored  : 63.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.01 (0.32), residues: 630
  helix:  2.46 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.89 (0.62), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  49 
 TYR   0.021   0.002   TYR B  62 
 PHE   0.013   0.001   PHE C 142 
 TRP   0.009   0.001   TRP A  71 
 HIS   0.005   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 5161)
  covalent geometry    : angle       0.67728 ( 7001)
  SS BOND              : bond        0.00125 (    4)
  SS BOND              : angle       0.88469 (    8)
  hydrogen bonds       : bond        0.04496 (  440)
  hydrogen bonds       : angle       3.63644 ( 1320)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 90
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8509 (ttp80)
REVERT: C  140 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6688 (tm-30)
REVERT: D   49 ARG cc_start: 0.9077 (mmm160) cc_final: 0.8864 (mmm160)
  outliers start: 30
  outliers final: 20
  residues processed: 112
  average time/residue: 0.0679
  time to fit residues: 9.5947
Evaluate side-chains
  106 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 GLU
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  173 ARG
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue   93 ASP
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  177 TRP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  150 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 38 optimal weight:    0.1980
   chunk 28 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0040
   chunk 23 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.147408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.106887 restraints weight = 9257.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.110598 restraints weight = 4850.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.112962 restraints weight = 3041.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.114485 restraints weight = 2206.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.115251 restraints weight = 1789.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.1479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5165  Z= 0.150
  Angle     :  0.680  10.577   7009  Z= 0.329
  Chirality :  0.039   0.212    792
  Planarity :  0.005   0.083    924
  Dihedral  :  3.277  14.720    712
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 31.45 %
    Favored  : 63.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.14 (0.32), residues: 630
  helix:  2.55 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.90 (0.61), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  91 
 TYR   0.032   0.002   TYR C 158 
 PHE   0.011   0.001   PHE C 142 
 TRP   0.007   0.001   TRP A  71 
 HIS   0.005   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 5161)
  covalent geometry    : angle       0.68028 ( 7001)
  SS BOND              : bond        0.00106 (    4)
  SS BOND              : angle       0.82761 (    8)
  hydrogen bonds       : bond        0.04402 (  440)
  hydrogen bonds       : angle       3.59411 ( 1320)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8210 (mmm-85)
REVERT: A  172 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8757 (pp30)
REVERT: A  173 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8504 (ttm170)
REVERT: B  154 TYR cc_start: 0.8134 (t80) cc_final: 0.7878 (t80)
REVERT: C  140 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6706 (tm-30)
  outliers start: 28
  outliers final: 19
  residues processed: 121
  average time/residue: 0.0776
  time to fit residues: 11.7450
Evaluate side-chains
  110 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ARG
Chi-restraints excluded: chain A residue  131 GLU
Chi-restraints excluded: chain A residue  172 GLN
Chi-restraints excluded: chain A residue  173 ARG
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue   93 ASP
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  184 GLU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  177 TRP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   83 LEU
Chi-restraints excluded: chain D residue  150 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 32 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 0 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  48 ASN
C 119 ASN
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.168565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.116272 restraints weight = 10307.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.119670 restraints weight = 5742.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.121956 restraints weight = 3793.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.123184 restraints weight = 2834.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.124242 restraints weight = 2361.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5165  Z= 0.181
  Angle     :  0.745  11.967   7009  Z= 0.359
  Chirality :  0.042   0.229    792
  Planarity :  0.006   0.081    924
  Dihedral  :  3.371  14.953    712
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 33.15 %
    Favored  : 61.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.92 (0.32), residues: 630
  helix:  2.41 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.99 (0.62), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  91 
 TYR   0.032   0.002   TYR C 158 
 PHE   0.015   0.002   PHE C 142 
 TRP   0.018   0.001   TRP A  71 
 HIS   0.005   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 5161)
  covalent geometry    : angle       0.74427 ( 7001)
  SS BOND              : bond        0.00121 (    4)
  SS BOND              : angle       0.94690 (    8)
  hydrogen bonds       : bond        0.04583 (  440)
  hydrogen bonds       : angle       3.75311 ( 1320)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 86
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8809 (pp30)
REVERT: A  173 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8615 (ttp80)
REVERT: B  154 TYR cc_start: 0.8361 (t80) cc_final: 0.8148 (t80)
REVERT: B  176 LYS cc_start: 0.9373 (tmmt) cc_final: 0.8996 (ptmm)
REVERT: C  140 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6813 (tm-30)
  outliers start: 30
  outliers final: 24
  residues processed: 108
  average time/residue: 0.0760
  time to fit residues: 10.4258
Evaluate side-chains
  110 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 GLU
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  172 GLN
Chi-restraints excluded: chain A residue  173 ARG
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue   93 ASP
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  177 TRP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   82 THR
Chi-restraints excluded: chain D residue   83 LEU
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  168 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 15 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9990
   chunk 7 optimal weight:    0.3980
   chunk 48 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  48 ASN
C 119 ASN
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.169596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.117482 restraints weight = 10134.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.120740 restraints weight = 5748.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.123068 restraints weight = 3847.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.124301 restraints weight = 2885.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.125333 restraints weight = 2408.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5165  Z= 0.161
  Angle     :  0.746  12.999   7009  Z= 0.359
  Chirality :  0.042   0.244    792
  Planarity :  0.005   0.080    924
  Dihedral  :  3.350  14.791    712
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 33.15 %
    Favored  : 60.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.98 (0.32), residues: 630
  helix:  2.46 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -1.02 (0.62), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  49 
 TYR   0.023   0.002   TYR C 158 
 PHE   0.012   0.001   PHE C 142 
 TRP   0.015   0.001   TRP A  71 
 HIS   0.006   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 5161)
  covalent geometry    : angle       0.74541 ( 7001)
  SS BOND              : bond        0.00083 (    4)
  SS BOND              : angle       0.85493 (    8)
  hydrogen bonds       : bond        0.04501 (  440)
  hydrogen bonds       : angle       3.70514 ( 1320)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 86
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8017 (mmm-85)
REVERT: A  131 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8100 (pm20)
REVERT: A  172 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8839 (pp30)
REVERT: A  173 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8676 (ttp80)
REVERT: B   85 TRP cc_start: 0.9070 (m-90) cc_final: 0.8636 (m-90)
REVERT: C  140 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6840 (tm-30)
  outliers start: 33
  outliers final: 24
  residues processed: 110
  average time/residue: 0.0787
  time to fit residues: 11.0461
Evaluate side-chains
  112 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ARG
Chi-restraints excluded: chain A residue  131 GLU
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  172 GLN
Chi-restraints excluded: chain A residue  173 ARG
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue   93 ASP
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   48 ASN
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   63 ASN
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  177 TRP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   82 THR
Chi-restraints excluded: chain D residue   83 LEU
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  168 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 38 optimal weight:    0.0770
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 60 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0010
   chunk 36 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.3944

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  58 GLN
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.148103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.106766 restraints weight = 9290.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.110473 restraints weight = 4804.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.112883 restraints weight = 2998.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.114245 restraints weight = 2167.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.115297 restraints weight = 1775.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5165  Z= 0.149
  Angle     :  0.752  13.272   7009  Z= 0.361
  Chirality :  0.042   0.253    792
  Planarity :  0.006   0.079    924
  Dihedral  :  3.303  14.450    712
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 33.52 %
    Favored  : 61.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.09 (0.33), residues: 630
  helix:  2.54 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -1.08 (0.61), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  49 
 TYR   0.050   0.002   TYR C 158 
 PHE   0.009   0.001   PHE C 142 
 TRP   0.023   0.001   TRP A  71 
 HIS   0.001   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5161)
  covalent geometry    : angle       0.75172 ( 7001)
  SS BOND              : bond        0.00081 (    4)
  SS BOND              : angle       0.77938 (    8)
  hydrogen bonds       : bond        0.04393 (  440)
  hydrogen bonds       : angle       3.64938 ( 1320)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 87
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8194 (mmm-85)
REVERT: A  131 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7959 (pm20)
REVERT: A  172 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8843 (pp30)
REVERT: A  173 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8705 (ttm170)
REVERT: A  209 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6536 (tt)
REVERT: B   85 TRP cc_start: 0.8778 (m-90) cc_final: 0.8480 (m-90)
REVERT: C  119 ASN cc_start: 0.8350 (t0) cc_final: 0.8140 (t0)
REVERT: C  140 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6738 (tm-30)
  outliers start: 28
  outliers final: 21
  residues processed: 107
  average time/residue: 0.0560
  time to fit residues: 7.8266
Evaluate side-chains
  109 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ARG
Chi-restraints excluded: chain A residue  131 GLU
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  172 GLN
Chi-restraints excluded: chain A residue  173 ARG
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue   93 ASP
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue  149 MET
Chi-restraints excluded: chain C residue  177 TRP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   82 THR
Chi-restraints excluded: chain D residue   83 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  168 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 58 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0470
   chunk 0 optimal weight:    9.9990
   chunk 52 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 114 ASN
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.147883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.106288 restraints weight = 9339.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.109989 restraints weight = 4859.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.112366 restraints weight = 3040.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.113735 restraints weight = 2210.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.114797 restraints weight = 1814.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.4102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5165  Z= 0.153
  Angle     :  0.756  13.548   7009  Z= 0.360
  Chirality :  0.042   0.264    792
  Planarity :  0.005   0.078    924
  Dihedral  :  3.318  14.320    712
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 33.33 %
    Favored  : 61.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.03 (0.32), residues: 630
  helix:  2.51 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -1.12 (0.61), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  49 
 TYR   0.045   0.002   TYR C 158 
 PHE   0.011   0.001   PHE C 142 
 TRP   0.020   0.001   TRP A  71 
 HIS   0.004   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 5161)
  covalent geometry    : angle       0.75552 ( 7001)
  SS BOND              : bond        0.00080 (    4)
  SS BOND              : angle       0.79681 (    8)
  hydrogen bonds       : bond        0.04405 (  440)
  hydrogen bonds       : angle       3.67676 ( 1320)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 89
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8181 (mmm-85)
REVERT: A  131 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7971 (pm20)
REVERT: A  172 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8834 (pp30)
REVERT: A  173 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8671 (ttm170)
REVERT: A  209 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6520 (tt)
REVERT: B   85 TRP cc_start: 0.8776 (m-90) cc_final: 0.8495 (m-90)
REVERT: C  119 ASN cc_start: 0.8381 (t0) cc_final: 0.8165 (t0)
REVERT: C  140 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6747 (tm-30)
  outliers start: 29
  outliers final: 23
  residues processed: 109
  average time/residue: 0.0598
  time to fit residues: 8.4399
Evaluate side-chains
  112 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ARG
Chi-restraints excluded: chain A residue  131 GLU
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  172 GLN
Chi-restraints excluded: chain A residue  173 ARG
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue   93 ASP
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   63 ASN
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  177 TRP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   82 THR
Chi-restraints excluded: chain D residue   83 LEU
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  168 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0970
   chunk 21 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0670
   chunk 7 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 162 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 = 0.4564 r_free = 0.4564 target = 0.147780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.106314 restraints weight = 9331.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.109926 restraints weight = 4838.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.112366 restraints weight = 3033.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.113856 restraints weight = 2196.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.114613 restraints weight = 1788.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5165  Z= 0.154
  Angle     :  0.775  14.000   7009  Z= 0.369
  Chirality :  0.043   0.264    792
  Planarity :  0.005   0.079    924
  Dihedral  :  3.334  14.220    712
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 33.52 %
    Favored  : 61.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.02 (0.32), residues: 630
  helix:  2.52 (0.21), residues: 535
  sheet:  None (None), residues: 0
  loop : -1.25 (0.61), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  49 
 TYR   0.045   0.002   TYR C 158 
 PHE   0.010   0.001   PHE C 142 
 TRP   0.025   0.001   TRP A  71 
 HIS   0.001   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5161)
  covalent geometry    : angle       0.77490 ( 7001)
  SS BOND              : bond        0.00076 (    4)
  SS BOND              : angle       0.76692 (    8)
  hydrogen bonds       : bond        0.04404 (  440)
  hydrogen bonds       : angle       3.69845 ( 1320)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 80
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8114 (mmm-85)
REVERT: A  131 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7952 (pm20)
REVERT: A  172 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8820 (pp30)
REVERT: A  209 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6512 (tt)
REVERT: B   85 TRP cc_start: 0.8783 (m-90) cc_final: 0.8501 (m-90)
REVERT: C  119 ASN cc_start: 0.8357 (t0) cc_final: 0.8140 (t0)
REVERT: C  140 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6766 (tm-30)
  outliers start: 29
  outliers final: 23
  residues processed: 101
  average time/residue: 0.0554
  time to fit residues: 7.2818
Evaluate side-chains
  107 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 80
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ARG
Chi-restraints excluded: chain A residue  131 GLU
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  172 GLN
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue   93 ASP
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   63 ASN
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  177 TRP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   82 THR
Chi-restraints excluded: chain D residue   83 LEU
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  168 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 42 optimal weight:    0.3980
   chunk 39 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   chunk 57 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0670
   chunk 26 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 162 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 = 0.4558 r_free = 0.4558 target = 0.147408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.109028 restraints weight = 9396.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.109996 restraints weight = 5366.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.112375 restraints weight = 3319.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.112906 restraints weight = 2458.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.113062 restraints weight = 2131.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5165  Z= 0.160
  Angle     :  0.771  13.861   7009  Z= 0.368
  Chirality :  0.043   0.265    792
  Planarity :  0.005   0.079    924
  Dihedral  :  3.332  14.286    712
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 33.52 %
    Favored  : 61.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.99 (0.32), residues: 630
  helix:  2.50 (0.21), residues: 535
  sheet:  None (None), residues: 0
  loop : -1.25 (0.61), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  49 
 TYR   0.014   0.002   TYR C 158 
 PHE   0.012   0.001   PHE C 142 
 TRP   0.023   0.001   TRP A  71 
 HIS   0.001   0.001   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 5161)
  covalent geometry    : angle       0.77142 ( 7001)
  SS BOND              : bond        0.00078 (    4)
  SS BOND              : angle       0.78693 (    8)
  hydrogen bonds       : bond        0.04430 (  440)
  hydrogen bonds       : angle       3.72858 ( 1320)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 935.82 seconds
wall clock time: 16 minutes 46.41 seconds (1006.41 seconds total)